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Sokal A, Royer G, Esposito-Farese M, Clermont O, Condamine B, Laouénan C, Lefort A, Denamur E, de Lastours V. Clinical and Bacteriological Specificities of Escherichia coli Bloodstream Infections From Biliary Portal of Entries. J Infect Dis 2024; 229:1679-1687. [PMID: 38214565 DOI: 10.1093/infdis/jiad586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Escherichia coli is frequently responsible for bloodstream infections (BSIs). Among digestive BSIs, biliary infections appear to be less severe. Respective roles of host factors, bacterial determinants (phylogroups, virulence, and antibiotic resistance), and portal of entry on outcome are unknown. METHODS Clinical characteristics and prognosis of 770 episodes of E coli BSI were analyzed and isolates sequenced (Illumina technology) comparing phylogroups, multilocus sequence type, virulence, and resistance gene content. BSI isolates were compared with 362 commensal E coli from healthy subjects. RESULTS Among 770 episodes, 135 were biliary, 156 nonbiliary digestive, and 479 urinary. Compared to urinary infections, BSIs of digestive origin occurred significantly more in men, comorbid, and immunocompromised patients. Digestive portal of entry was significantly associated with septic shock and death. Among digestive infections, patients with biliary infections were less likely to die (P = .032), despite comparable initial severity. Biliary E coli resembled commensals (phylogroup distribution, sequence type, and few virulence-associated genes) whereas nonbiliary digestive and urinary strains carried many virulence-associated genes. CONCLUSIONS Escherichia coli strains responsible for biliary infections exhibit commensal characteristics and are associated with lower mortality rates, despite similar initial severity, than other digestive BSIs. Biliary drainage in addition to antibiotics in the management of biliary infections may explain improved outcome.
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Affiliation(s)
- Aurélien Sokal
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
| | - Guilhem Royer
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, Unité mixte de recherche Centre National de la recherche Scientifique 6047, Université Paris Cité, Paris
| | | | - Olivier Clermont
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Bénédicte Condamine
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Cedric Laouénan
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Département d'épidémiologie, biostatistiques et recherche clinique
| | - Agnès Lefort
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Erick Denamur
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Victoire de Lastours
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
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Maldonado N, López-Hernández I, García-Montaner A, López-Cortés LE, Pérez-Crespo PMM, Retamar-Gentil P, Sousa-Domínguez A, Goikoetxea J, Pulido-Navazo Á, Labayru-Echeverría C, Natera-Kindelán C, Jover-Sáenz A, Del Arco-Jiménez A, Armiñanzas-Castillo C, Aller AI, Fernández-Suárez J, Marrodán-Ciordia T, Boix-Palop L, Smithson-Amat A, Reguera-Iglesias JM, Galán-Sánchez F, Bahamonde A, Sánchez Calvo JM, Gea-Lázaro I, Pérez-Camacho I, Reyes-Bertos A, Becerril-Carral B, Rodríguez-Baño J, Pascual Á. Whole-genome characterisation of Escherichia coli isolates from patients with bacteraemia presenting with sepsis or septic shock in Spain: a multicentre cross-sectional study. THE LANCET. MICROBE 2024; 5:e390-e399. [PMID: 38547882 DOI: 10.1016/s2666-5247(23)00369-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 04/08/2024]
Abstract
BACKGROUND Escherichia coli is the most frequent cause of bloodstream infections (BSIs). About one-third of patients with BSIs due to E coli develop sepsis or shock. The objective of this study is to characterise the microbiological features of E coli blood isolates causing sepsis or septic shock to provide exploratory information for future diagnostic, preventive, or therapeutic interventions. METHODS E coli blood isolates from a multicentre cross-sectional study of patients older than 14 years presenting with sepsis or septic shock (according to the Third International Consensus Definitions for Sepsis and Septic Shock criteria) from hospitals in Spain between Oct 4, 2016, and Oct 15, 2017, were studied by whole-genome sequencing. Phylogroups, sequence types (STs), serotype, FimH types, antimicrobial resistance (AMR) genes, pathogenicity islands, and virulence factors were identified. Susceptibility testing was performed by broth microdilution. The main outcome of this study was the characterisation of the E coli blood isolates in terms of population structure by phylogroups, groups (group 1: phylogroups B2, F, and G; group 2: A, B1, and C; group 3: D), and STs and distribution by geographical location and bloodstream infection source. Other outcomes were virulence score and prevalence of virulence-associated genes, pathogenicity islands, AMR, and AMR-associated genes. Frequencies were compared using χ² or Fisher's exact tests, and continuous variables using the Mann-Whitney test, with Bonferroni correction for multiple comparisons. FINDINGS We analysed 224 isolates: 140 isolates (63%) were included in phylogenetic group 1, 52 (23%) in group 2, and 32 (14%) in group 3. 85 STs were identified, with four comprising 44% (n=98) of the isolates: ST131 (38 [17%]), ST73 (25 [11%]), ST69 (23 [10%]), and ST95 (12 [5%]). No significant differences in phylogroup or ST distribution were found according to geographical areas or source of bloodstream infection, except for ST95, which was more frequent in urinary tract infections than in other sources (11 [9%] of 116 vs 1 [1%] of 108, p=0·0045). Median virulence score was higher in group 1 (median 25·0 [IQR 20·5-29·0) than in group 2 (median 14·5 [9·0-20·0]; p<0·0001) and group 3 (median 21 [16·5-23·0]; p<0·0001); prevalence of several pathogenicity islands was higher in group 1. No significant differences were found between phylogenetic groups in proportions of resistance to antibiotics. ST73 had higher median virulence score (32 [IQR 29-35]) than the other predominant clones (median range 21-28). Some virulence genes and pathogenicity islands were significantly associated with each ST. ST131 isolates had higher prevalence of AMR and a higher proportion of AMR genes, notably blaCTX-M-15 and blaOXA-1. INTERPRETATION In this exploratory study, the population structure of E coli causing sepsis or shock was similar to previous studies that included all bacteraemic isolates. Virulence genes, pathogenicity islands, and AMR genes were not randomly distributed among phylogroups or STs. These results provide a comprehensive characterisation of invasive E coli isolates causing severe response syndrome. Future studies are required to determine the contribution of these microbiological factors to severe clinical presentation and worse outcomes in patients with E coli bloodstream infection. FUNDING Instituto de Salud Carlos III.
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Affiliation(s)
- Natalia Maldonado
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain
| | - Inmaculada López-Hernández
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea García-Montaner
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain
| | - Luis Eduardo López-Cortés
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Pilar Retamar-Gentil
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | | | - Clara Natera-Kindelán
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario Reina Sofía, Córdoba, Spain
| | | | | | - Carlos Armiñanzas-Castillo
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario de Marqués de Valdecilla, Santander, Spain
| | | | - Jonathan Fernández-Suárez
- Hospital Universitario Central de Asturias, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | | | | | | | - José Mª Reguera-Iglesias
- Hospital Regional Universitario de Málaga, Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | | | | | - Juan Manuel Sánchez Calvo
- Hospital Universitario de Jerez, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Jerez de la Frontera, Spain
| | | | | | | | | | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamentos de Medicina y Microbiología, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F. The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLoS Genet 2023; 19:e1010842. [PMID: 37531401 PMCID: PMC10395866 DOI: 10.1371/journal.pgen.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Affiliation(s)
- Judit Burgaya
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, UMR CNRS 6047, Université Paris-Cité, Paris, France
| | | | | | | | | | | | - Agnès Lefort
- Université Paris Cité, INSERM, IAME, Paris, France
| | | | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR7241 / INSERM U1050, PSL Research University, Paris, France
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The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France. Appl Environ Microbiol 2022; 88:e0066422. [PMID: 35862685 PMCID: PMC9361829 DOI: 10.1128/aem.00664-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli is a commensal species of the lower intestine but is also a major pathogen causing intestinal and extraintestinal infections that is increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here, instead, we whole-genome sequenced a collection of 403 commensal E. coli isolates from fecal samples of healthy adult volunteers in France (1980 to 2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A; 16.3%), ST73 and ST95 (phylogroup B2; 6.3 and 5.0%, respectively), ST69 (phylogroup D; 4.2%), and ST59 (phylogroup F; 3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6, and O25 groups used in bioconjugate O-antigen vaccine against extraintestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistance was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independent of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies. IMPORTANCE Escherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an aging population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance takes place. Unfortunately, most whole-genome-sequenced strains are isolated from pathogenic conditions. Here, we whole-genome sequenced 403 E. coli commensals isolated from healthy French subjects over a 30-year period. Virulence genes increased in frequency by both clonal expansion of clones carrying them and increases in frequency within clones, whereas resistance genes increased by within-clone increased frequency. Prospective studies of E. coli commensals should be performed worldwide to have a broader picture of evolution and adaptation of this species.
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Freire CA, Silva RM, Ruiz RC, Pimenta DC, Bryant JA, Henderson IR, Barbosa AS, Elias WP. Secreted Autotransporter Toxin (Sat) Mediates Innate Immune System Evasion. Front Immunol 2022; 13:844878. [PMID: 35251044 PMCID: PMC8891578 DOI: 10.3389/fimmu.2022.844878] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Several strategies are used by Escherichia coli to evade the host innate immune system in the blood, such as the cleavage of complement system proteins by secreted proteases. Members of the Serine Proteases Autotransporters of Enterobacteriaceae (SPATE) family have been described as presenting proteolytic effects against complement proteins. Among the SPATE-encoding genes sat (secreted autotransporter toxin) has been detected in high frequencies among strains of E. coli isolated from bacteremia. Sat has been characterized for its cytotoxic action, but the possible immunomodulatory effects of Sat have not been investigated. Therefore, this study aimed to evaluate the proteolytic effects of Sat on complement proteins and the role in pathogenesis of BSI caused by extraintestinal E. coli (ExPEC). E. coli EC071 was selected as a Sat-producing ExPEC strain. Whole-genome sequencing showed that sat sequences of EC071 and uropathogenic E. coli CFT073 present 99% identity. EC071 was shown to be resistant to the bactericidal activity of normal human serum (NHS). Purified native Sat was used in proteolytic assays with proteins of the complement system and, except for C1q, all tested substrates were cleaved by Sat in a dose and time-dependent manner. Moreover, E. coli DH5α survived in NHS pre-incubated with Sat. EC071-derivative strains harboring sat knockout and in trans complementations producing either active or non-active Sat were tested in a murine sepsis model. Lethality was reduced by 50% when mice were inoculated with the sat mutant strain. The complemented strain producing active Sat partially restored the effect caused by the wild-type strain. The results presented in this study show that Sat presents immunomodulatory effects by cleaving several proteins of the three complement system pathways. Therefore, Sat plays an important role in the establishment of bloodstream infections and sepsis.
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Affiliation(s)
- Claudia A Freire
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil.,Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Rosa M Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rita C Ruiz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Daniel C Pimenta
- Laboratório de Bioquímica, Instituto Butantan, São Paulo, Brazil
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Angela S Barbosa
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
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de Lastours V, El Meouche I, Chau F, Beghain J, Chevret D, Aubert-Frambourg A, Clermont O, Royer G, Bouvet O, Denamur E, Fantin B. Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment. Int J Med Microbiol 2022; 312:151548. [PMID: 35030401 DOI: 10.1016/j.ijmm.2022.151548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Three healthy volunteers carried similar quinolone-resistant E. coli (QREC) (pulsed field gel electrophoresis profiles) in their gut before and after 14 days ciprofloxacin treatment. Given the intensity of the selective pressure and the mutagenic properties of quinolones, we determined whether these strains had evolved at the phenotypic and/or genomic levels. MATERIAL AND METHODS Commensal QREC from before day-0 (D0), and a month after 14 days of ciprofloxacin (D42) were compared in 3 volunteers. Growth experiments were performed; acetate levels, mutation frequencies, quinolone MICs and antibiotic tolerance were measured at D0 and D42. Genomes were sequenced and single nucleotide polymorphisms (SNPs) between D0 and D42 were analyzed using DiscoSNP and breseq methods. Cytoplasmic proteins were extracted, HPLC performed and proteins identified using X!tandem software; abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods. RESULTS No difference was found in MICs, growth characteristics, acetate concentrations, mutation frequencies, tolerance profiles, phylogroups, O-and H-types, fimH alleles and sequence types between D0 and D42. No SNP variation was evidenced between D0 and D42 isolates for 2/3 subjects; 2 SNP variations were evidenced in one. At the protein level, very few significant protein abundance differences were identified between D0 and D42. CONCLUSION No fitness, tolerance, metabolic or genomic evolution of commensal QREC was observed overtime, despite massive exposure to ciprofloxacin in the gut. The three strains behaved as if they had been unaffected by ciprofloxacin, suggesting that gut may act as a sanctuary where bacteria would be protected from the effect of antibiotics and survive without any detrimental effect of stress.
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Affiliation(s)
- V de Lastours
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France.
| | - I El Meouche
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - F Chau
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - J Beghain
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - D Chevret
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - A Aubert-Frambourg
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78150 Jouy-en-Josas, France
| | - O Clermont
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - G Royer
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - O Bouvet
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
| | - E Denamur
- IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France; Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance-Publique Hôpitaux de Paris, F-75018 Paris, France
| | - B Fantin
- Service de Médecine Interne, Hôpital Beaujon, Assistance-Publique Hôpitaux de Paris, F-92100 Clichy, France; IAME Research Group, UMR 1137, Université de Paris and INSERM, F-75018 Paris, France
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Grevskott DH, Ghavidel FZ, Svanevik CS, Marathe NP. Resistance profiles and diversity of β-lactamases in Escherichia coli strains isolated from city-scale sewage surveillance in Bergen, Norway mimic clinical prevalence. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112788. [PMID: 34571418 DOI: 10.1016/j.ecoenv.2021.112788] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
The aim of this study was to examine antibiotic resistance profiles and diversity of β-lactamases in Escherichia coli present within the population and the potential spread of resistant E. coli into the receiving environment using city-scale sewage surveillance. In E. coli isolates from ECC plates without antibiotics from ten influent samples (n = 300), highest resistance was observed against ampicillin (16.6%), sulfamethoxazole (9.7%) and trimethoprim (9.0%), while in effluent samples (n = 262) it was against sulfamethoxazole (11.8%), ampicillin (11.5%) and tetracycline (8.8%). All isolates (n = 123) obtained on cefotaxime-containing plates were multidrug-resistant. Several clinically important antibiotic resistance genes (ARGs) were detected in 46 E. coli isolates subjected to whole-genome sequencing, including carbapenemases like NDM-6, VIM-1 and OXA-48-variant, as well as tigecycline resistance gene tet(X4). CTX-M-15 was the most prevalent (42.9%) extended-spectrum β-lactamase among cefotaxime-resistant isolates, followed by CTX-M-27 (31.4%) and CTX-M-14 (17.1%), resembling clinical prevalence in Norway. Most of the sequenced isolates carried other clinically relevant ARGs, such as dfrA17, sul1, sul2, tet(A), aph(6)-Id, aph(3'')-Ib and aadA5. Sixteen different sequence types (STs) were identified, including ST131 (39.1%), ST38 (10.9%) and ST69 (8.7%). One E. coli isolate belonging to novel ST (ST11874) carried multiple virulence factors including genotoxin, salmochelin, aerobactin and yersiniabactin, suggesting that this isolate has potential to cause health concerns in future. Our study reveals presence of clinically relevant ARGs like blaNDM-6 and tet(X4) in pathogenic strains, which have so far not been reported from the clinics in Norway. Our study may thus, provide a framework for population-based surveillance of antibiotic resistance.
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Affiliation(s)
- Didrik H Grevskott
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Fatemeh Z Ghavidel
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Cecilie S Svanevik
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Nachiket P Marathe
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway.
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de Lastours V, Laouénan C, Royer G, Carbonnelle E, Lepeule R, Esposito-Farèse M, Clermont O, Duval X, Fantin B, Mentré F, Decousser JW, Denamur E, Lefort A. Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it. J Antimicrob Chemother 2021; 75:2334-2343. [PMID: 32417924 DOI: 10.1093/jac/dkaa161] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Escherichia coli bloodstream infections (BSIs) account for high mortality rates (5%-30%). Determinants of death are unclear, especially since the emergence of ESBL producers. OBJECTIVES To determine the relative weight of host characteristics, bacterial virulence and antibiotic resistance in the outcome of patients suffering from E. coli BSI. METHODS All consecutive patients suffering from E. coli BSI in seven teaching hospitals around Paris were prospectively included for 10 months. E. coli isolates were sequenced using Illumina NextSeq technology to determine the phylogroup, ST/ST complex (STc), virulence and antimicrobial resistance gene content. Risk factors associated with death at discharge or Day 28 were determined. RESULTS Overall, 545 patients (mean ± SD age 68.5 ± 16.5 years; 52.5% male) were included. Mean Charlson comorbidity index (CCI) was 5.6 (± 3.1); 19.6% and 12.8% presented with sepsis and septic shock, respectively. Portals of entry were mainly urinary (51.9%), digestive (41.9%) and pulmonary (3.5%); 98/545 isolates (18%) were third-generation cephalosporin resistant (3GC-R), including 86 ESBL producers. In-hospital death (or at Day 28) was 52/545 (9.5%). Factors independently associated with death were a pulmonary portal of entry [adjusted OR (aOR) 6.54, 95% CI 2.23-19.2, P = 0.0006], the iha_17 virulence gene (aOR 4.41, 95% CI 1.23-15.74, P = 0.022), the STc88 (aOR 3.62, 95% CI 1.30-10.09, P = 0.014), healthcare-associated infections (aOR 1.98, 95% CI 1.04-3.76, P = 0.036) and high CCI (aOR 1.14, 95% CI 1.04-1.26, P = 0.006), but not ESBL/3GC-R. CONCLUSIONS Host factors, portal of entry and bacterial characteristics remain major determinants associated with mortality in E. coli BSIs. Despite a high prevalence of ESBL producers, antibiotic resistance did not impact mortality. (ClinicalTrials.gov identifier: NCT02890901.).
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Affiliation(s)
- V de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
| | - C Laouénan
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - G Royer
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - E Carbonnelle
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Microbiologie, Hôpital Avicenne, AP-HP, F-93000 Bobigny, France
| | - R Lepeule
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - M Esposito-Farèse
- Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - O Clermont
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France
| | - X Duval
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Centre Investigation Clinique INSERM CIC-1425, Bichat Hospital, F-75018 France
| | - B Fantin
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
| | - F Mentré
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - J W Decousser
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - E Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018 Paris, France
| | - A Lefort
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
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9
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Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med 2021; 13:77. [PMID: 33952335 PMCID: PMC8097792 DOI: 10.1186/s13073-021-00892-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captured the emergence of some of them. However, data on within sequence type (ST) population genetic structure evolution are rare. Methods We compared whole genome sequences of 912 E. coli isolates responsible for bloodstream infections from two multicenter clinical trials that were conducted in the Paris area, France, 12 years apart, in teaching hospitals belonging to the same institution (“Assistance Publique-Hôpitaux de Paris”). We analyzed the strains at different levels of granularity, i.e., the phylogroup, the ST complex (STc), and the within STc clone taking into consideration the evolutionary history, the resistance, and virulence gene content as well as the antigenic diversity of the strains. Results We found a mix of stability and changes overtime, depending on the level of comparison. Overall, we observed an increase in antibiotic resistance associated to a restricted number of genetic determinants and in strain plasmidic content, whereas phylogroup distribution and virulence gene content remained constant. Focusing on STcs highlighted the pauci-clonality of the populations, with only 11 STcs responsible for more than 73% of the cases, dominated by five STcs (STc73, STc131, STc95, STc69, STc10). However, some STcs underwent dramatic variations, such as the global pandemic STc131, which replaced the previously predominant STc95. Moreover, within STc131, 95 and 69 genomic diversity analysis revealed a highly dynamic pattern, with reshuffling of the population linked to clonal replacement sometimes coupled with independent acquisitions of virulence factors such as the pap gene cluster bearing a papGII allele located on various pathogenicity islands. Additionally, STc10 exhibited huge antigenic diversity evidenced by numerous O:H serotype/fimH allele combinations, whichever the year of isolation. Conclusions Altogether, these data suggest that the bloodstream niche is occupied by a wide but specific phylogenetic diversity and that highly specialized extra-intestinal clones undergo frequent turnover at the within ST level. Additional worldwide epidemiological studies overtime are needed in different geographical and ecological contexts to assess how generalizable these data are. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00892-0.
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Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Mélanie Mercier Darty
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Jean-Winoc Decousser
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France. .,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018, Paris, France.
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10
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Success of Escherichia coli O25b:H4 Sequence Type 131 Clade C Associated with a Decrease in Virulence. Infect Immun 2020; 88:IAI.00576-20. [PMID: 32989036 PMCID: PMC7671891 DOI: 10.1128/iai.00576-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli O25b:H4 sequence type 131 (ST131), which is resistant to fluoroquinolones and which is a producer of CTX-M-15, is globally one of the major extraintestinal pathogenic E. coli (ExPEC) lineages. Phylogenetic analyses showed that multidrug-resistant ST131 strains belong to clade C, which recently emerged from clade B by stepwise evolution. It has been hypothesized that features other than multidrug resistance could contribute to this dissemination since other major global ExPEC lineages (ST73 and ST95) are mostly antibiotic susceptible. Escherichia coli O25b:H4 sequence type 131 (ST131), which is resistant to fluoroquinolones and which is a producer of CTX-M-15, is globally one of the major extraintestinal pathogenic E. coli (ExPEC) lineages. Phylogenetic analyses showed that multidrug-resistant ST131 strains belong to clade C, which recently emerged from clade B by stepwise evolution. It has been hypothesized that features other than multidrug resistance could contribute to this dissemination since other major global ExPEC lineages (ST73 and ST95) are mostly antibiotic susceptible. To test this hypothesis, we compared early biofilm production, presence of ExPEC virulence factors (VFs), and in vivo virulence in a mouse sepsis model in 19 and 20 epidemiologically relevant strains of clades B and C, respectively. Clade B strains were significantly earlier biofilm producers (P < 0.001), carriers of more VFs (P = 4e−07), and faster killers of mice (P = 2e−10) than clade C strains. Gene inactivation experiments showed that the H30-fimB and ibeART genes were associated with in vivo virulence. Competition assays in sepsis, gut colonization, and urinary tract infection models between the most anciently diverged strain (B1 subclade), one C1 subclade strain, and a B4 subclade recombining strain harboring some clade C-specific genetic events showed that the B1 strain always outcompeted the C1 strain, whereas the B4 strain outcompeted the C1 strain, depending on the mouse niches. All these findings strongly suggest that clade C evolution includes a progressive loss of virulence involving multiple genes, possibly enhancing overall strain fitness by avoiding severe infections, even if it comes at the cost of a lower colonization ability.
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11
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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12
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Hutinel M, Huijbers PMC, Fick J, Åhrén C, Larsson DGJ, Flach CF. Population-level surveillance of antibiotic resistance in Escherichia coli through sewage analysis. ACTA ACUST UNITED AC 2020; 24. [PMID: 31530345 PMCID: PMC6749774 DOI: 10.2807/1560-7917.es.2019.24.37.1800497] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
IntroductionThe occurrence of antibiotic resistance in faecal bacteria in sewage is likely to reflect the current local clinical resistance situation.AimThis observational study investigated the relationship between Escherichia coli resistance rates in sewage and clinical samples representing the same human populations.MethodsE. coli were isolated from eight hospital (n = 721 isolates) and six municipal (n = 531 isolates) sewage samples, over 1 year in Gothenburg, Sweden. An inexpensive broth screening method was validated against disk diffusion and applied to determine resistance against 11 antibiotics in sewage isolates. Resistance data on E. coli isolated from clinical samples from corresponding local hospital and primary care patients were collected during the same year and compared with those of the sewage isolates by linear regression.ResultsE. coli resistance rates derived from hospital sewage and hospital patients strongly correlated (r2 = 0.95 for urine and 0.89 for blood samples), as did resistance rates in E. coli from municipal sewage and primary care urine samples (r2 = 0.82). Resistance rates in hospital sewage isolates were close to those in hospital clinical isolates while resistance rates in municipal sewage isolates were about half of those measured in primary care isolates. Resistance rates in municipal sewage isolates were more stable between sampling occasions than those from hospital sewage.ConclusionOur findings provide support for development of a low-cost, sewage-based surveillance system for antibiotic resistance in E. coli, which could complement current monitoring systems and provide clinically relevant antibiotic resistance data for countries and regions where surveillance is lacking.
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Affiliation(s)
- Marion Hutinel
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Patricia Maria Catharina Huijbers
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Jerker Fick
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Christina Åhrén
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Dan Göran Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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13
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Santos ACDM, Santos FF, Silva RM, Gomes TAT. Diversity of Hybrid- and Hetero-Pathogenic Escherichia coli and Their Potential Implication in More Severe Diseases. Front Cell Infect Microbiol 2020; 10:339. [PMID: 32766163 PMCID: PMC7381148 DOI: 10.3389/fcimb.2020.00339] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
Although extraintestinal pathogenic Escherichia coli (ExPEC) are designated by their isolation site and grouped based on the type of host and the disease they cause, most diarrheagenic E. coli (DEC) are subdivided into several pathotypes based on the presence of specific virulence traits directly related to disease development. This scenario of a well-categorized E. coli collapsed after the German outbreak of 2011, caused by one strain bearing the virulence factors of two different DEC pathotypes (enteroaggregative E. coli and Shiga toxin-producing E. coli). Since the outbreak, many studies have shown that this phenomenon is more frequent than previously realized. Therefore, the terms hybrid- and hetero-pathogenic E. coli have been coined to describe new combinations of virulence factors among the classic E. coli pathotypes. In this review, we provide an overview of these classifications and highlight the E. coli genomic plasticity that results in some mixed E. coli pathotypes displaying novel pathogenic strategies, which lead to a new symptomatology related to E. coli diseases. In addition, as the capacity for genome interrogation has grown in the last few years, it is clear that genes encoding some virulence factors, such as Shiga toxin, are found among different E. coli pathotypes to which they have not traditionally been associated, perhaps foreshowing their emergence in new and severe outbreaks caused by such hybrid strains. Therefore, further studies regarding hetero-pathogenic and hybrid-pathogenic E. coli isolates are necessary to better understand and control the spread of these pathogens.
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Affiliation(s)
- Ana Carolina de Mello Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Clonal Structure, Virulence Factor-encoding Genes and Antibiotic Resistance of Escherichia coli, Causing Urinary Tract Infections and Other Extraintestinal Infections in Humans in Spain and France during 2016. Antibiotics (Basel) 2020; 9:antibiotics9040161. [PMID: 32260467 PMCID: PMC7235800 DOI: 10.3390/antibiotics9040161] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent, especially in Spain, while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of extended-spectrum beta-lactamase (ESBL) enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isolates belonged to only four of the dominant clones (B2-CH40-30-ST131, B2-CH40-41-ST131, C-CH4-39-ST88 and D-CH35-27-ST69). Among the remaining MDR isolates, two isolates belonged to B2-CH14-64-ST1193, i.e., the new global emergent MDR clone. Moreover, a hybrid extraintestinal pathogenic E.coli (ExPEC)/enteroaggregative isolate belonging to the A-CH11-54-ST10 clone was identified.
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15
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Vieira PCG, Espinoza-Culupú AO, Nepomuceno R, Alves MR, Lebrun I, Elias WP, Ruiz RC. Secreted autotransporter toxin (Sat) induces cell damage during enteroaggregative Escherichia coli infection. PLoS One 2020; 15:e0228959. [PMID: 32084148 PMCID: PMC7034920 DOI: 10.1371/journal.pone.0228959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 01/27/2020] [Indexed: 12/30/2022] Open
Abstract
Secreted autotransporter toxin (Sat) is a 107-kDa serine protease autotransporter of Enterobacteriaceae (SPATE) presenting cytotoxic activity in renal and bladder cells. Further studies have detected the Sat-encoding gene (sat) in enteroaggregative Escherichia coli (EAEC) and in E. coli strains isolated from neonatal septicemia and meningitis. Here, we investigated the role of Sat as a cytotoxin of EAEC. Sat was purified from a strain of E. coli harboring sat (DEC/Sat+, O126:H2) and used to raise antibodies in rabbit. The presence of Sat was detected by ELISA in the supernatant of 93.7% of EAEC strains harboring sat and in none lacking the gene. The effect of Sat during infection was investigated in polarized Caco-2 cells infected with Sat-producing EAEC (CV323/77, O125ab:H21). This strain induced intense cell detachment, which was inhibited by PMSF or Sat antiserum. Also, sat transcription and Sat production were detected during infection. Here we demonstrate that Sat is internalized in polarized cells leading to F-actin disruption which preceded cell detachment. A comparative study of the toxin action in cell lines corresponding to the infection sites in which bacteria carrying the sat gene have been isolated was performed. Cells originating from the gastrointestinal tract (Caco-2), urinary (LLC-PK1) and endothelium (HUVEC) were incubated with purified Sat. The time required for observation of cell damage differed according to the cell line. HUVEC cells were more sensitive to Sat than cells derived from urinary and intestinal tracts. The intense activity of Sat on the endothelial cells suggests that Sat could also be a virulence factor for the bacteria in the bloodstream. In addition, this is the first work demonstrating that Sat induces cytotoxic effect during EAEC infection in vitro. The cell damage observed during infection indicates that Sat may be another toxin with cytotoxic role in the EAEC pathogenesis.
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Affiliation(s)
| | | | | | - Marina R. Alves
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Ivo Lebrun
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
| | - Waldir P. Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Rita C. Ruiz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
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16
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Freire CA, Santos ACM, Pignatari AC, Silva RM, Elias WP. Serine protease autotransporters of Enterobacteriaceae (SPATEs) are largely distributed among Escherichia coli isolated from the bloodstream. Braz J Microbiol 2020; 51:447-454. [PMID: 31965549 DOI: 10.1007/s42770-020-00224-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/07/2020] [Indexed: 12/29/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the major cause of Gram-negative-related sepsis. Bacterial survival in the bloodstream is mediated by a variety of virulence traits, including those mediating immune system evasion. Serine protease autotransporters of Enterobacteriaceae (SPATE) constitute a superfamily of virulence factors that can cause tissue damage and cleavage of molecules of the complement system, which is a key feature for the establishment of infection in the bloodstream. In this study, we analyzed 278 E. coli strains isolated from human bacteremia from inpatients of both genders, different ages, and clinical conditions. These strains were screened for the presence of SPATE-encoding genes as well as for phylogenetic classification and intrinsic virulence of ExPEC. SPATE-encoding genes were detected in 61.2% of the strains and most of these strains (44.6%) presented distinct SPATE-encoding gene profiles. sat was the most frequent gene among the entire collection, found in 34.2%, followed by vat (28.4%), pic (8.3%), and tsh (4.7%). Although in low frequencies, espC (0.7%), eatA (1.1%), and espI (1.1%) were detected and are being reported for the first time in extraintestinal isolates. The presence of SPATE-encoding genes was positively associated to phylogroup B2 and intrinsic virulent strains. These findings suggest that SPATEs are highly prevalent and involved in diverse steps of the pathogenesis of bacteremia caused by E. coli.
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Affiliation(s)
- Claudia A Freire
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, SP, 05503-900, Brazil
| | - Ana Carolina M Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Antonio C Pignatari
- Laboratório Especial de Microbiologia Clínica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rosa M Silva
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, SP, 05503-900, Brazil.
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17
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La Combe B, Clermont O, Messika J, Eveillard M, Kouatchet A, Lasocki S, Corvec S, Lakhal K, Billard-Pomares T, Fernandes R, Armand-Lefevre L, Bourdon S, Reignier J, Fihman V, de Prost N, Bador J, Goret J, Wallet F, Denamur E, Ricard JD. Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012-2014. Emerg Infect Dis 2019; 25:710-718. [PMID: 30882313 PMCID: PMC6433033 DOI: 10.3201/eid2504.180944] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.
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18
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Billard-Pomares T, Clermont O, Castellanos M, Magdoud F, Royer G, Condamine B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Pognard D, Glodt J, Dion S, Rigal O, Picard B, Denamur E, Branger C. The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli. Antimicrob Agents Chemother 2019; 63:e00635-19. [PMID: 31138573 PMCID: PMC6658758 DOI: 10.1128/aac.00635-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023] Open
Abstract
We previously identified an operon involved in an arginine deiminase (ADI) pathway (arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-β-lactamase (ESBL)-producing E. coli strains. We studied two collections of human E. coli isolated in France (n = 493) and England (n = 1,509) and show that the prevalence of the arc operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.5%), (ii) is higher in CTX-M-producing strains (16%) than in other ESBL producers (3.5%), and (iii) increased over time in ESBL-producing strains from 0% before 2000 to 43.3% in 2011 to 2012. The arc operon, found in strains from various phylogenetic backgrounds, is carried by IncF plasmids (85%) or chromosomes (15%) in regions framed by numerous insertion sequences, indicating multiple arrivals. Competition experiments showed that the arc operon enhances fitness of the strain in vitro in lysogeny broth with arginine. In vivo competition experiments showed that the arc operon is advantageous for the strain in a mouse model of urinary tract infection (UTI), whereas it is a burden in a mouse model of intestinal colonization. In summary, we have identified a trait linked to CTX-M-producing strains that is responsible for a trade-off between two main E. coli lifestyles, UTI and gut commensalism. This trait alone cannot explain the wide spread of ESBLs in E. coli but merits epidemiological surveillance.
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Affiliation(s)
- Typhaine Billard-Pomares
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Olivier Clermont
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Miguel Castellanos
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Fatma Magdoud
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Guilhem Royer
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Bénédicte Condamine
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Stéphane Cruveiller
- UMR 8030, CNRS, Institut de Génomique-Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Évry-Val-d'Essonne, CEA, Évry, France
| | - Claudine Médigue
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Dominique Pognard
- APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France
| | - Jeremy Glodt
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France
| | - Sara Dion
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
| | - Odile Rigal
- Service de Biochimie-Hormonologie, Hôpital Robert Debré, Paris, France
| | - Bertrand Picard
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Hôpital Avicenne, Service de Microbiologie clinique, Bobigny, France
| | - Erick Denamur
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
- APHP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Catherine Branger
- IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris 13, Sorbonne Paris Cité, Paris, France
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Flament-Simon SC, Duprilot M, Mayer N, García V, Alonso MP, Blanco J, Nicolas-Chanoine MH. Association Between Kinetics of Early Biofilm Formation and Clonal Lineage in Escherichia coli. Front Microbiol 2019; 10:1183. [PMID: 31214138 PMCID: PMC6555128 DOI: 10.3389/fmicb.2019.01183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 01/27/2023] Open
Abstract
Background Escherichia coli biofilm formation has mostly been assessed in specific pathogenic E. coli groups. Here, we assessed the early biofilm formation (EBF), i.e., adhesion stage, using the BioFilm Ring Test® on 394 E. coli clinical isolates (EC) [196 consecutively isolated (CEC) in 2016 and 198 ESBL-producing E. coli (ESBLEC) isolated in 2015]. Then, biofilm-forming ability was contrasted with phylogroups, clonotypes (fumC-fimH), and sequence types (STs), all being used to define clones, virulence factors (VF), and FimB. Result According to both biofilm production levels at 2, 3, and 5 h, and EBF kinetics over 5 h, CEC and ESBLEC isolates segregated into three EBF groups: strong (G1), moderate (G2), and weak (G3) producers. At 2 h, strong producers were more frequent among CEC (n = 28; 14.3%) than among ESBLEC (n = 8; 4%) (P = 0.0004). As CEC and ESBLEC isolates showed similar individual EBF kinetics in each group, a comparison of isolate features between each group was applied to gathered CEC and ESBLEC isolates after 2 h of incubation, 2 h being the most representative time point of the CEC and ESBLEC isolate segregation into the three groups. Phylogroup B2 displayed by 51.3% of the 394 isolates was more frequent in G1 (77.8%) than in G3 (47.6%) (P = 0.0006). The 394 isolates displayed 153 clones, of which 31 included at least three isolates. B2-CH14-2-ST127, B2-CH40-22-ST131, B2-CH52-5/14-ST141, and E-CH100-96-ST362 clones were associated with G1 (P < 0.03) and accounted for 41.7% of G1 isolates. B2-CH40-30-ST131 clone was associated with G3 (P < 0.0001) and accounted for 25.5% of G3 isolates. VF mean was higher among G1 than among G3 isolates (P < 0.001). FimB-P2 variant was associated with G1 (P = 0.0011) and FimB-P1 variant was associated with G3 (P = 0.0023). Clone, some VF, and FimB were associated with EBF, with clonal lineage being able to explain 72% of the variability of EBF. Conclusion Among our 394 isolates, <10% are able to quickly and persistently produce high biofilm levels over 5 h. These isolates belong to a few clones previously described in various studies as dominant gut colonizers in mammalians and birds and comprised the B2-CH40-22-ST131 clone, i.e., the ancestor of the globally disseminated B2-CH40-30-ST131 clone that is the dominant clone among the weak biofilm producers.
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Affiliation(s)
- Saskia-Camille Flament-Simon
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Marion Duprilot
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.,IAME, UMR 1137, INSERM, Université Paris Diderot, Paris, France
| | - Noémie Mayer
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - María Pilar Alonso
- Unidade de Microbioloxía, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Marie-Hélène Nicolas-Chanoine
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France.,IAME, UMR 1137, INSERM, Université Paris Diderot, Paris, France
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20
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Bourrel AS, Poirel L, Royer G, Darty M, Vuillemin X, Kieffer N, Clermont O, Denamur E, Nordmann P, Decousser JW, LAFAURIE M, BERCOT B, WALEWSKI V, LESCAT M, CARBONNELLE E, OUSSER F, IDRI N, RICARD JD, LANDRAUD L, LE DORZE M, JACQUIER H, CAMBAU E, LEPEULE R, GOMART C. Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways. J Antimicrob Chemother 2019; 74:1521-1530. [DOI: 10.1093/jac/dkz090] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/04/2023] Open
Affiliation(s)
- Anne Sophie Bourrel
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Laurent Poirel
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Guilhem Royer
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mélanie Darty
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Xavier Vuillemin
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
| | - Nicolas Kieffer
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Olivier Clermont
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
| | - Erick Denamur
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Patrice Nordmann
- Laboratoire Européen Associé INSERM, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- National Reference Centre for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Jean-Winoc Decousser
- Laboratoire de Bactériologie et d’Hygiène Hospitalière, CHU Henri Mondor, Assistance Publique - Hôpitaux de Paris, Créteil, France
- IAME, UMR1137 INSERM, Université Paris Diderot, Université Paris Nord, Emerging Antibiotic Resistance in Gram-Negative Bacteria, Paris, France
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21
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Desroches M, Clermont O, Lafeuillade B, Rodriguez C, Darty M, Royer G, Bouvet O, Ounnoughene N, Noizat-Pirenne F, Denamur E, Decousser JW. Genotypic and phenotypic characteristics of Escherichia coli involved in transfusion-transmitted bacterial infections: implications for preventive strategies. Transfusion 2019; 58:1940-1950. [PMID: 30198609 DOI: 10.1111/trf.14812] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/05/2018] [Accepted: 04/09/2018] [Indexed: 01/23/2023]
Abstract
BACKGROUND Transfusion-transmitted bacterial infections (TTBIs) are the main residual infectious complications of transfusions. Escherichia coli and platelet (PLT) concentrates may be epidemiologically associated, leading to severe, if not lethal, TTBIs. We investigated the genotypic and phenotypic reasons for this clinically deleterious combination. STUDY DESIGN AND METHODS We investigated a French national E. coli strain collection related to six independent episodes of TTBIs. Their phenotypic characterizations included antibiotic susceptibility testing, growth testing under different culture conditions, serum survival assays, and virulence in a sepsis mouse model. Their genotypic characterizations included polymerase chain reaction phylotyping, whole genome sequencing, and a subsequent in silico analysis. RESULTS We highlighted a selection process of highly extraintestinal virulent strains, mainly belonging to the B2 phylogroup, adapted to the hostile environment (high citrate concentration and a bactericidal serum effect) of apheresis-collected platelet concentrates (PCs). Compared to controls, the E. coli TTBI strains grew faster in the PCs due to a superior ability to capture iron. The in vitro growth performances were highly compatible with blood-derived product real-life conditions, including storage conditions and delays. The consistent serum resistance of TTBI strains promotes their survival in both the donor's and the receiver's blood and in the PCs. CONCLUSION This study pointed out that E. coli strains responsible for TTBI exhibit very specific traits. They belong to the extraintestinal pathogenic phylogroups and have a high intrinsic virulence. They can be resistant to complement, capture iron, and grow in the apheresis-collected PCs. These findings therefore support the reinforcement of the postdonation information.
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Affiliation(s)
- Marine Desroches
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France.,Department of Bacteriology and Infection Control, University Hospital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Olivier Clermont
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France
| | - Bruno Lafeuillade
- Rhône-Alpes French Blood Establishment-Grenoble Site, La Tronche, France
| | - Christophe Rodriguez
- Next Generation Sequencing Platform, University Hospital Henri Mondor, Créteil, France
| | - Mélanie Darty
- Next Generation Sequencing Platform, University Hospital Henri Mondor, Créteil, France
| | - Guilhem Royer
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France.,Department of Bacteriology and Infection Control, University Hospital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | - Odile Bouvet
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France
| | | | | | - Erick Denamur
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France.,Department of Molecular Genetics, University Hospital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Winoc Decousser
- INSERM UMR1137, IAME, Paris Diderot University, Faculty of Medicine Xavier Bichat, Paris, France.,Department of Bacteriology and Infection Control, University Hospital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
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Clinical and Molecular Correlates of Escherichia coli Bloodstream Infection from Two Geographically Diverse Centers in Rochester, Minnesota, and Singapore. Antimicrob Agents Chemother 2018; 62:AAC.00937-18. [PMID: 30082285 DOI: 10.1128/aac.00937-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/26/2018] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated H30 subclone, H30R1 and H30Rx. We examined clinical and molecular correlates of E. coli bacteremia in two geographically distinct centers. We retrospectively studied 251 unique E. coli bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, blaCTX-M type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all E. coli bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated H30Rx clade was more prominent in SG than in MN (15% versus 4%; P = 0.04). In SG only, patients with STc131 (versus other E. coli STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; P = 0.005); this was true specifically for patients with H30Rx (odds ratio, 7.0; P = 0.005). H30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for H30Rx than for H30R1, non-H30 STc131, and non-STc131 isolates (P < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated H30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for H30/H30Rx might facilitate earlier prescribing of active therapy.
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Liu Y, Palmer SR, Chang H, Combs AN, Burne RA, Koo H. Differential oxidative stress tolerance of Streptococcus mutans isolates affects competition in an ecological mixed-species biofilm model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:12-22. [PMID: 29124888 PMCID: PMC5812797 DOI: 10.1111/1758-2229.12600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 05/10/2023]
Abstract
Streptococcus mutans strongly influences the development of pathogenic biofilms associated with dental caries. Our understanding of S. mutans behaviour in biofilms is based on a few well-characterized laboratory strains; however, individual isolates vary widely in genome content and virulence-associated phenotypes, such as biofilm formation and environmental stress sensitivity. Using an ecological biofilm model, we assessed the impact of co-cultivation of several S. mutans isolates with Streptococcus oralis and Actinomyces naeslundii on biofilm composition following exposure to sucrose. The laboratory reference strain S. mutans UA159 and clinical isolates Smu44 (most aciduric), Smu56 (altered biofilm formation) and Smu81 (more sensitive to oxidative stress) were used. Our data revealed S. mutans isolates varied in their ability to compete and become dominant in the biofilm after the addition of sucrose, and this difference correlated with sensitivity to H2 O2 produced by S. oralis. Smu81 was particularly sensitive to H2 O2 and could not compete with S. oralis in mixed-species biofilm, despite forming robust biofilms on its own. Thus, diminished oxidative stress tolerance in S. mutans isolates can impair their ability to compete in complex biofilms, even in the presence of sucrose, which could influence the progression of a healthy biofilm community to one capable of causing disease.
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Affiliation(s)
- Yuan Liu
- Department of Orthodontics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sara R. Palmer
- Division of Biosciences, The Ohio State University, Columbus, Ohio
| | - Hsiaochi Chang
- Division of Biosciences, The Ohio State University, Columbus, Ohio
| | - Ashton N. Combs
- Division of Biosciences, The Ohio State University, Columbus, Ohio
| | - Robert A. Burne
- Department of Oral Biology, University of Florida, Gainesville, Florida
| | - Hyun Koo
- Department of Orthodontics, University of Pennsylvania, Philadelphia, Pennsylvania
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24
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Messika J, Clermont O, Landraud L, Schmidt M, Aubry A, Sougakoff W, Fernandes R, Combes A, Denamur E, Ricard JD. Extra-corporeal membrane oxygenation-associated infections: implication of extra-intestinal pathogenic Escherichia coli clones. J Med Microbiol 2017; 66:1189-1195. [DOI: 10.1099/jmm.0.000554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jonathan Messika
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Luce Landraud
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Microbiologie, F-92700, Colombes, France
| | - Matthieu Schmidt
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Alexandra Aubry
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Wladimir Sougakoff
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Romain Fernandes
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Alain Combes
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, F-75018, Paris, France
| | - Jean-Damien Ricard
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
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