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Jamali H, Akrami F, Bouakkaz S, Dozois CM. Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis. Microb Pathog 2024; 194:106843. [PMID: 39117015 DOI: 10.1016/j.micpath.2024.106843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/22/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.
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Affiliation(s)
- Hossein Jamali
- Institut National de La Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada; Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Fariba Akrami
- Institut National de La Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada; Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Souhaib Bouakkaz
- École de Technologie Supérieure, 1100 R. Notre Dame Ouest, Montréal, QC H3C 1K3, Canada
| | - Charles M Dozois
- Institut National de La Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada; Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada.
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Heidari A, Emami MH, Maghool F, Mohammadzadeh S, Kadkhodaei Elyaderani P, Safari T, Fahim A, Kamali Dolatabadi R. Molecular epidemiology, antibiotic resistance profile and frequency of integron 1 and 2 in adherent-invasive Escherichia coli isolates of colorectal cancer patients. Front Microbiol 2024; 15:1366719. [PMID: 38939191 PMCID: PMC11208319 DOI: 10.3389/fmicb.2024.1366719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
This study explores the prevalence of adherent-invasive Escherichia coli (AIEC) in colorectal cancer (CRC) patients and investigates the potential of effective intracellular antibiotics as a therapeutic strategy for CRC patients with AIEC infections. Considering the pivotal role of integrons in bacterial antibiotic resistance, the frequency of class 1 and 2 integrons in AIEC isolated from CRC patients, in one of the referenced 3 gastroenterology clinics in Isfahan, Iran was examined. AIEC strains were isolated from the colorectal biopsies and their antimicrobial sensitivity was assessed using the disc diffusion method. Polymerase chain reaction (PCR) was employed to detect intl1 and intl2. The multilocus sequence typing (MLST) method was utilized to type 10 selected isolates. Of the 150 samples, 24 were identified as AIEC, with the highest number isolated from CRC2 (33.4%) and CRC1 (29.16%), and the least from the FH group (8.3%) and control group (12.5%). int1 in 79.2% and int2 in 45.8% of AIEC strains were found and 41.6% of strains had both integrons. AIEC isolates with int1 exhibited the highest sensitivity to trimethoprim-sulfamethoxazole (57.9%), while those with int2 showed the highest sensitivity to ciprofloxacin (63.6%). A significant association between resistance to rifampin and integron 2 presence in AIEC isolates was observed. Furthermore, a significant correlation between integron 1 presence, invasion, survival, and replication within macrophages in AIEC strains was identified. MLST analysis revealed ST131 from CC131 with integron 1 as the most common sequence type (ST). The emergence of such strains in CRC populations poses a serious public health threat. The distribution pattern of STs varied among studied groups, with pandemic STs highlighting the importance of examining and treating patients infected with these isolates. Comprehensive prospective clinical investigations are warranted to assess the prognostic value of detecting this pathovar in CRC and to evaluate therapeutic techniques targeting drug-resistant AIECs, such as phage therapy, bacteriocins, and anti-adhesion compounds, for CRC prevention and treatment.
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Affiliation(s)
- Aida Heidari
- Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hassan Emami
- Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Maghool
- Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Samane Mohammadzadeh
- Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Tahereh Safari
- Physiology Department, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Alireza Fahim
- Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Razie Kamali Dolatabadi
- Department of Medicine, Najafabad Branch, Islamic Azad University, Najafabad, Iran
- Clinical Research Development Center, Najafabad Branch, Islamic Azad University, Najafabad, Iran
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Sereme Y, Schrimp C, Faury H, Agapoff M, Lefebvre-Wloszczowski E, Chang Marchand Y, Ageron-Ardila E, Panafieu E, Blec F, Coureuil M, Frapy E, Tsatsaris V, Bonacorsi S, Skurnik D. A live attenuated vaccine to prevent severe neonatal Escherichia coli K1 infections. Nat Commun 2024; 15:3021. [PMID: 38589401 PMCID: PMC11001983 DOI: 10.1038/s41467-024-46775-x] [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: 08/25/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Preterm birth is currently the leading cause of neonatal morbidity and mortality. Genetic, immunological and infectious causes are suspected. Preterm infants have a higher risk of severe bacterial neonatal infections, most of which are caused by Escherichia coli an in particular E. coli K1strains. Women with history of preterm delivery have a high risk of recurrence and therefore constitute a target population for the development of vaccine against E. coli neonatal infections. Here, we characterize the immunological, microbiological and protective properties of a live attenuated vaccine candidate in adult female mice and their pups against after a challenge by K1 and non-K1 strains of E. coli. Our results show that the E. coli K1 E11 ∆aroA vaccine induces strong immunity, driven by polyclonal bactericidal antibodies. In our model of meningitis, mothers immunized prior to mating transfer maternal antibodies to pups, which protect newborn mice against various K1 and non-K1 strains of E. coli. Given the very high mortality rate and the neurological sequalae associated with neonatal E. coli K1 meningitis, our results constitute preclinical proof of concept for the development of a live attenuated vaccine against severe E. coli infections in women at risk of preterm delivery.
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Affiliation(s)
- Youssouf Sereme
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
| | - Cécile Schrimp
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
| | - Helène Faury
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
- Department of Microbiology, Necker Hospital, University de Paris, Paris, France
| | - Maeva Agapoff
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
| | | | | | | | - Emilie Panafieu
- LEAT antenne Imagine- SFR Necker INSERM US 24, Paris, France
| | - Frank Blec
- LEAT antenne Imagine- SFR Necker INSERM US 24, Paris, France
| | - Mathieu Coureuil
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
| | - Eric Frapy
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France
| | - Vassilis Tsatsaris
- Maternité Port-Royal, hôpital Cochin, GHU Centre Paris cité, AP-HP, Paris, France
- FHU PREMA, Maternité Port-Royal, Paris, France
| | - Stephane Bonacorsi
- IAME, UMR 1137, INSERM, Université Paris Cité, Paris, France
- Laboratoire de Microbiologie, Hôpital Robert Debré, AP-HP, Paris, France
| | - David Skurnik
- Université Paris Cité, CNRS, INSERM, Institut Necker Enfants Malades, Paris, France.
- Department of Microbiology, Necker Hospital, University de Paris, Paris, France.
- FHU PREMA, Maternité Port-Royal, Paris, France.
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Tenderenda A, Łysakowska ME, Gawron-Skarbek A. The Prevalence of Alert Pathogens and Microbial Resistance Mechanisms: A Three-Year Retrospective Study in a General Hospital in Poland. Pathogens 2023; 12:1401. [PMID: 38133286 PMCID: PMC10746124 DOI: 10.3390/pathogens12121401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
The development of antibiotic resistance mechanisms hinders the treatment process. So far, there is limited data on the problem of bacterial resistance in hospitals in Central and Eastern Europe. Therefore, this study aimed to assess the prevalence of resistance mechanisms and alert pathogens based on reports regarding cultures of samples collected from general hospital patients in Poland in the period 2019-2021. This study examined the prevalence of resistance mechanisms and alert pathogens and the structure of microorganisms, including the type of diagnostic material in the hospital department. The frequency of occurrence and the trends were analysed based on Cochran's Q-test, relative change and the average annual rate of change (AARC). Of all 14,471 cultures, 3875 were positive for bacteria, and 737 were characterised by resistance mechanisms (19.0%). Alert pathogens were identified in 983 cases (24.6%), including pathogens isolated from blood samples. The most commonlyisolated bacteria were Escherichia coli (>20% of positive cultures), Enterococcus faecalis (7%), and Klebsiella pneumoniae (6%) increasing over time; Staphylococcus aureus (13%) was also found, but its proportion was decreasing over time. Extended-spectrum β-lactamase (ESBL) was the most frequent resistance mechanism in Internal Medicine (IM) (p < 0.001) and the Intensive Care Unit (ICU) (p < 0.01), as well as in ICU-COVID; this increased over the study period (AARC ↑34.9%). Methicillin-resistant Staphylococcus aureus (MRSA) (AARC ↓50.82%) and AmpC beta-lactamase (AARC ↓24.77%) prevalence fell over time. Also, the number of alert pathogens was dominant in the IM (p < 0.01) and ICU (p < 0.001). The most common alert pathogen was ESBL-positive E. coli. Gram-negative rods constitute a significant epidemiological problem in hospitals, especially the growing trend of ESBL in IM and ICU, which calls for increased control of sanitary procedures.
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Affiliation(s)
- Anna Tenderenda
- Department of Geriatrics, Medical University of Lodz, 90-647 Lodz, Poland;
| | - Monika Eliza Łysakowska
- Department of Microbiology and Medical Laboratory Immunology, Medical University of Lodz, 90-213 Lodz, Poland
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Praça J, Furtado R, Coelho A, Correia CB, Borges V, Gomes JP, Pista A, Batista R. Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal. Microorganisms 2023; 11:322. [PMID: 36838288 PMCID: PMC9964920 DOI: 10.3390/microorganisms11020322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Traditional cheeses are part of the Portuguese gastronomic identity, and raw milk of autochthonous species is a common primary ingredient. Here, we investigated the presence of Listeria monocytogenes, Coagulase Positive Staphylococci (CPS) and pathogenic Escherichia coli, as well as of indicator microorganisms (E. coli and other Listeria spp.) in 96 cured raw milk cheeses from the Alentejo region. Whole genome sequencing (WGS) of pathogenic E. coli and Listeria spp. as well as antimicrobial resistance (AMR) screening of E. coli isolates was also performed. L. monocytogenes, CPS > 104 cfu/g and Extraintestinal E. coli were detected in 15.6%, 16.9% and 10.1% of the samples, respectively. Moreover, L. monocytogenes > 102 cfu/g and Staphylococcal enterotoxins were detected in 4.2% and 2.2% of the samples, respectively. AMR was observed in 27.3% of the E. coli isolates, six of which were multidrug resistant. WGS analysis unveiled clusters of high closely related isolates for both L. monocytogenes and L. innocua (often correlating with the cheese producer). This study can indicate poor hygiene practices during milk collection/preservation or during cheese-making procedures and handling, and highlights the need of more effective prevention and control measures and of multi-sectoral WGS data integration, in order to prevent and detect foodborne bacterial outbreaks.
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Affiliation(s)
- Joana Praça
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
- Faculty of Farmacy, University of Lisbon, Avenida Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rosália Furtado
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Anabela Coelho
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Cristina Belo Correia
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
| | - Rita Batista
- Food Microbiology Laboratory, Food and Nutrition Department, National Institute of Health Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisbon, Portugal
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Lemlem M, Aklilu E, Mohammed M, Kamaruzzaman F, Zakaria Z, Harun A, Devan SS. Molecular detection and antimicrobial resistance profiles of Extended-Spectrum Beta-Lactamase (ESBL) producing Escherichia coli in broiler chicken farms in Malaysia. PLoS One 2023; 18:e0285743. [PMID: 37205716 DOI: 10.1371/journal.pone.0285743] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Antimicrobial resistance is one of the major public health threats globally. This challenge has been aggravated with the overuse and misuse of antibiotics in food animals and humans. The present study aimed to investigate the prevalence of Extended-Spectrum β-lactamase (ESBL) genes in Escherichia coli (E. coli) isolated from broiler chickens in Kelantan, Malaysia. A total of 320 cloacal swabs were collected from farms in different districts of Kelantan and were analyzed using routine bacteriology, antimicrobial susceptibility test, and molecular techniques for further identification and characterization of ESBL encoding genes. Based on PCR detection for the E. coli species-specific Pho gene, 30.3% (97/320) of isolates were confirmed as E. coli, and 84.5% (82/97) of the isolates were positive for at least one ESBL gene. Majority of the isolates, 62.9% (61/97) were harboring blaCTX-M followed by 45.4% (44/97) of blaTEM genes, while 16.5% (16/97) of the isolates were positive for both mcr-1 and ESBL genes. Overall, 93.8% (90/97) of the E. coli were resistant to three or more antimicrobials; indicating that the isolates were multi-drug resistance. 90.7% of multiple antibiotic resistance (MAR) index value greater than 0.2, would also suggest the isolates were from high-risk sources of contamination. The MLST result shows that the isolates are widely diverse. Our findings provide insight into the alarmingly high distribution of antimicrobial resistant bacteria, mainly ESBL producing E. coli in apparently healthy chickens indicating the role of food animals in the emergence and spread of antimicrobial resistance, and the potential public health threats it may pose.
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Affiliation(s)
- Mulu Lemlem
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
- Department of Medical Microbiology and Immunology, College of Health Science, Mekelle University, Tigray, Ethiopia
| | - Erkihun Aklilu
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
| | - Maizan Mohammed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
| | | | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Azian Harun
- School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Susmita Seenu Devan
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Kota Baharu, Malaysia
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Mercato A, Cortimiglia C, Abualsha’ar A, Piazza A, Marchesini F, Milani G, Bonardi S, Cocconcelli PS, Migliavacca R. Wild Boars as an Indicator of Environmental Spread of ESβL-Producing Escherichia coli. Front Microbiol 2022; 13:838383. [PMID: 35432265 PMCID: PMC9011151 DOI: 10.3389/fmicb.2022.838383] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) represents an increasing issue worldwide, spreading not only in humans and farmed animals but also in wildlife. One of the most relevant problems is represented by Extended-Spectrum Beta-Lactamases (ESβLs) producing Escherichia coli because they are the cause of important infections in human. Wild boars (Sus scrofa) as a source of ESβLs attracted attention due to their increasing density and their habits that lead them to be at the human-livestock-wildlife interface. The aim of this study was to increase the knowledge about the ESβLs E. coli strains carried by wild boars living in a particularly high-density area of Northern Italy. The analysis of 60 animals allowed to isolate 16 ESβL-producing E. coli strains (prevalence 23.3%), which were characterised from a phenotypical and molecular point of view. The overall analysis revealed that the 16 isolates were all not only ESβL producers but also multidrug resistant and carried different types of plasmid replicons. The genome analysis performed on a subset of isolates confirmed the heterogeneity observed with pulsed-field gel electrophoresis (PFGE) and highlighted the presence of two pandemic sequence types, ST131 and ST10, with different collections of virulence factors. The genomic context of ESβL genes further evidenced that all of them were surrounded by transposons and insertion sequences, suggesting the possibility to exchange AMR genes. Overall, this study shows the worrying dissemination of ESβL-producing E. coli in wild boars in Northern Italy, suggesting the role of these animals as a spreader of AMR and their inclusion in surveillance programmes, to shed light on the “One Health” complex interactions.
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Affiliation(s)
- Alessandra Mercato
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Claudia Cortimiglia
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Aseel Abualsha’ar
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Aurora Piazza
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Federica Marchesini
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Giovanni Milani
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Silvia Bonardi
- Department of Veterinary Science, Unit of Food Inspection, University of Parma, Parma, Italy
| | - Pier Sandro Cocconcelli
- Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
- *Correspondence: Pier Sandro Cocconcelli,
| | - Roberta Migliavacca
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
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Molecular Epidemiology of Multidrug-Resistant Uropathogenic Escherichia coli O25b Strains Associated with Complicated Urinary Tract Infection in Children. Microorganisms 2021; 9:microorganisms9112299. [PMID: 34835425 PMCID: PMC8623209 DOI: 10.3390/microorganisms9112299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Uropathogenic Escherichia coli (UPEC) has increased the incidence of urinary tract infection (UTI). It is the cause of more than 80% of community-acquired cystitis cases and more than 70% of uncomplicated acute pyelonephritis cases. Aim: The present study describes the molecular epidemiology of UPEC O25b clinical strains based on their resistance profiles, virulence genes, and genetic diversity. Methods: Resistance profiles were identified using the Kirby–Bauer method, including the phenotypic production of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). The UPEC serogroups, phylogenetic groups, virulence genes, and integrons were determined via multiplex PCR. Genetic diversity was established using pulsed-field gel electrophoresis (PFGE), and sequence type (ST) was determined via multilocus sequence typing (MLST). Results: UPEC strains (n = 126) from hospitalized children with complicated UTIs (cUTIs) were identified as O25b, of which 41.27% were multidrug resistant (MDR) and 15.87% were extensively drug resistant (XDR). The O25b strains harbored the fimH (95.23%), csgA (91.26%), papGII (80.95%), chuA (95.23%), iutD (88.09%), satA (84.92%), and intl1 (47.61%) genes. Moreover, 64.28% were producers of ESBLs and had high genetic diversity. ST131 (63.63%) was associated primarily with phylogenetic group B2, and ST69 (100%) was associated primarily with phylogenetic group D. Conclusion: UPEC O25b/ST131 harbors a wide genetic diversity of virulence and resistance genes, which contribute to cUTIs in pediatrics.
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Castanheira M, Simner PJ, Bradford PA. Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection. JAC Antimicrob Resist 2021; 3:dlab092. [PMID: 34286272 PMCID: PMC8284625 DOI: 10.1093/jacamr/dlab092] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.
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Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. Microorganisms 2021; 9:microorganisms9061299. [PMID: 34203637 PMCID: PMC8232093 DOI: 10.3390/microorganisms9061299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.
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Vianello MA, Cardoso B, Fuentes-Castillo D, Moura Q, Esposito F, Fuga B, Lincopan N, Egito EST. International high-risk clone of fluoroquinolone-resistant Escherichia coli O15:H1-D-ST393 in remote communities of Brazilian Amazon. INFECTION GENETICS AND EVOLUTION 2021; 91:104808. [PMID: 33737229 DOI: 10.1016/j.meegid.2021.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/07/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
The global dissemination of multidrug-resistant Escherichia coli lineages belonging to high- risk clones poses a significant public health threat. Herein we report the identification and genomic profiling of two multidrug-resistant E. coli strains [BL-II-03(2) and BL-II-11(3)] belonging to the O15:H1-D-ST393 (clonal complex 31) worldwide spread clone, isolated from fecal samples of indigenous peoples belonging to two different ethnic groups of remote communities of Brazilian Amazon. Genomic analysis revealed genes and mutations conferring resistance to β-lactams [blaTEM-1], aminoglycosides [aadA5, aph(3″)-Ib, aph(6)-Id], tetracyclines [tetB], sulfamethoxazole/trimethoprim [sul1, sul2, dfrA17], and fluoroquinolones [gyrA (D87N, S83L), parC (S80I, S57T), parE (L416F)]; and presence of IncQ1, IncFIA, and IncFIB(pB171) plasmids. On the other hand, phylogenomics of globally reported E. coli ST393 assigned E. coli strains BL-II-03(2) and BL-II-11(3) to a cluster comprising human isolates from Australia, Canada, China, Sweden, and United States of America. These results might provide valuable information for understanding dissemination of intercontinental multidrug-resistant clones in remote communities with low levels of antibiotic exposure.
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Affiliation(s)
- Marco Aurelio Vianello
- Graduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Brenda Cardoso
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil.
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Development of a chitosan-modified PLGA nanoparticle vaccine for protection against Escherichia coli K1 caused meningitis in mice. J Nanobiotechnology 2021; 19:69. [PMID: 33673858 PMCID: PMC7934409 DOI: 10.1186/s12951-021-00812-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background Escherichia coli K1 (E. coli K1) caused neonatal meningitis remains a problem, which rises the urgent need for an effective vaccine. Previously, we rationally designed and produced the recombinant protein OmpAVac (Vo), which elicited protective immunity against E. coli K1 infection. However, Vo has limited stability, which hinders its future industrial application. Method Chitosan-modified poly (lactic-co-glycolic acid) (PLGA) nanoparticles were prepared and used as carried for the recombinant Vo. And the safety, stability and immunogenicity of Vo delivered by chitosan-modified PLGA nanoparticles were tested in vitro and in a mouse model of bacteremia. Results We successfully generated chitosan-modified PLGA nanoparticles for the delivery of recombinant Vo (VoNP). In addition, we found that a freeze-drying procedure increases the stability of the VoNPs without changing the shape, size distribution and encapsulation of the Vo protein. Unlike aluminum adjuvant, the nanoparticles that delivered Vo were immunoprotective in mice even after storage for as long as 180 days. Conclusions We identified an effective strategy to improve the stability of Vo to maintain its immunogenicity, which will contribute to the future development of vaccines against E. coli K1.![]()
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Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12010009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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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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Prevalence of fluoroquinolone-resistant and broad-spectrum cephalosporin-resistant community-acquired urinary tract infections in Rio de Janeiro: Impact of genotypes ST69 and ST131. INFECTION GENETICS AND EVOLUTION 2020; 85:104452. [DOI: 10.1016/j.meegid.2020.104452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
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Cha MH, Ryu JG, Chi YM, Woo GJ. Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Fresh Produce and Agricultural Environments in Korea. J Food Prot 2020; 83:1115-1124. [PMID: 32083678 DOI: 10.4315/jfp-19-483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/20/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT This study was conducted to characterize Escherichia coli strains and evaluate the spread of antimicrobial resistance among these strains from fresh produce and farm environments in Korea. We then conducted phenotypic and genetic studies on antimicrobial-resistant isolates. We determined the genetic epidemiological characteristics of isolates that produced extended-spectrum β-lactamase (ESBL) and confirmed plasmid transfer in isolates that carried blaCTX-M-type genes. E. coli strains were isolated from 8 samples of fresh produce and 152 samples from the farm environment collected from May 2014 to June 2016. Cephalosporin resistance was the most prevalent (61.8%) type of resistance among the isolates. Five ESBL-producing strains with high genetic homology with E. coli of human or livestock origin were identified. Lateral transfer of plasmids harboring blaCTX-M-type genes to transconjugants was successful. Two isolates from Chinese cabbage and from water samples collected from a nearby stream harbored the ISEcp1-blaCTX-M-55-orf477 operon and were confirmed as sequence type 1196 and the same type of plasmid replicon, suggesting that cross-contamination was highly likely. A high-risk clone of sequence type 69 (clonal complex 69) isolates was also recovered from the farm environment. This study provides genetic evidence that antimicrobial resistance factors in E. coli from farm environments originate in the clinic or in livestock, highlighting the fact that good agricultural practices in farming are important to inhibit the spread of antimicrobial resistance to bacteria on fresh produce. HIGHLIGHTS
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Affiliation(s)
- Min-Hyeok Cha
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Graduate School, Korea University Seoul, Republic of Korea.,Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju, Republic of Korea
| | - Jae-Gee Ryu
- Microbial Safety Team, National Academy of Agricultural Science, Rural Development Administration, Wanju, Republic of Korea
| | - Young-Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University Seoul, Republic of Korea
| | - Gun-Jo Woo
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Graduate School, Korea University Seoul, Republic of Korea
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Kim B, Seo MR, Kim J, Kim Y, Wie SH, Ki M, Cho YK, Lim S, Lee JS, Kwon KT, Lee H, Cheong HJ, Park DW, Ryu SY, Chung MH, Pai H. Molecular Epidemiology of Ciprofloxacin-Resistant Escherichia coli Isolated from Community-Acquired Urinary Tract Infections in Korea. Infect Chemother 2020; 52:194-203. [PMID: 32406212 PMCID: PMC7335657 DOI: 10.3947/ic.2020.52.2.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/28/2020] [Indexed: 12/29/2022] Open
Abstract
Background Escherichia coli is the predominant causative pathogen for community-acquired urinary tract infections (UTIs), and the increase in fluoroquinolone-resistant E. coli is of great concern in Korea. The objectives of this study were to investigate the genotypic characteristics and molecular epidemiology of ciprofloxacin-resistant (CIP-R) E. coli isolated from community-acquired UTIs in Korea. Materials and Methods E. coli samples isolated from the blood or urine were collected from patients with community-acquired acute pyelonephritis aged 15 years and more who were admitted to 12 Korean hospitals from 1st April 2010 to 29th February 2012. Phylogenetic typing, multilocus sequence typing, and molecular characterization of β-lactamase and plasmid-mediated quinolone resistance determinants were performed for CIP-R E. coli isolates. Results A total of 569 E. coli isolates were collected, and 122 (21.4%) isolates were CIP-R isolates. The most prevalent sequence type (ST) was ST131 (28.7%, 35/122), followed by ST393 (14.7%, 18/122), ST1193 (13.1%, 16/122), ST38 (9.0%, 11/122), and ST405 (8.2%, 10/122). The antimicrobial resistance rates of ST131 to cefepime (22.9%, 8/35), ST38 to gentamicin (100%, 11/11), and ST405 to cefotaxime (66.7%, 6/9) were significantly higher than the resistance rates of all other STs combined. Notably, 40% (4/10) of ST405 clones produced extended-spectrum β-lactamases and were co-resistant to trimethoprim/sulfamethoxazole. aac(6′)-1b-cr (20%, 7/35) and CTX-M-14 (40%, 4/10) were more frequently observed in ST131 and ST405 compared with other clones, respectively. Conclusions Among the CIP-R uropathogenic E. coli isolates in this study, ST131, ST38, and ST405 were specifically associated with antimicrobial resistance.
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Affiliation(s)
- Bongyoung Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Mi Ran Seo
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Jieun Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Yeonjae Kim
- Division of Infectious Diseases, National Medical Center, Seoul, Korea
| | - Seong Heon Wie
- Division of Infectious Diseases, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Moran Ki
- Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Yong Kyun Cho
- Department of Internal Medicine, Medical College, Gacheon University, Incheon, Korea
| | - Seungkwan Lim
- Department of Internal Medicine, Ansung Hospital, Gyeonggi Provincial Medical Center, Ansung, Korea
| | - Jin Seo Lee
- Division of Infectious Diseases, Kangdong Sacred Heart Hospital, Hallym University, Seoul, Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyuck Lee
- Division of Infectious Diseases, Dong-A University Hospital, Dong-A University, Busan, Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Korea University Guro Hospital, Seoul, Korea
| | - Dae Won Park
- Division of Infectious Diseases, Korea University Ansan Hospital, Ansan, Korea
| | - Seong Yeol Ryu
- Division of Infectious Diseases, Dongsan Hosptial, Keimyeong University, Daegu, Korea
| | - Moon Hyun Chung
- Division of Infectious Diseases, Seogwipo Medical Center, Jeju, Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea.
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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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Abstract
In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.
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Affiliation(s)
- Lee W. Riley
- School of Public Health, University of California, Berkeley, California 94720, USA
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Epidemiology and genotypic characterisation of dissemination patterns of uropathogenic Escherichia coli in a community. Epidemiol Infect 2020; 147:e148. [PMID: 30869058 PMCID: PMC6518783 DOI: 10.1017/s0950268819000426] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To characterise the dissemination patterns of uropathogenic Escherichia coli (UPEC) in a community, we conducted a study utilising molecular and fundamental descriptive epidemiology. The subjects, consisted of women having community-acquired acute urinary tract infection (UTI), were enrolled in the study from 2011 to 2012. UPEC isolates were subjected to antibacterial-susceptibility testing, O serogrouping, phylotyping, multilocus-sequence typing with phylogenetic-tree analysis and pulsed-field-gel electrophoresis (PFGE). From the 209 unique positive urinary samples 166 UPEC were isolated, of which 129 were fully susceptible to the tested antibiotics. Of the 53 sequence types (STs), the four most prevalent STs (ST95, ST131, ST73 and ST357) accounted for 60% of all UPEC strains. Antimicrobial resistance was less frequently observed for ST95 and ST73 than for the others. A majority of rare STs and a few common STs constituted the diversity pattern within the population structure, which was composed of the two phylogenetically distinct clades. Eleven genetically closely related groups were determined by PFGE, which accounted for 42 of the 166 UPEC isolates, without overt geo-temporal clustering. Our results indicate that a few major lineages of UPEC, selected by unidentified factors, are disseminated in this community and contribute to a large fraction of acute UTIs.
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Fuzi M, Rodriguez Baño J, Toth A. Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents. Front Microbiol 2020; 11:271. [PMID: 32158437 PMCID: PMC7052298 DOI: 10.3389/fmicb.2020.00271] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum β-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Jesus Rodriguez Baño
- Unit of Infectious Diseases, Clinical Microbiology and Preventive Medicine, Department of Medicine, Hospital Universitario Virgen Macarena, University of Seville - Biomedicine Institute of Seville (IBiS), Seville, Spain
| | - Akos Toth
- Department of Bacteriology, Mycology and Parasitology, National Public Health Center, Budapest, Hungary
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Chen YC, Chang CC, Chiu THT, Lin MN, Lin CL. The risk of urinary tract infection in vegetarians and non-vegetarians: a prospective study. Sci Rep 2020; 10:906. [PMID: 32001729 PMCID: PMC6992707 DOI: 10.1038/s41598-020-58006-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infection (UTI) is caused principally by ascending Escherichia coli infection via an intestine-stool-urethra route. Recent studies found that the strains of E. coli causing UTIs, called extra-intestinal pathogenic E. coli (ExPEC), were distinct from the intestinal pathogenic strains and normal commensal strains. Further analysis found the meat including poultry and pork is the major reservoir for ExPECs. Vegetarians avoid meat and should theoretically have less exposure to ExPEC. However, no study thus far has examined whether vegetarian diets reduce the risk of UTI. Our aim was to examine the association between vegetarian diet and UTI risk in a Taiwanese Buddhist population. We prospectively followed 9724 Buddhists free of UTI from 2005 to 2014. During the 10-year follow-up, 661 incident UTI cases were confirmed. Diet was assessed through a food frequency questionnaire. Cox regression was used to evaluate the prospective association between a vegetarian diet on risk of UTI while adjusting for age, sex, educational level, alcohol-drinking, smoking, hypertension, diabetes mellitus, hyperlipidemia, and disease conditions predisposing to UTIs. Overall, vegetarian diet was associated with 16% lower hazards (hazard ratio [HR]: 0.84, 95% confidence interval [CI]: 0.71-0.99). In subgroup analysis, the protective association between vegetarian diet and UTI is observed mainly in the female (HR: 0.82, 95% CI: 0.69-0.99), never smokers (HR: 0.80, 95% CI: 0.67-0.95), and for uncomplicated UTI (HR: 0.81, 95% CI: 0.68-0.98).
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Affiliation(s)
- Yen-Chang Chen
- Department of Anatomical Pathology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Chia-Chen Chang
- Department of Medical Research, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Tina H T Chiu
- Department of Nutritional Science, Fu-Jen Catholic University, Taipei, Taiwan
| | - Ming-Nan Lin
- Department of Family Medicine, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi County, Taiwan
- Department of Family Medicine, College of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Chin-Lon Lin
- Department of Cardiology, Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Chiayi County, Taiwan.
- Department of Internal Medicine, College of Medicine, Tzu Chi University, Hualien, Taiwan.
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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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Cho S, Gupta SK, McMillan EA, Sharma P, Ramadan H, Jové T, Jackson CR, Frye JG. Genomic Analysis of Multidrug-Resistant Escherichia coli from Surface Water in Northeast Georgia, United States: Presence of an ST131 Epidemic Strain Containing blaCTX-M-15 on a Phage-Like Plasmid. Microb Drug Resist 2019; 26:447-455. [PMID: 31725354 DOI: 10.1089/mdr.2019.0306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Surface water is suspected of playing a role in the development and spread of antimicrobial-resistant (AR) bacteria, including human pathogens. In our previous study, 496 Escherichia coli isolates were recovered from water samples collected over a 2-year period from the Upper Oconee watershed, Athens, GA, United States, of which 34 (6.9%) were AR isolates. Of these, six isolates were selected based on their multidrug resistance (MDR) phenotypes, the presence of mobile genetic elements, and their pathogenic potential and were subjected to whole-genome sequence (WGS) analysis to enhance our understanding of environmental MDR E. coli isolates. This study is the first report on genomic characterization of MDR E. coli from environmental water in the United States through a WGS approach. The sequences of the six MDR E. coli isolates were analyzed and the locations of their AR genes were identified. One of the E. coli isolates was an ST131 epidemic strain, which also produced an extended-spectrum β-lactamase encoded by the blaCTX-M-15 gene, carried on a plasmid that is a member of a very rarely reported family of phage-like plasmids. This is the first time an in-depth sequence analysis has been done on a blaCTX-M-15- containing phage-like plasmid, the presence of which suggests a new emerging mechanism of AR gene transmission.
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Affiliation(s)
- Sohyun Cho
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | | | - Poonam Sharma
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Thomas Jové
- Univ. Limoges, INSERM, CHU Limoges, RESINFIT, U1092, Limoges, France
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, Georgia, USA
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Neamati F, Khorshidi A, Moniri R, Hosseini Tafreshi SA. Molecular Epidemiology of Antimicrobial Resistance of Uropathogenic Escherichia coli Isolates from Patients with Urinary Tract Infections in a Tertiary Teaching Hospital in Iran. Microb Drug Resist 2019; 26:60-70. [PMID: 31526226 DOI: 10.1089/mdr.2019.0184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To characterize the resistance patterns of uropathogenic Escherichia coli (UPEC) in a Tertiary Teaching Hospital in Iran, we conducted a descriptive epidemiology study using molecular techniques. The subjects consisted of patients having acute urinary tract infection, who were enrolled in the study from 2014 to 2017. The antimicrobial susceptibility profile of 101 UPEC isolates was determined by Kirby-Bauer disc diffusion method. Extended spectrum β-lactamase (ESBL) was detected by the double-disk synergy test. Biofilm formation was done using microtiter plates. The presence of virulence genes (pai, pap, hly, traT, pai, cnf-1, sfa, and afa) was evaluated by a PCR. Molecular typing of UPEC E. coli isolates was performed with fimH and multilocus sequence typing (MLST). 70.3% of isolates were multidrug-resistant. 37.6% of isolates were Extended spectrum β-lactamases (ESBLs) producer. Strong biofilm formation was seen in 27.7%. Forty-seven different fimH allelic variants were identified. Among identified fimH allelic variants, the most common types were f1 (18.8%) and f14 (18.8%). ST131 (54.5%) was the most prevalent clonal group significantly correlated with the pai gene. Seven sequence types (STs) were detected only once (ST405, ST410, ST450, ST636, ST648, ST1193, and ST6451). Clonal groups showed no significant differences in terms of antibiotic resistance patterns. There was no significant difference between virulence genes and antibiotic resistance patterns in the studied clonal groups. To our knowledge, the present study is the first study in Iran that investigated the genotypic diversity of UPEC isolates by MLST and fimH typing methods. The two methods might serve as a useful molecular test for surveillance and epidemiological studies of isolates.
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Affiliation(s)
- Foroogh Neamati
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ahmad Khorshidi
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Rezvan Moniri
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran.,Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
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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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Mamani R, Flament-Simon SC, García V, Mora A, Alonso MP, López C, García-Meniño I, Díaz-Jiménez D, Blanco JE, Blanco M, Blanco J. Sequence Types, Clonotypes, Serotypes, and Virotypes of Extended-Spectrum β-Lactamase-Producing Escherichia coli Causing Bacteraemia in a Spanish Hospital Over a 12-Year Period (2000 to 2011). Front Microbiol 2019; 10:1530. [PMID: 31379759 PMCID: PMC6646471 DOI: 10.3389/fmicb.2019.01530] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to examine the prevalence and determine the molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) causing bacteraemia in a Spanish Hospital over a 12-year period (2000 to 2011). As far as we know, this is the first study which has investigated and compared the serotypes, phylogroups, clonotypes, virotypes, and PFGE profiles of ST131 and non-ST131 clones of bacteraemia ESBL-EC isolates. Of the 2,427 E. coli bloodstream isolates, 96 (4.0%) were positive for ESBL production: 40 for CTX-M-15, 36 for CTX-M-14, eight for CTX-M-1, four for CTX-M-9, CTX-M-32, and SHV-12. The number of ESBL-EC increased from 1.0% during 2000 to 2005 to 5.5% during 2006-2011 (P < 0.001). The 96 ESBL-EC isolates belonged to 36 different STs. The commonest was ST131 (41 isolates), followed by ST58, ST354, ST393 and ST405 (four isolates each). Most CTX-M-15 isolates (87.5%, 35/40) were ST131, whereas the 36 CTX-M-14 isolates belonged to 23 different STs and only 3 (8.3%) of them were ST131. The 35 ST131 CTX-M-15-producing isolates belonged to the H30Rx subclone and 29 of them showed the virotype A. A drastic change in ST131 virotypes happened in 2011 due to the emergence of the virotypes E (sat, papGII, cnf1, hlyA, and kpsMII-K5) and F (sat, papGII, and kpsMII-K5) which displaced virotype A (afa/draBC, afa operon FM955459, sat, and kpsMII-K2). Although the 96 ESBL-EC isolates showed 21 O serogroups and 17 H flagellar antigens, 39 belonged to serotype O25b:H4 (ST131 isolates). The second most prevalent serotype (O15:H1) was found to be associated with another important high-risk clone (ST393). In conclusion, the ST131 was the most frequent sequence type, being the H30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H30Rx subclone emerged in 2011. Future molecular studies are needed to understand the dynamics of expansion of this successful high-risk subclone in order to prevent its spread and establish the importance of the two new virotypes.
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Affiliation(s)
- Rosalia Mamani
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Saskia Camille Flament-Simon
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Vanesa García
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - María Pilar Alonso
- Unidade de Microbioloxía Clínica, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Cecilia López
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dafne Díaz-Jiménez
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jesús E Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Hawkey PM, Warren RE, Livermore DM, McNulty CAM, Enoch DA, Otter JA, Wilson APR. Treatment of infections caused by multidrug-resistant Gram-negative bacteria: report of the British Society for Antimicrobial Chemotherapy/Healthcare Infection Society/British Infection Association Joint Working Party. J Antimicrob Chemother 2019. [PMID: 29514274 DOI: 10.1093/jac/dky027] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Working Party makes more than 100 tabulated recommendations in antimicrobial prescribing for the treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria (GNB) and suggest further research, and algorithms for hospital and community antimicrobial usage in urinary infection. The international definition of MDR is complex, unsatisfactory and hinders the setting and monitoring of improvement programmes. We give a new definition of multiresistance. The background information on the mechanisms, global spread and UK prevalence of antibiotic prescribing and resistance has been systematically reviewed. The treatment options available in hospitals using intravenous antibiotics and in primary care using oral agents have been reviewed, ending with a consideration of antibiotic stewardship and recommendations. The guidance has been derived from current peer-reviewed publications and expert opinion with open consultation. Methods for systematic review were NICE compliant and in accordance with the SIGN 50 Handbook; critical appraisal was applied using AGREE II. Published guidelines were used as part of the evidence base and to support expert consensus. The guidance includes recommendations for stakeholders (including prescribers) and antibiotic-specific recommendations. The clinical efficacy of different agents is critically reviewed. We found there are very few good-quality comparative randomized clinical trials to support treatment regimens, particularly for licensed older agents. Susceptibility testing of MDR GNB causing infection to guide treatment needs critical enhancements. Meropenem- or imipenem-resistant Enterobacteriaceae should have their carbapenem MICs tested urgently, and any carbapenemase class should be identified: mandatory reporting of these isolates from all anatomical sites and specimens would improve risk assessments. Broth microdilution methods should be adopted for colistin susceptibility testing. Antimicrobial stewardship programmes should be instituted in all care settings, based on resistance rates and audit of compliance with guidelines, but should be augmented by improved surveillance of outcome in Gram-negative bacteraemia, and feedback to prescribers. Local and national surveillance of antibiotic use, resistance and outcomes should be supported and antibiotic prescribing guidelines should be informed by these data. The diagnosis and treatment of both presumptive and confirmed cases of infection by GNB should be improved. This guidance, with infection control to arrest increases in MDR, should be used to improve the outcome of infections with such strains. Anticipated users include medical, scientific, nursing, antimicrobial pharmacy and paramedical staff where they can be adapted for local use.
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Affiliation(s)
- Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | | | - Cliodna A M McNulty
- Microbiology Department, Gloucestershire Royal Hospital, Great Western Road, Gloucester GL1 3NN, UK
| | - David A Enoch
- Public Health England, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - A Peter R Wilson
- Department of Microbiology and Virology, University College London Hospitals, London, UK
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31
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Mostafavi SKS, Najar‐Peerayeh S, Mobarez AM, Parizi MK. Characterization of uropathogenic
E. coli
O25b‐B2‐ST131, O15:K52:H1, and CGA: Neutrophils apoptosis, serum bactericidal assay, biofilm formation, and virulence typing. J Cell Physiol 2019; 234:18272-18282. [DOI: 10.1002/jcp.28459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/05/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
| | - Shahin Najar‐Peerayeh
- Department of Bacteriology Faculty of Medical Sciences, Tarbiat Modares University Tehran Iran
| | | | - Mehdi Kardoust Parizi
- Department of Urology Shariati Hospital, Tehran University of Medical Sciences Tehran Iran
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32
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Self-reported risk factors for having Escherichia coli sequence type 131 or its H30 subclone among US Veterans with a clinical E. coli isolate. Epidemiol Infect 2018; 147:e55. [PMID: 30501663 PMCID: PMC6518554 DOI: 10.1017/s0950268818003114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among 469 US military veterans with an Escherichia coli clinical isolate (2012-2013), we explored healthcare and non-healthcare risk factors for having E. coli sequence type 131 and its H30 subclone (ST131-H30). Overall, 66 (14%) isolates were ST131; 51 (77%) of these were ST131-H30. After adjustment for healthcare-associated factors, ST131 remained positively associated with medical lines and nursing home residence. After adjustment for environmental factors, ST131 remained associated with wild animal contact (positive), meat consumption (negative) and pet cat exposure (negative). Thus, ST131 was associated predominantly with healthcare-associated exposures, while non-ST131 E. coli were associated with some environmental exposures.
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Bozcal E, Eldem V, Aydemir S, Skurnik M. The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey. PeerJ 2018; 6:e5470. [PMID: 30155366 PMCID: PMC6110251 DOI: 10.7717/peerj.5470] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/21/2018] [Indexed: 12/25/2022] Open
Abstract
Background Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages. Methods Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended-Spectrum β-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated. Results Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n = 1), ST14 (n = 1), ST10 (n = 1), ST69 (n = 1), ST1722 (n = 2), ST141 (n = 1), ST88 (n = 1), ST80 (n = 1), and ST998 (n = 1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates. Conclusion The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics.
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Affiliation(s)
- Elif Bozcal
- Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Zoology Section, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Sohret Aydemir
- Department of Medical Microbiology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
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Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4. [PMID: 30080134 PMCID: PMC6202452 DOI: 10.1099/mgen.0.000203] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.
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Affiliation(s)
- Catherine Branger
- 1IAME, UMR1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, UFR de Medecine, 16 Rue Henri Huchard, Paris 75018, France
| | - Alice Ledda
- 2Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, UK
| | | | - Benoît Doublet
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Stéphanie Fouteau
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - Valérie Barbe
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - David Roche
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Stéphane Cruveiller
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Claudine Médigue
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Miguel Castellanos
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Dominique Decré
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Laurence Drieux-Rouze
- 9APHP, Hôpital de la Pitié-Salpêtrière Service de Bactériologie-Hygiène, 75015, Paris, France
| | - Olivier Clermont
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Jérémy Glodt
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Olivier Tenaillon
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Axel Cloeckaert
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Guillaume Arlet
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Erick Denamur
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
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Alousi S, Salloum T, Arabaghian H, Matar GM, Araj GF, Tokajian ST. Genomic Characterization of MDR Escherichia coli Harboring blaOXA-48 on the IncL/M-type Plasmid Isolated from Blood Stream Infection. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3036143. [PMID: 30050923 PMCID: PMC6046176 DOI: 10.1155/2018/3036143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Escherichia coli is responsible for a wide variety of community and hospital acquired extraintestinal infections, and the emergence of ESBL resistant isolates is a major clinical concern. In this study, we characterized the genomic attributes of an OXA-48 and CTX-M-3 producing E. coli EC-IMP153. Whole-genome initial assembly produced 146 contigs with a combined 5,504,170 bp in size and a G+C content of 50.5%. wgSNPs-based phylogenetic comparison with 36 publically available genomes was also performed. Comprehensive genomic analysis showed that EC-IMP153 belonged to sequence type ST-405 and harbored several resistance determinants including the β-lactam resistance genes blaOXA-48, blaCTX-M-3, blaTEM-1B, blaOXA-1, and blaCMY-70, aminoglycoside fyuA and aac(3)IId, tetracycline tet(A) and tet(R), and fluoroquinolone gyrA, parC, and mfd resistance determinants. Plasmids with the following incompatibility groups were detected in silico and confirmed using PBRT: IncI1-α, IncL, IncW, Col (BS512), and IncF. To our knowledge this is the first in-depth genomic analysis of an OXA-48 producing E. coli ST-405 isolated from a patient in Lebanon and linked to a blood stream infection. Continuous monitoring is necessary to better understand the continued diffusion of such pathogens, especially in view of the population movements triggered by unrest in the Middle East.
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Affiliation(s)
- S. Alousi
- Department of Natural Sciences, School of Arts & Sciences, Lebanese American University, Byblos, Lebanon
| | - T. Salloum
- Department of Natural Sciences, School of Arts & Sciences, Lebanese American University, Byblos, Lebanon
| | - H. Arabaghian
- Department of Natural Sciences, School of Arts & Sciences, Lebanese American University, Byblos, Lebanon
| | - G. M. Matar
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Experimental Pathology, Immunology & Microbiology, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - G. F. Araj
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - S. T. Tokajian
- Department of Natural Sciences, School of Arts & Sciences, Lebanese American University, Byblos, Lebanon
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36
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Torres E, López-Cerero L, Morales I, Navarro M, Rodríguez-Baño J, Pascual A. Prevalence and transmission dynamics of Escherichia coli ST131 among contacts of infected community and hospitalized patients. Clin Microbiol Infect 2018; 24:618-623. [DOI: 10.1016/j.cmi.2017.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/18/2017] [Accepted: 09/12/2017] [Indexed: 11/24/2022]
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37
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Ahlstrom CA, Bonnedahl J, Woksepp H, Hernandez J, Olsen B, Ramey AM. Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis. Sci Rep 2018; 8:7361. [PMID: 29743625 PMCID: PMC5943298 DOI: 10.1038/s41598-018-25474-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/23/2018] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens threatens global health, though the spread of AMR bacteria and AMR genes between humans, animals, and the environment is still largely unknown. Here, we investigated the role of wild birds in the epidemiology of AMR Escherichia coli. Using next-generation sequencing, we characterized cephalosporin-resistant E. coli cultured from sympatric gulls and bald eagles inhabiting a landfill habitat in Alaska to identify genetic determinants conferring AMR, explore potential transmission pathways of AMR bacteria and genes at this site, and investigate how their genetic diversity compares to isolates reported in other taxa. We found genetically diverse E. coli isolates with sequence types previously associated with human infections and resistance genes of clinical importance, including blaCTX-M and blaCMY. Identical resistance profiles were observed in genetically unrelated E. coli isolates from both gulls and bald eagles. Conversely, isolates with indistinguishable core-genomes were found to have different resistance profiles. Our findings support complex epidemiological interactions including bacterial strain sharing between gulls and bald eagles and horizontal gene transfer among E. coli harboured by birds. Results suggest that landfills may serve as a source for AMR acquisition and/or maintenance, including bacterial sequence types and AMR genes relevant to human health.
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Affiliation(s)
| | - Jonas Bonnedahl
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, SE-58183, Sweden.,Department of Infectious Diseases, Kalmar County Hospital, Kalmar, SE-39185, Sweden
| | - Hanna Woksepp
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, SE-39185, Sweden
| | - Jorge Hernandez
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, SE-75185, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, SE-75185, Sweden
| | - Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, 99508, USA.
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Genome-Wide Identification of Fitness Factors in Mastitis-Associated Escherichia coli. Appl Environ Microbiol 2018; 84:AEM.02190-17. [PMID: 29101196 DOI: 10.1128/aem.02190-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
Virulence factors of mammary pathogenic Escherichia coli (MPEC) have not been identified, and it is not known how bacterial gene content influences the severity of mastitis. Here, we report a genome-wide identification of genes that contribute to fitness of MPEC under conditions relevant to the natural history of the disease. A highly virulent clinical isolate (M12) was identified that killed Galleria mellonella at low infectious doses and that replicated to high numbers in mouse mammary glands and spread to spleens. Genome sequencing was combined with transposon insertion site sequencing to identify MPEC genes that contribute to growth in unpasteurized whole milk, as well as during G. mellonella and mouse mastitis infections. These analyses show that strain M12 possesses a unique genomic island encoding a group III polysaccharide capsule that greatly enhances virulence in G. mellonella Several genes appear critical for MPEC survival in both G. mellonella and in mice, including those for nutrient-scavenging systems and resistance to cellular stress. Insertions in the ferric dicitrate receptor gene fecA caused significant fitness defects under all conditions (in milk, G. mellonella, and mice). This gene was highly expressed during growth in milk. Targeted deletion of fecA from strain M12 caused attenuation in G. mellonella larvae and reduced growth in unpasteurized cow's milk and lactating mouse mammary glands. Our results confirm that iron scavenging by the ferric dicitrate receptor, which is strongly associated with MPEC strains, is required for MPEC growth and may influence disease severity in mastitis infections.IMPORTANCE Mastitis caused by E. coli inflicts substantial burdens on the health and productivity of dairy animals. Strains causing mastitis may express genes that distinguish them from other E. coli strains and promote infection of mammary glands, but these have not been identified. Using a highly virulent strain, we employed genome-wide mutagenesis and sequencing to discover genes that contribute to mastitis. This extensive data set represents a screen for mastitis-associated E. coli fitness factors and provides the following contributions to the field: (i) global comparison of genes required for different aspects of mastitis infection, (ii) discovery of a unique capsule that contributes to virulence, and (iii) conclusive evidence for the crucial role of iron-scavenging systems in mastitis, particularly the ferric dicitrate transport system. Similar approaches applied to other mastitis-associated strains will uncover conserved targets for prevention or treatment and provide a better understanding of their relationship to other E. coli pathogens.
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ESBL-producing Escherichia coli
and Its Rapid Rise among Healthy People. Food Saf (Tokyo) 2017; 5:122-150. [PMID: 32231938 DOI: 10.14252/foodsafetyfscj.2017011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/11/2017] [Indexed: 02/06/2023] Open
Abstract
Since around the 2000s, Escherichia coli (E. coli) resistant to both oxyimino-cephalosporins and fluoroquinolones has remarkably increased worldwide in clinical settings. The kind of E. coli is also identified in patients suffering from community-onset infectious diseases such as urinary tract infections. Moreover, recoveries of multi-drug resistant E. coli from the feces of healthy people have been increasingly documented in recent years, although the actual state remains uncertain. These E. coli isolates usually produce extended-spectrum β-lactamase (ESBL), as well as acquisition of amino acid substitutions in the quinolone-resistance determining regions (QRDRs) of GyrA and/or ParC, together with plasmid-mediated quinolone resistance determinants such as Qnr, AAC(6')-Ib-cr, and QepA. The actual state of ESBL-producing E. coli in hospitalized patients has been carefully investigated in many countries, while that in healthy people still remains uncertain, although high fecal carriage rates of ESBL producers in healthy people have been reported especially in Asian and South American countries. The issues regarding the ESBL producers have become very complicated and chaotic due to rapid increase of both ESBL variants and plasmids mediating ESBL genes, together with the emergence of various "epidemic strains" or "international clones" of E. coli and Klebsiella pneumoniae harboring transferable-plasmids carrying multiple antimicrobial resistance genes. Thus, the current state of ESBL producers outside hospital settings was overviewed together with the relation among those recovered from livestock, foods, pets, environments and wildlife from the viewpoint of molecular epidemiology. This mini review may contribute to better understanding about ESBL producers among people who are not familiar with the antimicrobial resistance (AMR) threatening rising globally.
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40
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Fuzi M, Szabo D, Csercsik R. Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria. Front Microbiol 2017; 8:2261. [PMID: 29250038 PMCID: PMC5715326 DOI: 10.3389/fmicb.2017.02261] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/02/2017] [Indexed: 01/06/2023] Open
Abstract
The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Rita Csercsik
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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Nowak K, Fahr J, Weber N, Lübke-Becker A, Semmler T, Weiss S, Mombouli JV, Wieler LH, Guenther S, Leendertz FH, Ewers C. Highly diverse and antimicrobial susceptible Escherichia coli display a naïve bacterial population in fruit bats from the Republic of Congo. PLoS One 2017; 12:e0178146. [PMID: 28700648 PMCID: PMC5507484 DOI: 10.1371/journal.pone.0178146] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 05/09/2017] [Indexed: 01/30/2023] Open
Abstract
Bats are suspected to be a reservoir of several bacterial and viral pathogens relevant to animal and human health, but studies on Escherichia coli in these animals are sparse. We investigated the presence of E. coli in tissue samples (liver, lung and intestines) collected from 50 fruit bats of five different species (Eidolon helvum, Epomops franqueti, Hypsignathus monstrosus, Myonycteris torquata, Rousettus aegyptiacus) of two different areas in the Republic of Congo between 2009 and 2010. To assess E. coli pathotypes and phylogenetic relationships, we determined the presence of 59 virulence associated genes and multilocus sequence types (STs). Isolates were further tested for their susceptibility to several antimicrobial substances by agar disk diffusion test and for the presence of an Extended-Spectrum Beta-Lactamase phenotype. E. coli was detected in 60% of the bats analysed. The diversity of E. coli strains was very high, with 37 different STs within 40 isolates. Occasionally, we detected sequence types (e.g. ST69, ST127, and ST131) and pathotypes (e.g. ExPEC, EPEC and atypical EPEC), which are known pathogens in human and/or animal infections. Although the majority of strains were assigned to phylogenetic group B2 (46.2%), which is linked with the ExPEC pathovar, occurrence of virulence-associated genes in these strains were unexpectedly low. Due to this, and as only few of the E. coli isolates showed intermediate resistance to certain antimicrobial substances, we assume a rather naïve E. coli population, lacking contact to humans or domestic animals. Future studies featuring in depth comparative whole genome sequence analyses will provide insights into the microevolution of this interesting strain collection.
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Affiliation(s)
- Kathrin Nowak
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
- * E-mail:
| | - Jakob Fahr
- Department of Migration and Immuno-Ecology, Vogelwarte Radolfzell, Max Planck Institute for Ornithology, Radolfzell, Germany
- Zoological Institute, TU Braunschweig, Braunschweig, Germany
| | - Natalie Weber
- Institute of Evolutionary Ecology and Conservation Genomics, Universität Ulm, Ulm, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Torsten Semmler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Sabrina Weiss
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | | | - Lothar H. Wieler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Fabian H. Leendertz
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | - Christa Ewers
- Veterinary Faculty, Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Giessen, Germany
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42
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Genome sequence of lung pathogenic Escherichia coli O78, a chimeric strain isolated from pneumonia forest musk deer. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0545-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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43
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Ojer-Usoz E, González D, Vitas AI. Clonal Diversity of ESBL-Producing Escherichia coli Isolated from Environmental, Human and Food Samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017. [PMID: 28644413 PMCID: PMC5551114 DOI: 10.3390/ijerph14070676] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study presents a comprehensive approach of a clonal diversity analysis of 448 Extended-spectrum β-lactamase (ESBL)-producing E. coli isolated from environmental, human and food samples in Spain. The phenotypic confirmation of ESBL production was performed by disc diffusion and microdilution methods, while Polymerase Chain Reaction (PCR) and sequencing were used for the molecular characterization of β-lactamase genes (blaCTX-M, blaSHV, blaTEM, blaOXA). Clonal relationship of isolates was determined by multi-locus sequence typing (MLST). Multidrug resistant strains were present in all the studied niches, with percentages above 50.0%. The most prevalent β-lactamase genes were blaCTXM-14 (26%) and blaCTXM-1 (21.4%), followed by blaSHV-12, blaCTX-M-15 and blaTEM-42. MLST isolates were grouped into 26 clonal complexes (CC) and 177 different sequence types (ST) were detected. Despite the high clonal diversity observed, CC10 was the prevalent and the only CC detected in all niches, while other complexes as CC131 were mainly associated to human isolates. The observed prevalence and diversity of these resistant bacteria across the different environments encourages a One Health approach to prevent and control ESBL dissemination between environment and consumers.
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Affiliation(s)
- Elena Ojer-Usoz
- Department of Microbiology and Parasitology, University of Navarra, 31080 Pamplona, Spain.
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31080 Pamplona, Spain.
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31080 Pamplona, Spain.
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44
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Molecular epidemiology of Escherichia coli sequence type 131 and its H30/H30-Rx subclones recovered from extra-intestinal infections: first report of OXA-48 producing ST131 clone from Iran. Eur J Clin Microbiol Infect Dis 2017; 36:1859-1866. [DOI: 10.1007/s10096-017-3021-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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45
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de Souza da-Silva AP, de Sousa VS, Martins N, da Silva Dias RC, Bonelli RR, Riley LW, Moreira BM. Escherichia coli sequence type 73 as a cause of community acquired urinary tract infection in men and women in Rio de Janeiro, Brazil. Diagn Microbiol Infect Dis 2017; 88:69-74. [PMID: 28214224 PMCID: PMC5392417 DOI: 10.1016/j.diagmicrobio.2017.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/25/2017] [Accepted: 01/31/2017] [Indexed: 12/22/2022]
Abstract
Escherichia coli clones ST131, ST69, ST95, and ST73 are frequent causes of urinary tract infections (UTI) and bloodstream infections. Specific clones and virulence profiles of E. coli causing UTI in men has been rarely described. The aim of this study was to characterize patient and clonal characteristics of community-acquired UTI caused by E. coli in men (n=12) and women (n=127) in Rio de Janeiro, Brazil, complementing a previous work. We characterized isolates in phylogenetic groups, ERIC2-PCR and PFGE types, MLST, genome similarity and virulence gene-profiles. UTI from men were more frequently caused by phylogenetic group B2 isolates (83% versus 42%, respectively, P = 0.01), a group with significantly higher virulence scores compared with women. ST73 was the predominant clone in men (50%) and the second most frequent in women (12%), with the highest virulence score (mean and median=9) among other clones. ST73 gnomes formed at least six clusters. E. coli from men carried significantly higher numbers of virulence genes, such as sfa/focDE (67% versus 27%), hlyA (58% versus 24%), cnf 1 (58% versus 16%), fyuA (100% versus 82%) and MalX (92% versus 44%), compared with isolates from women. These data suggest the predominance and spread of ST73 isolates likely relates to an abundance of virulence determinants.
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Affiliation(s)
| | - Viviane Santos de Sousa
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Natacha Martins
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | | | - Raquel Regina Bonelli
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA
| | - Beatriz Meurer Moreira
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Rio de Janeiro, 21941-902, Brazil.
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46
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Lara FBM, Nery DR, de Oliveira PM, Araujo ML, Carvalho FRQ, Messias-Silva LCF, Ferreira LB, Faria-Junior C, Pereira AL. Virulence Markers and Phylogenetic Analysis of Escherichia coli Strains with Hybrid EAEC/UPEC Genotypes Recovered from Sporadic Cases of Extraintestinal Infections. Front Microbiol 2017; 8:146. [PMID: 28217123 PMCID: PMC5290387 DOI: 10.3389/fmicb.2017.00146] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/19/2017] [Indexed: 11/13/2022] Open
Abstract
Virulence genes from different E. coli pathotypes are blended in hybrid strains. E. coli strains with hybrid enteroaggregative/uropathogenic (EAEC/UPEC) genotypes have sporadically emerged causing outbreaks of extraintestinal infections, however their association with routine infections is yet underappreciated. We assessed 258 isolates of E. coli recovered from 86 consecutive cases of extraintestinal infections seeking EAEC and hybrid genotype (EAEC/UPEC) strains. Extensive virulence genotyping was carried out to detect 21 virulence genes, including molecular predictors of EAEC and UPEC strains. Phylogenetic groups and sequence types (STs) were identified, as well as it was performed phylogenetic analyses in order to evaluate whether hybrid EAEC/UPEC strains belonged to intestinal or extraintestinal lineages of E. coli. Adhesion assays were performed to evaluate the biofilm formation by hybrid strains in human urine and cell culture medium (DMEM). Molecular predictors of UPEC were detected in more than 70% of the strains (chuA in 85% and fyuA in 78%). Otherwise, molecular predictors of EAEC (aatA and aggR) were detected in only 3.4% (9/258) of the strains and always along with the UPEC predictor fyuA. Additionally, the pyelonephritis-associated pilus (pap) gene was also detected in all of the hybrid EAEC/UPEC strains. EAEC/UPEC strains were recovered from two cases of community-onset urinary tract infections (UTI) and from a case of bacteremia. Analyses revealed that hybrid EAEC/UPEC strains were phylogenetically positioned in two different clades. Two representative strains, each recovered from UTI and bacteremia, were positioned into a characteristic UPEC clade marked by strains belonging to phylogenetic group D and ST3 (Warwick ST 69). Another hybrid EAEC/UPEC strain was classified as phylogroup A-ST478 and positioned in a commensal clade. Hybrid EAEC/UPEC strains formed biofilms at modest, but perceptible levels either in DMEM or in urine samples. We showed that different lineages of E. coli, at least phylogenetic group A and D, can acquire and gather EAEC and UPEC virulence genes promoting the emergence of hybrid EAEC/UPEC strains.
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Affiliation(s)
- Flaviane B M Lara
- Graduate Program in Microbial Biology, Biology Institute, University of Brasília Brasília, Brazil
| | - Danielly R Nery
- Campus of Ceilândia, University of Brasília Brasília, Brazil
| | | | - Mayana L Araujo
- Campus of Ceilândia, University of Brasília Brasília, Brazil
| | | | | | | | - Celio Faria-Junior
- Central Laboratory for Public Health, Secretary of State for Health Brasília, Brazil
| | - Alex L Pereira
- Graduate Program in Microbial Biology, Biology Institute, University of BrasíliaBrasília, Brazil; Campus of Ceilândia, University of BrasíliaBrasília, Brazil
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Manjarrez-Hernandez A, Molina-López J, Gavilanes-Parra S, Hernandez-Castro R. Escherichia coli clonal group A among uropathogenic infections in Mexico City. J Med Microbiol 2016; 65:1438-1444. [DOI: 10.1099/jmm.0.000389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Angel Manjarrez-Hernandez
- Dirección de Investigación, Hospital General Dr. Gea González, Tlalpan, Ciudad de México 14080, Mexico
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
| | - José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
- Laboratorio de Patogenicidad Bacteriana, Edificio de Investigación Hemato-Oncología 5to, Piso Hospital Infantil de México ‘Federico Gómez’, C.P. 06720 Ciudad de México, Mexico
| | - Sandra Gavilanes-Parra
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
- Dirección de Investigación, Hospital General Dr. Gea González, Tlalpan, Ciudad de México 14080, Mexico
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Abstract
The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.
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Pathoadaptive Mutations of Escherichia coli K1 in Experimental Neonatal Systemic Infection. PLoS One 2016; 11:e0166793. [PMID: 27861552 PMCID: PMC5115809 DOI: 10.1371/journal.pone.0166793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/03/2016] [Indexed: 12/04/2022] Open
Abstract
Although Escherichia coli K1 strains are benign commensals in adults, their acquisition at birth by the newborn may result in life-threatening systemic infections, most commonly sepsis and meningitis. Key features of these infections, including stable gastrointestinal (GI) colonization and age-dependent invasion of the bloodstream, can be replicated in the neonatal rat. We previously increased the capacity of a septicemia isolate of E. coli K1 to elicit systemic infection following colonization of the small intestine by serial passage through two-day-old (P2) rat pups. The passaged strain, A192PP (belonging to sequence type 95), induces lethal infection in all pups fed 2–6 x 106 CFU. Here we use whole-genome sequencing to identify mutations responsible for the threefold increase in lethality between the initial clinical isolate and the passaged derivative. Only four single nucleotide polymorphisms (SNPs), in genes (gloB, yjgV, tdcE) or promoters (thrA) involved in metabolic functions, were found: no changes were detected in genes encoding virulence determinants associated with the invasive potential of E. coli K1. The passaged strain differed in carbon source utilization in comparison to the clinical isolate, most notably its inability to metabolize glucose for growth. Deletion of each of the four genes from the E. coli A192PP chromosome altered the proteome, reduced the number of colonizing bacteria in the small intestine and increased the number of P2 survivors. This work indicates that changes in metabolic potential lead to increased colonization of the neonatal GI tract, increasing the potential for translocation across the GI epithelium into the systemic circulation.
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50
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Abstract
Several potential reservoirs for the Escherichia coli strains that cause most human extraintestinal infections (extraintestinal pathogenic E. coli; ExPEC) have been identified, including the human intestinal tract and various non-human reservoirs, such as companion animals, food animals, retail meat products, sewage, and other environmental sources. Understanding ExPEC reservoirs, chains of transmission, transmission dynamics, and epidemiologic associations will assist greatly in finding ways to reduce the ExPEC-associated disease burden. The need to clarify the ecological behavior of ExPEC is all the more urgent because environmental reservoirs may contribute to acquisition of antimicrobial resistance determinants and selection for and amplification of resistant ExPEC. In this chapter, we review the evidence for different ExPEC reservoirs, with particular attention to food and food animals, and discuss the public health implications of these reservoirs for ExPEC dissemination and transmission.
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