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Korkmazer R, Kayaaslan B, Kaya-Kalem A, Oktay Z, Eser F, Hasanoğlu İ, Güner R. Causative Microorganisms in Community-Acquired Urinary Tract Infections and Risk Factors for the Development of Infection with Extended-Spectrum β-Lactamase-Producing Species. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2024; 6:112-122. [PMID: 39005695 PMCID: PMC11243775 DOI: 10.36519/idcm.2024.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/18/2024] [Indexed: 07/16/2024]
Abstract
Objective This study aimed to determine the microorganisms grown in the urine cultures of patients followed up with the diagnosis of community-acquired urinary tract infection (CA-UTI), their antibiotic susceptibility, and the risk factors that cause extended-spectrum β-lactamase (ESBL) production in microorganisms. Materials and Methods Patients diagnosed with CA-UTI in the Yıldırım Beyazıt University City Hospital Infectious Diseases and Clinical Microbiology Clinic between February 2019 and February 2020 were prospectively analyzed. The microorganisms grown in the urine cultures and antibiotic susceptibility rates were examined. The clinical and demographic characteristics of the patients were compared in terms of the isolated agent producing ESBL. Results Escherichia coli (63.8%) and Klebsiella pneumoniae (22.0%) were the most common microorganisms detected in the urine cultures; the rate of those producing ESBL was 46.6%. Antibiotics with high resistance rates were ampicillin (74.2%), cefuroxime (49.6%), and ceftriaxone (49%). Male gender, complicating factors, immunosuppression, kidney transplantation and history of antibiotic use were determined as significant risk factors for ESBL production. Male gender, immunosuppression, and history of antibiotic use were also independent risk factors. ROC analysis of risk factors showed ESBL-producing bacteria were isolated at a high rate in patients having ≥3 risk factors. Conclusion The resistance rates in our study are quite high. Male gender, history of antibiotic use and immunosuppression status were found to be independent risk factors for ESBL positivity in patients with CA-UTI, and the more risk factors a patient has, the higher the risk of ESBL positivity.
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Affiliation(s)
- Rüveyda Korkmazer
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - Bircan Kayaaslan
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - Ayşe Kaya-Kalem
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - Zeynep Oktay
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - Fatma Eser
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - İmran Hasanoğlu
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
| | - Rahmet Güner
- Department of Infectious Disease and Clinical Microbiology, Yıldırım Beyazıt University School of Medicine, Ankara City Hospital, Ankara, Türkiye
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Song H, Yoo JS, Unno T. Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172068. [PMID: 38554973 DOI: 10.1016/j.scitotenv.2024.172068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.
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Affiliation(s)
- Hokyung Song
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Jung Sik Yoo
- Division of Antimicrobial Resistance Research, National Institute of Health, Korea Disease Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea
| | - Tatsuya Unno
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Seowon-Gu, Cheongju 28644, Republic of Korea.
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Wyrsch ER, Hoye BJ, Sanderson-Smith M, Gorman J, Maute K, Cummins ML, Jarocki VM, Marenda MS, Dolejska M, Djordjevic SP. The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170815. [PMID: 38336047 DOI: 10.1016/j.scitotenv.2024.170815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Wildlife are implicated in the dissemination of antimicrobial resistance, but their roles as hosts for Escherichia coli that pose a threat to human and animal health is limited. Gulls (family Laridae) in particular, are known to carry diverse lineages of multiple-antibiotic resistant E. coli, including extra-intestinal pathogenic E. coli (ExPEC). Whole genome sequencing of 431 E. coli isolates from 69 healthy Australian silver gulls (Chroicocephalus novaehollandiae) sampled during the 2019 breeding season, and without antibiotic selection, was undertaken to assess carriage in an urban wildlife population. Phylogenetic analysis and genotyping resolved 123 sequence types (STs) representing most phylogroups, and identified diverse ExPEC, including an expansive phylogroup B2 cluster comprising 103 isolates (24 %; 31 STs). Analysis of the mobilome identified: i) widespread carriage of the Yersinia High Pathogenicity Island (HPI), a key ExPEC virulence determinant; ii) broad distribution of two novel phage elements, each carrying sitABCD and iii) carriage of the transmissible locus of stress tolerance (tLST), an element linked to sanitation resistance. Of the 169 HPI carrying isolates, 49 (48 %) represented diverse B2 isolates hosting FII-64 ColV-like plasmids that lacked iutABC and sitABC operons typical of ColV plasmids, but carried the serine protease autotransporter gene, sha. Diverse E. coli also carried archetypal ColV plasmids (52 isolates; 12 %). Clusters of closely related E. coli (<50 SNVs) from ST58, ST457 and ST746, sourced from healthy gulls, humans, and companion animals, were frequently identified. In summary, anthropogenically impacted gulls host an expansive E. coli population, including: i) putative ExPEC that carry ColV virulence gene cargo (101 isolates; 23.4 %) and HPI (169 isolates; 39 %); ii) atypical enteropathogenic E. coli (EPEC) (17 isolates; 3.9 %), and iii) E. coli that carry the tLST (20 isolates; 4.6 %). Gulls play an important role in the evolution and transmission of E. coli that impact human health.
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Affiliation(s)
- Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Martina Sanderson-Smith
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jody Gorman
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Marc S Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic; CEITEC VETUNI, University of Veterinary Sciences Brno, Czech Republic; Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Czech Republic; Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czech Republic
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
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Fang Y, Tao S, Chen H, Xu Y, Chen L, Liang W. ESBL-Producing and Non-ESBL-Producing Escherichia coli Isolates from Urinary Tract Differ in Clonal Distribution, Virulence Gene Content and Phylogenetic Group. Infect Drug Resist 2023; 16:5563-5571. [PMID: 37641799 PMCID: PMC10460598 DOI: 10.2147/idr.s423860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Purpose The objectives of this study are to determine the differences in clonality, virulence gene (VG) content and phylogenetic group between non extended-spectrum beta-lactamase-producing E. coli (non-ESBL-EC) and ESBL-EC isolates from urine. Patients and Methods This study characterized a total of 100 clinical E. coli isolates consecutively obtained from the inpatients hospitalized in The First Affiliated Hospital of Ningbo University in China by polymerase-chain reaction (PCR). Results Phylogenetic group B2 was found to be the most prevalent in both ESBL-EC and non-ESBL-EC group. Among 100 clinical isolates, the count of acquired virulence genes in group B2 was found to be significantly higher than that in group A, B1, and D (p <0.001). Additionally, the presence of content within virulence genes (the total number of virulence genes detected per isolate) in B2 of non-ESBL-EC and ESBL-EC showed a significant difference (p<0.001). ST131 was detected exclusively in ESBL-EC, while ST95 and ST73 were the main sequence types in non-ESBL-EC. Conclusion Our study demonstrated the different distribution of MLST, phylogenetic group in ESBL-EC and non-ESBL-EC group. The inverse association between beta-lactamase resistance and VG content performed in this study should get a lot more attention. At the same time, we should also be wary of the appearance of non-ESBL-EC isolates of group B2 harboring more virulence genes which will lead to high pathogenicity.
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Affiliation(s)
- Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, People’s Republic of China
| | - Shuan Tao
- School of Medicine, Jiangsu University, Zhejiang, People’s Republic of China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhejiang, People’s Republic of China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, People’s Republic of China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, People’s Republic of China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, People’s Republic of China
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Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens 2022; 11:pathogens11121528. [PMID: 36558862 PMCID: PMC9782660 DOI: 10.3390/pathogens11121528] [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: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) may inhabit the human gut microbiota without causing disease. However, if they reach extra-intestinal sites, common cystitis to bloodstream infections may occur, putting patients at risk. To examine the human gut as a source of endogenous infections, we evaluated the E. coli clonal diversity of 18 inpatients' guts and their relationship with strains isolated from urinary tract infection (UTI) in the same hospital. Random amplified polymorphic DNA evaluated the clonal diversity, and the antimicrobial susceptibility was determined by disk diffusion. One isolate of each clone detected was sequenced, and their virulome and resistome were determined. Overall, 177 isolates were screened, among which 32 clones were identified (mean of two clones per patient), with ExPEC strains found in over 75% of the inpatients' guts. Endogenous infection was confirmed in 75% of the cases. ST10, ST59, ST69, ST131, and ST1193 clones and critical mobile drug-resistance encoding genes (blaCTX-M-15, blaOXA-1, blaDHA-1, aac(6')-lb-cr, mcr-1.26, qnrB4, and qnrB19) were identified in the gut of inpatients. The genomic analysis highlighted the diversity of the fecal strains, colonization by lactose-negative E. coli, the high frequency of ExPEC in the gut of inpatients without infections, and the presence of β-lactamase producing E. coli in the gut of inpatients regardless of the previous antibiotics' usage. Considering that we found more than one ExPEC clone in the gut of several inpatients, surveillance of inpatients' fecal pathogens may prevent UTI caused by E. coli in the hospital and dissemination of risk clones.
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Nüesch-Inderbinen M, Tresch S, Zurfluh K, Cernela N, Biggel M, Stephan R. Finding of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in wild game meat originating from several European countries: predominance of Moellerella wisconsensis producing CTX-M-1, November 2021. Euro Surveill 2022; 27:2200343. [PMID: 36695441 PMCID: PMC9732924 DOI: 10.2807/1560-7917.es.2022.27.49.2200343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
IntroductionMeat can be a vehicle for food-borne transmission of antimicrobial resistant bacteria and antimicrobial resistance genes. The occurrence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales has been observed in meat from livestock production but has not been well studied in meat from wild game.AimWe aimed to investigate, particularly in central Europe, to what extent ESBL-producing Enterobacterales may be present in wild game meat.MethodsA total of 111 samples of different types of game meat supplied by butchers, hunters, retail stores and a large game-processing establishment in Europe were screened for ESBL-producing Enterobacterales using a selective culture medium. Isolates were genotypically and phenotypically characterised.ResultsThirty-nine samples (35% of the total) yielded ESBL-producing Enterobacterales, with most (35/39) supplied by the game-processing establishment. Isolates included 32 Moellerella wisconsensis, 18 Escherichia coli and one Escherichia marmotae. PCR screening identified bla CTX-M-1 (n = 31), bla CTX-M-32 (n = 8), bla CTX-M-65 (n = 4), bla CTX-M-15 (n = 3), bla CTX-M-8 (n = 1), bla CTX-M-14 (n = 1), bla CTX-M-55 (n = 1), and bla SHV-12 (n = 2). Most E. coli belonged to phylogenetic group A (n = 7) or B1 (n = 9), but several isolates belonged to extraintestinal pathogenic E. coli (ExPEC) sequence types (ST)58 (n = 4), ST68 (n = 1) and ST540 (n = 1). Whole genome sequencing of six selected isolates localised bla CTX-M-1 on megaplasmids in four M. wisconsensis and bla CTX-M-32 on IncN_1 plasmids in one M. wisconsensis and one E. marmotae. Forty-eight isolates (94%) exhibited a multidrug-resistance phenotype.ConclusionWe found a high occurrence of ESBL-producing Enterobacterales in wild game meat, suggesting wildlife habitat pollution and possible microbial contamination events occurring during skinning or cutting carcasses.
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Affiliation(s)
| | - Silvan Tresch
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
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7
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Dreyer S, Globig A, Bachmann L, Schütz AK, Schaufler K, Homeier-Bachmann T. Longitudinal Study on Extended-Spectrum Beta-Lactamase- E. coli in Sentinel Mallard Ducks in an Important Baltic Stop-Over Site for Migratory Ducks in Germany. Microorganisms 2022; 10:1968. [PMID: 36296245 PMCID: PMC9612239 DOI: 10.3390/microorganisms10101968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 08/17/2023] Open
Abstract
Antimicrobial resistance (AMR) is a serious global health threat with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales as the most critical ones. Studies on AMR in wild birds imply a possible dissemination function and indicate their potential role as sentinel animals. This study aimed to gain a deeper insight into the AMR burden of wild waterfowl by sampling semi-wild mallard ducks used as sentinels and to identify if AMR bacteria could be recommended to be added to the pathogens of public health risks to be screened for. In total, 376 cloacal and pooled fecal samples were collected from the sentinel plant over a period of two years. Samples were screened for ESBL-carrying E. coli and isolates found further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. Over the sampling period, 4.26% (16/376) of the samples were positive for ESBL-producing E. coli. BlaCTX-M-1 and blaCTX-M-32 were the most abundant CTX-M types. Although none of the top global sequence types (ST) could be detected, poultry-derived ST115 and non-poultry-related STs were found and could be followed over time. The current study revealed low cases of ESBL-producing E. coli in semi-wild mallard ducks, which proves the suitability of sentinel surveillance for AMR detection in water-associated wildlife.
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Affiliation(s)
- Sylvia Dreyer
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Lisa Bachmann
- Faculty of Agriculture and Food Science, University of Applied Science Neubrandenburg, 17033 Neubrandenburg, Germany
| | - Anne K. Schütz
- Institute of Epidemiology, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
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Tsoumtsa Meda LL, Landraud L, Petracchini S, Descorps-Declere S, Perthame E, Nahori MA, Ramirez Finn L, Ingersoll MA, Patiño-Navarrete R, Glaser P, Bonnet R, Dussurget O, Denamur E, Mettouchi A, Lemichez E. The cnf1 gene is associated with an expanding Escherichia coli ST131 H30Rx/C2 subclade and confers a competitive advantage for gut colonization. Gut Microbes 2022; 14:2121577. [PMID: 36154446 PMCID: PMC9519008 DOI: 10.1080/19490976.2022.2121577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract and a source of urinary tract pathogens. Bioinformatics analyses of a large collection of E. coli genomes from EnteroBase, enriched in clinical isolates of worldwide origins, suggest the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, is preferentially distributed in four common sequence types (ST) encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment, with known enhanced capacities to colonize the gastrointestinal tract. Statistical projections based on this dataset point to a global expansion of cnf1-positive multidrug-resistant ST131 strains from subclade H30Rx/C2, accounting for a rising prevalence of cnf1-positive strains in ST131. Despite the absence of phylogeographical signals, cnf1-positive isolates segregated into clusters in the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. The suggested dominant expansion of cnf1-positive strains in ST131-H30Rx/C2 led us to uncover the competitive advantage conferred by cnf1 for gut colonization to the clinical strain EC131GY ST131-H30Rx/C2 versus cnf1-deleted isogenic strain. Complementation experiments showed that colon tissue invasion was compromised in the absence of deamidase activity on Rho GTPases by CNF1. Hence, gut colonization factor function of cnf1 was confirmed for another clinical strain ST131-H30Rx/C2. In addition, functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2 and a cnf1-deleted isogenic strain showed no detectable impact of the CNF1 gene on bacterial fitness and inflammation during the acute phase of bladder monoinfection. Together these data argue for an absence of role of CNF1 in virulence during UTI, while enhancing gut colonization capacities of ST131-H30Rx/C2 and suggested expansion of cnf1-positive MDR isolates in subclade ST131-H30Rx/C2.
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Affiliation(s)
- Landry L. Tsoumtsa Meda
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Luce Landraud
- Université Paris Cité et Université Sorbonne Paris Nord, INSERM U1137, IAME, Paris, France,Laboratoire Microbiologie-hygiène, AP-HP, Hôpital Louis Mourier, Colombes, France
| | - Serena Petracchini
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Stéphane Descorps-Declere
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France,Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Emeline Perthame
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Marie-Anne Nahori
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Laura Ramirez Finn
- Institut Pasteur, Department of Immunology, Mucosal Inflammation and Immunity group, Paris, France,Université Paris Cité, Institut Cochin, CNRS UMR8104, INSERM U1016, Paris, France
| | - Molly A. Ingersoll
- Institut Pasteur, Department of Immunology, Mucosal Inflammation and Immunity group, Paris, France,Université Paris Cité, Institut Cochin, CNRS UMR8104, INSERM U1016, Paris, France
| | - Rafael Patiño-Navarrete
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Département de Microbiologie, Paris, France
| | - Philippe Glaser
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Département de Microbiologie, Paris, France
| | - Richard Bonnet
- UMR INSERM U1071, INRA USC-2018, Université Clermont Auvergne, Clermont-Ferrand, France,Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, Clermont-Ferrand, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, Département de Microbiologie, Paris, France
| | - Erick Denamur
- Université Paris Cité et Université Sorbonne Paris Nord, INSERM U1137, IAME, Paris, France,AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Amel Mettouchi
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France,Amel Mettouchi Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, 75015Paris, France
| | - Emmanuel Lemichez
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France,CONTACT Emmanuel Lemichez
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Bong CW, Low KY, Chai LC, Lee CW. Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River. Front Public Health 2022; 10:794513. [PMID: 35356018 PMCID: PMC8960044 DOI: 10.3389/fpubh.2022.794513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.
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Affiliation(s)
- Chui Wei Bong
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Chui Wei Bong ;
| | - Kyle Young Low
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lay Ching Chai
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Choon Weng Lee
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
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10
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Valdez C, Costa C, Simões M, de Carvalho CCCR, Baptista T, Campos MJ. Detection of mcr-1 Gene in Undefined Vibrio Species Isolated from Clams. Microorganisms 2022; 10:microorganisms10020394. [PMID: 35208850 PMCID: PMC8876837 DOI: 10.3390/microorganisms10020394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
The increase of antimicrobial resistant strains is leading to an emerging threat to public health. Pathogenic Vibrio are responsible for human and animal illness. The Enterobacteriaceae family includes microorganisms that affect humans, causing several infections. One of the main causes of human infection is related to the ingestion of undercooked seafood. Due to their filter-feeding habit, marine invertebrates, such as clams, are known to be a natural reservoir of specific microbial communities. In the present study, Vibrionaceae and coliforms microorganisms were isolated from clams. A microbial susceptibility test was performed using the disk diffusion method. From 43 presumptive Vibrio spp. and 17 coliforms, three Vibrio spp. with MICs to colistin >512 mg L−1 were found. From the 23 antimicrobial resistance genes investigated, only the three isolates that showed phenotypic resistance to colistin contained the mcr-1 gene. Genotypic analysis for virulence genes in EB07V indicated chiA gene presence. The results from the plasmid cure and transformation showed that the resistance is chromosomally mediated. Biochemical analysis and MLSA, on the basis of four protein-coding gene sequences (recA, rpoB, groEL and dnaJ), grouped the isolates into the genus Vibrio but distinguished them as different from any known Vibrio spp.
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Affiliation(s)
- Christian Valdez
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Cátia Costa
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Marco Simões
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Carla C. C. R. de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Teresa Baptista
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
| | - Maria J. Campos
- MARE-Marine and Environmental Sciences Centre, ESTM, Polytechnic of Leiria, 2520-630 Peniche, Portugal; (C.V.); (C.C.); (M.S.); (T.B.)
- Correspondence:
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11
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Genomic analysis of the zoonotic ST73 lineage containing avian and human extraintestinal pathogenic Escherichia coli (ExPEC). Vet Microbiol 2022; 267:109372. [DOI: 10.1016/j.vetmic.2022.109372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022]
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12
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Masui T, Nakano R, Nakano A, Saito K, Suzuki Y, Kakuta N, Horiuchi S, Tsubaki K, Kitahara T, Yano H. Predominance of CTX-M-9 Group Among ESBL-Producing Escherichia coli Isolated from Healthy Individuals in Japan. Microb Drug Resist 2022; 28:355-360. [PMID: 34990283 DOI: 10.1089/mdr.2021.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The detection rate of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, microorganisms associated with health care settings, has significantly increased worldwide. Moreover, their community incidence has increased in several countries. In this study, we investigated the prevalence and genetic diversity of ESBL-producing Escherichia coli isolated from 547 nonduplicated stool specimens from healthy Japanese individuals, between 2015 and 2019. E. coli were isolated on deoxycholate-hydrogen sulfide-lactose (DHL) agar and identified by MALDI-TOF MS, ESBL were screened through disk diffusion method (cefotaxime with or without clavulanate), and genetic detection and genotyping were performed by PCR and DNA sequencing. Clonal similarities between ESBL-producing and nonproducing isolates were assessed by multilocus sequence typing (MLST). The prevalence of ESBL-producing E. coli was 9.7% (53/547). These bacteria harbored CTX-M genes, from which CTX-M-9 (31/53, 58.5%) and CTX-M-1 (13/53, 24.5%) groups were the predominant. The MLST analysis revealed that ST131 genotype prevailed within ESBL-producing E. coli (15/53), whereas ST95 (10/53) and ST73 (8/53) prevailed among non-ESBL producers, with ST131 being present in only four isolates. Overall, a high prevalence rate of CTX-M-type ESBL-producing E. coli was detected. CTX-M-9 group-producing ST131 predominated among healthy Japanese individuals, similar to that observed in hospital isolates. CTX-M-type ESBL may disseminate clonally among hospital patients and subsequently, within the community.
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Affiliation(s)
- Takashi Masui
- Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, Kashihara, Japan.,Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Kai Saito
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Naoki Kakuta
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Kousuke Tsubaki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Tadashi Kitahara
- Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, Kashihara, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
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13
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Elankumaran P, Browning GF, Marenda MS, Reid CJ, Djordjevic SP. Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100106. [PMID: 35128493 PMCID: PMC8803956 DOI: 10.1016/j.crmicr.2022.100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
ST127 is an established extra-intestinal pathogen of humans and companion animals with high virulence gene carriage A dominant sub-lineage of ST127 contains closely related human and companion animal sequences that are globally distributed The dominant sub-lineage characteristically contains specific alleles of important virulence-associated and metabolic genes This work supports the global expansion of a dominant sub-lineage of ST127 with extensive transfer occurring between humans and companion animals
Escherichia coli ST127, a recently emerged global pathogen noted for high virulence gene carriage, is a leading cause of urinary tract and blood stream infections. ST127 is frequently isolated from humans and companion animals; however, it is unclear if they are distinct or related populations of ST127. We performed a phylogenomic analysis of 299 E. coli ST127 of diverse epidemiological origin to characterize their population structure, genetic determinants of virulence, antimicrobial resistance, and repertoire of mobile genetic elements with a focus on plasmids. The core gene phylogeny was divided into 13 clusters, the largest of which (BAP4) contained the majority of human and companion animal origin isolates. This dominant cluster displayed genetic differences to the remainder of the phylogeny, most notably alternative gene alleles encoding important virulence factors including lipid A, flagella, and K capsule. Furthermore, numerous close genetic linkages (<30 SNPs) between human and companion animal isolates were observed within the cluster. Carriage of antimicrobial resistance genes in the collection was limited, but virulence gene carriage was extensive. We found evidence of pUTI89-like virulence plasmid carriage in over a third of isolates, localised to four of the major phylogenetic clusters. Our study supports global scale repetitive transfer of E. coli ST127 lineages between humans and companion animals, particularly within the dominant BAP4 cluster.
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14
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Fecal Carriage and Epidemiology of Extended-Spectrum Beta-Lactamase/Carbapenemases Producing Enterobacterales Isolates in Bulgarian Hospitals. Antibiotics (Basel) 2021; 10:antibiotics10060747. [PMID: 34202982 PMCID: PMC8234131 DOI: 10.3390/antibiotics10060747] [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: 05/04/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022] Open
Abstract
The gastrointestinal tract is an important reservoir of extended spectrum beta-lactamase (ESBL)/carbapenemase-producing Enterobacterales isolates. This study included patients from two Bulgarian hospitals. Overall, 98 ESBL producers (including 68 Escherichia coli and 20 Klebsiella pneumoniae isolates) were detected among 99 hospitalized patients, 212 patients at admission, and 92 hospital staff in 42.4%, 24.5%, and 4%, respectively. We observed blaCTX-M-15 in 47% of isolates, blaCTX-M-3 in 39% and blaCTX-M-14 in 11%. Three blaCTX-M-15 positive isolates were also blaKPC-2 positive. High transferability was detected for blaCTX-M-3 carrying plasmids (55%) with L/M and I1 replicon plasmids, followed by CTX-M-14 (36.4%) and CTX-M-15 (27.9%) with IncF plasmids. BlaKPC-2 was carried by FIIAs plasmids. Epidemiology typing revealed 8 K. pneumoniae ST types—ST15(8/20), ST17(4/20), ST37(2/20) and 9 E. coli ST types—ST131 (30.9%, 21/68), ST38 (8/68), ST95(7/68) and ST316(7/68). All ST131 isolates but one was from the highly virulent epidemic clone O25bST131. This is the first report in Bulgaria about ESBL/carbapenemase faecal carriage. We observed high ESBL/carbapenemases prevalence. A predominant number of isolates were members of highly epidemic and virulent PanEuropean clones ST15 K. pneumoniae and O25bST131 E. coli. High antibiotics usage during the COVID pandemic will worsen the situation. Routine screenings and strict infection control measures should be widely implemented.
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15
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Song J, Kim J, Oh SS, Shin J. Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Vegetable Farm Soil in South Korea. Microb Drug Resist 2021; 27:1489-1494. [PMID: 33926223 DOI: 10.1089/mdr.2020.0542] [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] [Indexed: 12/20/2022] Open
Abstract
The populations of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have increasingly disseminated in humans, animals, and the environment. This study aimed to determine the prevalence, antimicrobial susceptibilities, and molecular characteristics of ESBL-EC isolates obtained from vegetable farm soil. In total, 200 soil samples were collected from vegetable farms in Incheon, South Korea, between 2018 and 2019 and cultured on MacConkey screening plates supplemented with 2 μg/mL cefotaxime. Cefotaxime-resistant ESBL-EC isolates were recovered from 4.0% (8/200) of the soil samples. All eight isolates were nonsusceptible to ampicillin, piperacillin, cefazolin, cefotaxime, and cefepime and harbored blaCTX-M-type ESBL genes, including blaCTX-M-15 (50.0%), blaCTX-M-55 (25.0%), and blaCTX-M-14 (25.0%). Phylogenetic analysis showed that the B1 lineage was predominant (75.0%), followed by A (12.5%) and B2 (12.5%) lineages. Multilocus sequence typing revealed eight different E. coli sequence types (STs), including ST10, ST73, ST155, ST847, ST2521, ST3285, ST5173, and ST9479. Notably, ST10 and ST73 belong to the global extraintestinal pathogenic E. coli lineages. Our findings demonstrated that the farm soil environment may serve as a reservoir of human-associated multidrug-resistant ESBL-producing pathogens.
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Affiliation(s)
- Jihyun Song
- Department of Microbiology, Inha University College of Medicine, Incheon, South Korea
| | - Junghee Kim
- Incheon Research Institute of Public Health and Environment, Incheon, South Korea
| | - Sung-Suck Oh
- Incheon Research Institute of Public Health and Environment, Incheon, South Korea
| | - Jinwook Shin
- Department of Microbiology, Inha University College of Medicine, Incheon, South Korea
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16
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Birgy A, Madhi F, Jung C, Levy C, Cointe A, Bidet P, Hobson CA, Bechet S, Sobral E, Vuthien H, Ferroni A, Aberrane S, Cuzon G, Beraud L, Gajdos V, Launay E, Pinquier D, Haas H, Desmarest M, Dommergues MA, Cohen R, Bonacorsi S. Diversity and trends in population structure of ESBL-producing Enterobacteriaceae in febrile urinary tract infections in children in France from 2014 to 2017. J Antimicrob Chemother 2021; 75:96-105. [PMID: 31617912 DOI: 10.1093/jac/dkz423] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/21/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E). OBJECTIVES To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E. METHODS A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined. RESULTS E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs. cgMLST enabled discrimination of clusters within the main STs. CONCLUSIONS The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.
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Affiliation(s)
- André Birgy
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | - Fouad Madhi
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, France.,Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
| | - Camille Jung
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
| | - Corinne Levy
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, ACTIV, 94000, Créteil, France
| | - Aurélie Cointe
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | - Philippe Bidet
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | | | - Stéphane Bechet
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France
| | - Elsa Sobral
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France
| | - Hoang Vuthien
- AP-HP, HU-Est Parisien site Trousseau, Service de Bactériologie, F-75012, Paris, France
| | - Agnès Ferroni
- AP-HP, Hopital Necker, Service de Microbiologie, University Paris Descartes, Paris, France
| | - Saïd Aberrane
- Microbiology Laboratory, Créteil Hospital, Créteil, France
| | - Gaëlle Cuzon
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Université Paris Sud, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur, APHP-Université Paris Sud, Paris, France
| | - Laetitia Beraud
- Centre National de Référence des Légionelles, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Vincent Gajdos
- Service de Pédiatrie, Antoine Béclère University Hospital, Assistance Publique-Hôpitaux de Paris, Clamart, France.,Centre for Research in Epidemiology and Population Health, Villejuif, France
| | - Elise Launay
- Service de Pédiatrie Générale et Infectiologie Pédiatrique, Hôpital Femme-Enfant-Adolescent, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Didier Pinquier
- Unité de Pneumologie et Allergologie pédiatriques & CRCM mixte, Pédiatrie Médicale, CHU Charles Nicolle, Rouen, France
| | - Hervé Haas
- Hôpitaux pédiatriques CHU Lenval, Nice, France
| | - Marie Desmarest
- Service d'Accueil des Urgences Pédiatriques, AP-HP, Hôpital Robert Debré, Paris, France
| | - Marie-Aliette Dommergues
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Service de pédiatrie, centre hospitalier de Versailles, Le Chesnay, France
| | - Robert Cohen
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France.,Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, ACTIV, 94000, Créteil, France.,Unité Court Séjour, Petits Nourrisson, Service de Néonatologie, Centre Hospitalier Intercommunal de Créteil, France
| | - Stéphane Bonacorsi
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
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17
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Valiatti TB, Santos FF, Santos ACM, Nascimento JAS, Silva RM, Carvalho E, Sinigaglia R, Gomes TAT. Genetic and Virulence Characteristics of a Hybrid Atypical Enteropathogenic and Uropathogenic Escherichia coli (aEPEC/UPEC) Strain. Front Cell Infect Microbiol 2020; 10:492. [PMID: 33134184 PMCID: PMC7550682 DOI: 10.3389/fcimb.2020.00492] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022] Open
Abstract
Hybrid strains of Escherichia coli combine virulence traits of diarrheagenic (DEC) and extraintestinal pathogenic E. coli (ExPEC), but it is poorly understood whether these combined features improve the virulence potential of such strains. We have previously identified a uropathogenic E. coli (UPEC) strain (UPEC 252) harboring the eae gene that encodes the adhesin intimin and is located in the locus of enterocyte effacement (LEE) pathogenicity island. The LEE-encoded proteins allow enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) to form attaching and effacing (A/E) lesions in enterocytes. We sought to characterize UPEC 252 through whole-genome sequencing and phenotypic virulence assays. Genome analysis unveiled that this strain harbors a complete LEE region, with more than 97% of identity comparing to E2348/69 (EPEC) and O157:H7 Sakai (EHEC) prototype strains, which was functional, since UPEC 252 expressed the LEE-encoded proteins EspB and intimin and induced actin accumulation foci in HeLa cells. Phylogenetic analysis performed comparing 1,000 single-copy shared genes clustered UPEC 252 with atypical EPEC strains that belong to the sequence type 10, phylogroup A. Additionally, UPEC 252 was resistant to the bactericidal power of human serum and colonized cells of the urinary (T24 and HEK293-T) and intestinal (Caco-2 and LS174T) tracts. Our findings suggest that UPEC 252 is an atypical EPEC strain that emerges as a hybrid strain (aEPEC/UPEC), which could colonize new niches and potentially cause intestinal and extraintestinal infections.
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Affiliation(s)
- Tiago B Valiatti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda F Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana C M Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Júllia A S Nascimento
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa M Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Eneas Carvalho
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Rita Sinigaglia
- Centro de Microscopia Eletrônica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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18
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Mostafa HH, Cameron A, Taffner SM, Wang J, Malek A, Dumyati G, Hardy DJ, Pecora ND. Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase bla CTX-M-27 Is Emerging on Distinct Plasmids in ST38. Front Microbiol 2020; 11:1747. [PMID: 32849376 PMCID: PMC7406970 DOI: 10.3389/fmicb.2020.01747] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the blaCTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The blaCTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the blaCTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the blaCTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the blaCTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the blaCTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.
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Affiliation(s)
- Heba H Mostafa
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Samantha M Taffner
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Adel Malek
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Ghinwa Dumyati
- Department of Medicine, Infectious Diseases, University of Rochester Medical Center, Rochester, NY, United States
| | - Dwight J Hardy
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Nicole D Pecora
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, United States.,Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
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19
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Draft Genome Sequence of an Escherichia coli Sequence Type 420 Isolate from a Patient with Urinary Tract Infection in Northern California. Microbiol Resour Announc 2020; 9:9/23/e00251-20. [PMID: 32499367 PMCID: PMC7272548 DOI: 10.1128/mra.00251-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of a uropathogenic Escherichia coli sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3. The genome sequence of a uropathogenic Escherichia coli sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3.
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Valat C, Drapeau A, Beurlet S, Bachy V, Boulouis HJ, Pin R, Cazeau G, Madec JY, Haenni M. Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages. Front Microbiol 2020; 11:580. [PMID: 32373083 PMCID: PMC7186358 DOI: 10.3389/fmicb.2020.00580] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/17/2020] [Indexed: 12/12/2022] Open
Abstract
Escherichia coli is a ubiquitous commensal and pathogen that has also been recognized as a multi-sectoral indicator of antimicrobial resistance (AMR). Given that latter focus, such as on resistances to extended-spectrum cephalosporins (ESC) and carbapenems, the reported population structure of E. coli is generally biased toward resistant isolates, with sequence type (ST)131 being widely reported in humans, and ST410 and ST648 being reported in animals. In this study, we characterized 618 non-duplicate E. coli isolates collected throughout France independently of their resistance phenotype. The B2 phylogroup was over-represented (79.6%) and positively associated with the presence of numerous virulence factors (VFs), including those defining the extra-intestinal pathogenic E. coli isolates (presence of ≥2 VFs: papA, sfaS, focG, afaD, iutA, and kpsMTII) and those more specifically related to uropathogenic E. coli (cnf1, hlyD). The major STs associated with clinical isolates from dogs were by far the dog-associated ST372 (20.7%) and ST73 (20.1%), a lineage that had commonly been considered until now as human-associated. Resistance to ESC was found in 33 isolates (5.3%), along with one carbapenemase-producing isolate, and was mostly restricted to non-B2 isolates. In conclusion, the presence of virulent E. coli lineages may be the issue, rather than the presence of ESC-resistant isolates, and the risk of transmission of such virulent isolates to humans needs to be further studied.
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Affiliation(s)
- Charlotte Valat
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon – Université de Lyon, Lyon, France
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon – Université de Lyon, Lyon, France
| | | | | | - Henri-Jean Boulouis
- Unité de Bactériologie, BioPôle, Ecole Nationale Vétérinaire d’Alfort, Maisons-Alfort, France
| | | | - Géraldine Cazeau
- Unité Epidémiologie et Appui à la Surveillance, ANSES Laboratoire de Lyon – Université de Lyon, Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon – Université de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon – Université de Lyon, Lyon, France
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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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van Hout D, Verschuuren TD, Bruijning-Verhagen PCJ, Bosch T, Schürch AC, Willems RJL, Bonten MJM, Kluytmans JAJW. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content. PLoS One 2020; 15:e0227604. [PMID: 31935253 PMCID: PMC6959556 DOI: 10.1371/journal.pone.0227604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec isolates from ECB episodes with different epidemiological characteristics. METHODS A random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG. RESULTS ST73 was most prevalent among the 212 non-ESBL-Ec (N = 26, 12.3%) and ST131 among the 69 ESBL-Ec (N = 30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N = 22, P value < .001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1-6) and 7 (IQR 4-9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < .001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1-8). Median VG scores were 13 (IQR 9-20) and 12 (IQR 8-14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = .002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11-21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 5-13) or hepatic-biliary focus (median 11, IQR 5-18) (P values = .007 and .04, respectively). VG content varied between different E. coli STs. CONCLUSIONS Non-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.
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Affiliation(s)
- Denise van Hout
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- * E-mail:
| | - Tess D. Verschuuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Patricia C. J. Bruijning-Verhagen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thijs Bosch
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Marc J. M. Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Jan A. J. W. Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
- Microvida Laboratory for Medical Microbiology and Department of Infection Control, Amphia Hospital, Breda, The Netherlands
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Anes J, Nguyen SV, Eshwar AK, McCabe E, Macori G, Hurley D, Lehner A, Fanning S. Molecular characterisation of multi-drug resistant Escherichia coli of bovine origin. Vet Microbiol 2020; 242:108566. [PMID: 32122581 DOI: 10.1016/j.vetmic.2019.108566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/05/2019] [Accepted: 12/26/2019] [Indexed: 12/27/2022]
Abstract
Antimicrobial resistance reported in bacteria of animal origin is considered a major challenge to veterinary public health. In this study, the genotypic and phenotypic characterisation of twelve Escherichia coli isolates of bovine origin is reported. Twelve bacterial isolates of animal origin were selected from a previous study based on their multidrug resistant (MDR) profile. Efflux pump activity was measured using ethidium bromide (EtBr) and the biofilm forming ability of the individual strains was assessed using a number of phenotypic assays. All isolates were resistant to tetracyclines and a number of isolates expressed resistance to fluoroquinolones which was also confirmed in silico by the presence of these resistance markers. Amino acid substitutions in the quinolone resistance-determining regions were identified in all isolates and the presence of several siderophores were also noted. Whole genomesequence (WGS) data showed different STs that were not associated with epidemic STs or virulent clonal complexes. Seven isolates formed biofilms in minimal media with some isolates showing better adaptation at 25 °C while others at 37 °C. The capacity to efflux EtBr was found to be high in 4 isolates and impaired in 4 others. The pathogenicity of three selected isolates was assessed in zebrafish embryo infection models, revealing isolates CFS0355 and CFS0356 as highly pathogenic. These results highlight the application of NGS technologies combined with phenotypic assays in providing a better understanding of E. coli of bovine origin and their adaptation to this niche environment.
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Affiliation(s)
- João Anes
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Scott V Nguyen
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland.
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Evonne McCabe
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Guerrino Macori
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Daniel Hurley
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Séamus Fanning
- UCD School of Public Health, Physiotherapy and Sports Science, UCD-Centre for Food Safety, UCD Centre for Molecular Innovation and Drug Discovery, Science Centre South, Room S1.05, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom.
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High occurrence of CMY-2-type beta-lactamase-producing Escherichia coli among broiler flocks in Turkey. Trop Anim Health Prod 2019; 52:1681-1689. [PMID: 31858371 DOI: 10.1007/s11250-019-02167-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/01/2019] [Indexed: 10/25/2022]
Abstract
In this study, the prevalence of ESBL/pAmpC-producing Escherichia coli and their molecular characterization from cloacal swab samples were investigated. All samples were obtained from broiler flocks that are located in Hatay, Adana, and Mersin provinces of Turkey. Antimicrobial susceptibilities of the isolates were determined by disk diffusion method following the CLSI criteria. Genetic mechanisms mediating resistance in ESBL/pAmpC-producing E. coli isolates were identified by polymerase chain reaction (PCR) and followed by DNA sequencing. Phylogenetic groups and plasmid replicon types of the isolates were also investigated by PCR. The clonal relationship of selected isolates was investigated by enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing (MLST) method. Of 430 cloacal swab samples, 154 (35.8%) were positive for ESBL/pAmpC-producing E. coli. The ESBL/pAmpC type beta-lactamases were as follows: CMY-2 (n = 46), CMY-2 + TEM-1b (n = 63), SHV-12 (n = 5), SHV-12 + TEM-1b (n = 12), CTX-M-3 (n = 14), CTX-M-3 + TEM-1b (n = 1), CTX-M-15 (n = 4), CTX-M-15 + TEM-1b (n = 4), and CTX-M-1 (n = 3). Moreover, various rates of resistance to different antimicrobials were determined such as nalidixic acid (92.9%), ciprofloxacin (76%), sulfamethoxazole-trimethoprim (78.6%), tetracycline (73.4%), streptomycin (52.6%), chloramphenicol (44.2%), kanamycin (27.9%), tobramycin (24.7%), gentamicin (19.5%), and amikacin (0.6%). Furthermore, 148 (96.1%) isolates were found to be MDR. The ESBL/pAmpC-producing isolates were distributed into the following phylogroups: E (n = 61), B1 (n = 30), F (n = 20), A (n = 19), B2 (n = 11), D (n = 10), and C (n = 3). ERIC-PCR analysis showed 51 unrelated patterns. Out of the 28 selected isolates, the following sequence types (STs) were detected: ST354 (n = 3), ST114 (n = 3), ST5696 (n = 2), ST156 (n = 2), ST174 (n = 2), ST362 (n = 2), ST157 (n = 2), ST5114 (n = 2), ST6635, ST539, ST457, ST1640, ST95, ST5843, ST1158, ST10, ST648, and ST4248. The results of the current study revealed that broilers in Turkey are important reservoir of ESBL/pAmpC-producing E. coli, which suggest that these agents have a great potential of transmission to humans by food chain or direct contact.
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Rodríguez-Villodres Á, Bonnin RA, Ortiz de la Rosa JM, Álvarez-Marín R, Naas T, Aznar J, Pachón J, Lepe JA, Smani Y. Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections. J Clin Med 2019; 8:E2118. [PMID: 31810308 PMCID: PMC6947626 DOI: 10.3390/jcm8122118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli is the most frequent Gram-negative bacilli involved in intra-abdominal infections. However, despite high mortality rates associated with biliary tract infections due to E. coli, there is no study focusing on this pathogen. In this study, we have characterized a group of 15 E. coli isolates obtained from 12 patients with biliary tract infections. Demographic and clinical data of the patients were recovered. Phylogeny, resistome, and virulome analysis through whole genome sequencing and biofilm formation were investigated. Among the 15 E. coli isolates, no predominant sequence type (ST) was identified, although 3 of them belonged to unknown STs (20%). Resistance to ampicillin, amoxicillin/clavulanic acid, cotrimoxazole, and quinolones was more present in these isolates; whereas, third and fourth generation cephalosporins, carbapenems, amikacin, tigecycline, and colistin were highly active. Moreover, high diversity of virulence factors has been found, with sfa, fimH, and gad the most frequently detected genes. Interestingly, 26.6% of the E. coli isolates were high biofilm-producers. Altogether, our data characterized for the first time E. coli isolates associated with biliary tract infections in terms of genomic relationship, resistome, and virulome.
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Affiliation(s)
- Ángel Rodríguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Rémy A. Bonnin
- LabEx Lermit, EA7361, Université Paris-Sud, Université Paris-Saclay, 91190 Saint-Aubin, France; (R.A.B.); (T.N.)
- The Evolution and Ecology of Resistance to Antibiotics” Unit, Institut Pasteur-APHP-Université Paris Sud, 91400 Orsay, France
| | - José Manuel Ortiz de la Rosa
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Rocío Álvarez-Marín
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Thierry Naas
- LabEx Lermit, EA7361, Université Paris-Sud, Université Paris-Saclay, 91190 Saint-Aubin, France; (R.A.B.); (T.N.)
- The Evolution and Ecology of Resistance to Antibiotics” Unit, Institut Pasteur-APHP-Université Paris Sud, 91400 Orsay, France
- Bacteriology Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, 94270 Paris, France
| | - Javier Aznar
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
- Department of Microbiology, University of Seville, 41009 Seville, Spain
| | - Jerónimo Pachón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
- Department of Medicine, University of Seville, 41009 Seville, Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Younes Smani
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
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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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Thingholm KR, Hertz FB, Løbner-Olesen A, Frimodt-Møller N, Nielsen KL. Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli. Infect Drug Resist 2019; 12:2429-2435. [PMID: 31496755 PMCID: PMC6689528 DOI: 10.2147/idr.s208536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023] Open
Abstract
Background Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) causing urinary tract infections often belong to sequence type 131 (ST131), serotype O25, carrying bla CTX-M-15. Aim The main aim of this study was to examine the conjugational frequencies of E. coli with plasmids carrying bla CTX-M-15 to E. coli isolates from the fecal flora of healthy humans to determine whether ST131 is more likely to uptake or donate ESBL resistance compared to other E. coli clones. Methods Donors and recipients were all clinical isolates and did not harbor plasmids with identical incompatibility groups (Inc-groups) based on in silico analyses of Inc-groups and restriction/modification systems (R/M-systems). The in vitro conjugation experiments were performed as filter conjugation with verification of transconjugants by random amplified polymorphic DNA (RAPD) PCR and bla CTX-M-15 PCR. Results The frequencies of conjugation with bla CTX-M-15-carrying plasmids were found to be very rare with detectable conjugation frequencies in the range of 4x10-9-7x10-7 transconjugants/recipient. Recipients of O25/ST131 type yielded significantly lower conjugation frequencies compared to recipients of other O-types (P=0.004). The applied ST131/O25 donors did not yield detectable levels of transconjugants regardless of the applied recipient. Presence of sub-MIC levels of ampicillin increased plasmid transfer frequencies x100 fold (P=0.07). Conclusion The results indicate that bla CTX-M-15 is rarely transferred by conjugation to E. coli isolates of the intestinal flora, even when the gene is plasmid-borne.
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Affiliation(s)
| | - Frederik Boëtius Hertz
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark.,Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev 2730, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Section for Functional Genomics and Center for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | | | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark
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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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Arana DM, Sánchez A, Bautista V, Oteo-Iglesias J, Alós JI. ESBL-producing-multidrug resistant E. coli population from urinary tract infections is less diverse than non-ESBL-multidrug resistant population. Enferm Infecc Microbiol Clin 2019; 37:652-655. [PMID: 30979526 DOI: 10.1016/j.eimc.2019.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The aim of this study was to compare the population structure of three different representative groups of E. coli isolates causing urinary tract infections in a large area of Madrid, Spain: two groups of multidrug resistant isolates (MDR), ESBL- and non-ESBL producers, and one of fully-susceptible isolates (35 isolates in each group). METHODS Epidemiological relatedness was studied by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The presence of genes encoding ESBL was determined by using PCR and sequencing. Antimicrobial susceptibility testing was performed by broth microdilution. RESULTS PFGE analysis revealed a high degree of genetic diversity in susceptible and non-ESBL-MDR groups. However, the ESBL-MDR E. coli population was less diverse and a large cluster consisting of ST131 and CTX-M-15-producing isolates was detected. CONCLUSIONS The present study revealed that ESBL-producing-MDR E. coli population was less diverse than the non-ESBL MDR group and that ST131 was dominant among CTX-M-15-producing isolates that reflects the spread of this successful MDR lineage.
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Affiliation(s)
- David M Arana
- Servicio de Microbiología, Hospital Universitario Getafe, Madrid, Spain
| | - Aída Sánchez
- Servicio Microbiología, Laboratorio Clínico General BR Salud, Hospital Infanta Sofía, San Sebastián de los Reyes, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan-Ignacio Alós
- Servicio de Microbiología, Hospital Universitario Getafe, Madrid, Spain.
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Genotypic analysis of uropathogenic Escherichia coli to understand factors that impact the prevalence of β-lactam-resistant urinary tract infections in a community. J Glob Antimicrob Resist 2019; 19:173-180. [PMID: 30872040 DOI: 10.1016/j.jgar.2019.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES To determine the contribution of specific uropathogenic Escherichia coli (UPEC) lineages, drug resistance genes, and plasmid incompatibility/replicon (Inc) groups to the prevalence of β-lactam-resistant urinary tract infections (UTIs) in a university community. METHODS Urine samples were consecutively collected and cultured over a 2-year period from patients presenting to a university health centre with symptoms of UTI. Isolated UPEC were subtyped by multilocus sequence typing and fimH typing, and tested by PCR and sequencing for β-lactamase genes and plasmid Inc groups. RESULTS Among 273 UPEC isolates, 85 (31%) were ampicillin-resistant (AMP-R) and 188 (69%) were susceptible to all β-lactam drugs (AMP-S). Six lineages accounted for two-thirds of the isolates: ST95 (21%), ST69 (11%), ST420 (11%), ST73 (10%), ST127 (8%), and ST404 (3%). ST69 and ST404 were associated with AMP-R (P=0.003, P=0.0005), while ST420 and ST127 were associated with AMP-S (P<0.0001, P=0.027). ST95 contained four fimH types; the ST95/f-6 sublineage was more frequently identified among the AMP-R population (P = 0.009), while the ST95/f-47 sublineage was more frequently identified among the AMP-S population (P=0.007). The most common β-lactamase gene was blaTEM, which was identified in 81 (95%) AMP-R isolates. IncFIB, IncFIA, and IncB/O type plasmids were the most commonly identified types, and were associated with β-lactam resistance (P<0.001 for all). CONCLUSIONS These observations indicate that the prevalence of β-lactam-resistant UTIs in this community was largely determined by a limited set of circulating UPEC STs and sublineages, carrying TEM β-lactamase genes that were likely encoded on one of three Inc type plasmids.
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Prevalence of Extended-Spectrum β-Lactamases Among Klebsiella pneumoniae Isolated from Intensive Care Unit Patients in a Tertiary Hospital. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.69199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rapid detection of extra-intestinal pathogenic Escherichia coli multi-locus sequence type 127 using a specific PCR assay. J Med Microbiol 2019; 68:188-196. [DOI: 10.1099/jmm.0.000902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Cummins ML, Reid CJ, Roy Chowdhury P, Bushell RN, Esbert N, Tivendale KA, Noormohammadi AH, Islam S, Marenda MS, Browning GF, Markham PF, Djordjevic SP. Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene. Microb Genom 2019; 5. [PMID: 30672731 PMCID: PMC6421350 DOI: 10.1099/mgen.0.000250] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes blaTEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.
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Affiliation(s)
- Max L Cummins
- 1The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cameron J Reid
- 1The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Piklu Roy Chowdhury
- 1The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Rhys N Bushell
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Nicolas Esbert
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Kelly A Tivendale
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Amir H Noormohammadi
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Shaiful Islam
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Marc S Marenda
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Glenn F Browning
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Philip F Markham
- 2Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, and Werribee, Victoria 3030, Australia
| | - Steven P Djordjevic
- 1The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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Population Structure and Antimicrobial Resistance of Canine Uropathogenic Escherichia coli. J Clin Microbiol 2018; 56:JCM.00788-18. [PMID: 29997200 DOI: 10.1128/jcm.00788-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/30/2018] [Indexed: 01/04/2023] Open
Abstract
Escherichia coli is the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of the E. coli population that causes human UTI. While little is known about the population structure of E. coli that causes UTI in dogs, there is evidence that dogs and humans can share fecal strains of E. coli and that human-associated strains can cause disease in dogs. In order to better characterize the E. coli strains that cause canine UTI, we analyzed 295 E. coli isolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates with blaCTX-M genes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenic E. coli.
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2018; 9:243. [PMID: 29503639 PMCID: PMC5821075 DOI: 10.3389/fmicb.2018.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Ismail MD, Ali I, Hatt S, Salzman EA, Cronenwett AW, Marrs CF, Rickard AH, Foxman B. Association of Escherichia coli ST131 lineage with risk of urinary tract infection recurrence among young women. J Glob Antimicrob Resist 2017; 13:81-84. [PMID: 29258889 DOI: 10.1016/j.jgar.2017.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/30/2017] [Accepted: 12/10/2017] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The aim of this study was to test the hypothesis that urinary tract infections (UTIs) caused by Escherichia coli of the sequence type 131 (ST131) lineage are more likely to recur than UTIs caused by other E. coli lineages. METHODS Isolates from 221 young women with UTI caused by E. coli participating in a randomised controlled trial were used. Participants were followed for 6 months or until UTI recurrence. RESULTS Sequence type was not associated with risk of recurrence. Isolates in the ST131 lineage were more resistant than other STs to quinolones (6.2% vs. 1.3%) but not trimethoprim/sulfamethoxazole (15.4% vs. 15.0%). CONCLUSIONS These results do not support an increased risk of recurrent UTI among otherwise healthy women with UTI caused by E. coli ST131.
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Affiliation(s)
- Miriam D Ismail
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Ihsan Ali
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Savannah Hatt
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Elizabeth A Salzman
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Anna W Cronenwett
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Carl F Marrs
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Alexander H Rickard
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA
| | - Betsy Foxman
- The Center for Molecular and Clinical Epidemiology of Infectious Diseases (MAC-EPID), Department of Epidemiology, University of Michigan, School of Public Health, Ann Arbor, MI 48109, USA.
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Alonso CA, González-Barrio D, Ruiz-Fons F, Ruiz-Ripa L, Torres C. High frequency of B2 phylogroup among non-clonally related fecal Escherichia coli isolates from wild boars, including the lineage ST131. FEMS Microbiol Ecol 2017; 93:3003317. [PMID: 28365752 DOI: 10.1093/femsec/fix016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/11/2017] [Indexed: 11/14/2022] Open
Abstract
Wild boars are worldwide distributed mammals which population is increasing in many regions, like the Iberian Peninsula, leading to an increased exposition to humans. They are considered reservoirs of different zoonotic pathogens and have been postulated as potential vectors of antimicrobial-resistant (AMR) bacteria. This study aimed to determine the prevalence of antimicrobial resistance and phylogenetic distribution of Escherichia coli from wild boar feces. Antimicrobial resistance and integron content was genetically characterized and E. coli of B2 phylogroup was further analyzed by molecular typing and virulence genotyping. The prevalence of AMR E. coli was low, with only 7.5% of isolates being resistant against at least one antimicrobial, mainly ampicillin, tetracycline and/or sulfonamide. An unexpected elevated rate of B2 phylogroup (47.5%) was identified, most of them showing unrelated pulsed-field-gel-electrophoresis patterns. ST131/B2 (fimH 22 sublineage), ST28/B2, ST1170/B2, ST681/B2 and ST625/B2 clones, previously described in extraintestinal infections in humans, were detected in B2 isolates, and carried one or more genes associated with extraintestinal pathogenic E. coli (ExPEC). This study demonstrated a low prevalence of antimicrobial resistance in E. coli from wild boars, although they are not exempt of AMR bacteria, and a predominance of genetically diverse B2 phylogroup, including isolates carrying ExPEC which may contribute to the spread of virulence determinants among different ecosystems.
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Affiliation(s)
- Carla Andrea Alonso
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - David González-Barrio
- Health and Biotechnology (SaBio) Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), 13071 Ciudad Real, Spain
| | - Francisco Ruiz-Fons
- Health and Biotechnology (SaBio) Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), 13071 Ciudad Real, Spain
| | - Laura Ruiz-Ripa
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
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Grevskott DH, Svanevik CS, Sunde M, Wester AL, Lunestad BT. Marine Bivalve Mollusks As Possible Indicators of Multidrug-Resistant Escherichia coli and Other Species of the Enterobacteriaceae Family. Front Microbiol 2017; 8:24. [PMID: 28149295 PMCID: PMC5241299 DOI: 10.3389/fmicb.2017.00024] [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: 11/24/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022] Open
Abstract
The mechanisms for the development and spread of antibacterial resistance (ABR) in bacteria residing in environmental compartments, including the marine environment, are far from understood. The objective of this study was to examine the ABR rates in Escherichia coli and other Enterobacteriaceae isolates obtained from marine bivalve mollusks collected along the Norwegian coast during a period from October 2014 to November 2015. A total of 549 bivalve samples were examined by a five times three tube most probable number method for enumeration of E. coli in bivalves resulting in 199 isolates from the positive samples. These isolates were identified by biochemical reactions and matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, showing that 90% were E. coli, while the remaining were species within the genera Klebsiella, Citrobacter, and Enterobacter. All 199 isolates recovered were susceptibility tested following the European Committee on Antimicrobial Susceptibility Testing disk diffusion method. In total, 75 of 199 (38%) isolates showed resistance to at least one antibacterial agent, while multidrug-resistance were seen in 9 (5%) isolates. One isolate conferred resistance toward 15 antibacterial agents. Among the 75 resistant isolates, resistance toward extended-spectrum penicillins (83%), aminoglycosides (16%), trimethoprim (13%), sulfonamides (11%), tetracyclines (8%), third-generation cephalosporins (7%), amphenicols (5%), nitrofurans (5%), and quinolones (5%), were observed. Whole-genome sequencing on a selection of 10 E. coli isolates identified the genes responsible for resistance, including blaCTX-M genes. To indicate the potential for horizontal gene transfer, conjugation experiments were performed on the same selected isolates. Conjugative transfer of resistance was observed for six of the 10 E. coli isolates. In order to compare E. coli isolates from bivalves with clinical strains, multiple-locus variable number tandem repeats analysis (MLVA) was applied on a selection of 30 resistant E. coli isolates. The MLVA-profiles were associated with community-acquired E. coli strains causing bacteremia. Our study indicates that bivalves represent an important tool for monitoring antibacterial resistant E. coli and other members of the Enterobacteriaceae family in the coastal environment.
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Affiliation(s)
| | | | - Marianne Sunde
- Norwegian Veterinary InstituteOslo, Norway; Norwegian Institute of Public HealthOslo, Norway
| | | | - Bjørn T Lunestad
- National Institute of Nutrition and Seafood Research Bergen, Norway
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Helldal L, Karami N, Welinder-Olsson C, Moore ERB, Åhren C. Evaluation of MLVA for epidemiological typing and outbreak detection of ESBL-producing Escherichia coli in Sweden. BMC Microbiol 2017; 17:8. [PMID: 28061803 PMCID: PMC5217547 DOI: 10.1186/s12866-016-0922-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To identify the spread of nosocomial infections and halt outbreak development caused by Escherichia coli that carry multiple antibiotic resistance factors, such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases, is becoming demanding challenges due to the rapid global increase and constant and increasing influx of these bacteria from the community to the hospital setting. Our aim was to assess a reliable and rapid typing protocol for ESBL-E. coli, with the primary focus to screen for possible clonal relatedness between isolates. All clinical ESBL-E. coli isolates, collected from hospitals (n = 63) and the community (n = 41), within a single geographical region over a 6 months period, were included, as well as clinical isolates from a polyclonal outbreak (ST131, n = 9, and ST1444, n = 3). The sporadic cases represented 36 STs, of which eight STs dominated i.e. ST131 (n = 33 isolates), ST648 (n = 10), ST38 (n = 9), ST12 and 69 (each n = 4), ST 167, 405 and 372 (each n = 3). The efficacy of multiple-locus variable number tandem repeat analysis (MLVA) was evaluated using three, seven or ten loci, in comparison with that of pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST). RESULTS MLVA detected 39, 55 and 60 distinct types, respectively, using three (GECM-3), seven (GECM-7) or ten (GECM-10) loci. For GECM-7 and -10, 26 STs included one type and eleven STs each included several types, the corresponding numbers for GECM-3 were 29 and 8. The highest numbers were seen for ST131 (7,7 and 8 types, respectively), ST38 (5,5,8) and ST648 (4,5,5). Good concordance was observed with PFGE and GECM-7 and -10, despite fewer types being identified with MLVA; 78 as compared to 55 and 60 types. The lower discriminatory power of MLVA was primarily seen within the O25b-ST131 lineage (n = 34) and its H30-Rx subclone (n = 21). Epidemiologically unrelated O25b-ST131 isolates were clustered with O25b-ST131 outbreak isolates by MLVA, whereas the ST1444 outbreak isolates were accurately distinguished from unrelated isolates. CONCLUSION MLVA, even when using only three loci, represents an easy initial typing tool for epidemiological screening of ESBL-E. coli. For the ST131-O25b linage, complementary methods may be needed to obtain sufficient resolution.
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Affiliation(s)
- Lisa Helldal
- Department of Infectious Diseases, Institution of Biomedicine, Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
- Clinical Microbiology/Section for Bacteriology, Sahlgrenska University Hospital, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institution of Biomedicine, Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
| | - Christina Welinder-Olsson
- Department of Infectious Diseases, Institution of Biomedicine, Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institution of Biomedicine, Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhren
- Department of Infectious Diseases, Institution of Biomedicine, Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, Gothenburg, Sweden
- Swedish strategic programme against antibiotic resistance, Region Västra Götaland, Gothenburg, Sweden
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Hertz FB, Nielsen JB, Schønning K, Littauer P, Knudsen JD, Løbner-Olesen A, Frimodt-Møller N. Erratum to: Population structure of Drug-Susceptible,-Resistant and ESBL-producing Escherichia coli from community-acquired urinary tract infections. BMC Microbiol 2016; 16:114. [PMID: 27324943 PMCID: PMC4913426 DOI: 10.1186/s12866-016-0725-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/06/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- Frederik Boëtius Hertz
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Boye Nielsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Pia Littauer
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Jenny Dahl Knudsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
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