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Belmont-Monroy L, Merida-Vieyra J, Bautista-Hernandez R, Mateo-Arreola JA, de Colsa-Ranero A, Medina-Vera I, Jandete-Martinez EE, Aquino-Andrade A. Escherichia coli causing bloodstream infections in Mexican paediatric patients: molecular typing, antimicrobial resistance, virulence factors, and clinical features. BMC Infect Dis 2025; 25:764. [PMID: 40426089 PMCID: PMC12117857 DOI: 10.1186/s12879-025-11163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Accepted: 05/23/2025] [Indexed: 05/29/2025] Open
Abstract
BACKGROUND Escherichia coli is one of the main pathogens causing bloodstream infections (BSIs) in paediatric patients. It is classified into pathogenic (B2, D and F) and commensal (A, B1 and C) phylogroups, with virulence mainly attributed to adhesins, toxins and iron acquisition systems. In recent years, the global spread of high-risk clones such as ST131 and ST405, often associated with extended-spectrum beta-lactamases (ESBLs), has contributed to increased resistance and limited treatment options. The BSI mortality rate in children varies from 14 to 21.6%. This study aimed to describe resistant mechanisms; virulence factors and clonal distribution of E. coli isolates that cause BSIs in children in Mexico and clinical features. METHODS Thirty-eight ceftriaxone (CRO)-resistant E. coli isolates were included. Beta-lactamase and virulence genes were detected by PCR. Molecular typing included phylogroup determination, sequence types (ST), and pulsed-field gel electrophoresis (PFGE). Clinical information was acquired. RESULTS CTX-M was the most frequently identified beta-lactamase (82%) and aac(6')-Ib-cr was present in 45%. Phylogroup distribution was A (21.1%), C (7.9%), D (28.9%), B2 (23.7%), and F (18.4%). The most common virulence factor was fimH (71%), while papC, sat and irp2 were significantly more frequently in the pathogenic phylogroups (P = 0.029, 0.011 and 0.006, respectively). PFGE identified 5 clusters, 20 non-related isolates and 4 non-typeable. Predominant clonal complexes (CC) were CC405 (23.7%) and CC131 (21.1%), with 82% of isolates belonging to high-risk clones. Survival rates differed significantly with moderate high-grade fever (P = 0.022). All patients who died had complications, compared to 34.8% of survivors (P < 0.0001). Mortality was higher in adolescents (53.3%), patients with leukaemia or lymphoma (40%), those with hospital-acquired infections (86.8%), those with an abdominal or pulmonary focus (33.3% each). No significant differences were found in of haematological parameters. CONCLUSIONS Both commensal and pathogenic E. coli strains cause BSIs in paediatric patients with underlying diseases. Resistance to 3GCs and 4GCs is mainly mediated by CTX-M, hence treatment with carbapenems was used. Infection-related deaths were more frequent in patients infected by pathogenic phylogroups, where papC, sat, and irp2 were more prevalent. High-risk clones were widely distributed among isolates.
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Affiliation(s)
- Laura Belmont-Monroy
- Laboratory of Molecular Microbiology, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Jocelin Merida-Vieyra
- Laboratory of Molecular Microbiology, Instituto Nacional de Pediatria, Mexico City, Mexico
| | | | | | - Agustín de Colsa-Ranero
- Department of Pediatric Infectious Diseases, Instituto Nacional de Pediatria, Mexico City, Mexico
| | - Isabel Medina-Vera
- Department of Research Methodology, Instituto Nacional de Pediatria, Mexico City, Mexico
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Tanaka M, Hanawa T, Suda T, Tanji Y, Minh LN, Kondo K, Azam AH, Kiga K, Yonetani S, Yashiro R, Ohmori T, Matsuda T. Comparative analysis of virulence-associated genes in ESBL-producing Escherichia coli isolates from bloodstream and urinary tract infections. Front Microbiol 2025; 16:1571121. [PMID: 40342604 PMCID: PMC12058657 DOI: 10.3389/fmicb.2025.1571121] [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: 02/05/2025] [Accepted: 04/03/2025] [Indexed: 05/11/2025] Open
Abstract
The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) is a global health concern due to the multidrug antimicrobial resistance in extraintestinal pathogenic E. coli (ExPEC). ExPEC causes severe infections such as bloodstream infections, meningitis, and sepsis. Uropathogenic E. coli (UPEC), a subset of ExPEC, is responsible for urinary tract infections (UTIs), ranging from asymptomatic bacteriuria and cystitis to more severe conditions, such as pyelonephritis, bacteremia, and sepsis (urosepsis). Although ESBL-producing E. coli may have a significant impact on patient outcomes, comparisons of genotype and virulence factors between ESBL-producing and non-ESBL-producing E. coli have not fully elucidated the factors influencing its pathogenicity. Therefore, in the present study, we analyzed the genotypes and virulence-associated genes of ESBL-producing strains isolated from the blood of patients with UTIs to determine the characteristics of ESBL-producing UPEC strains associated with severe infections. Most of the clinical isolates belonged to phylogroup B2, with the exception of three strains from phylogroup D. The MLST was ST131, followed by ST73, ST95, and ST38, which are commonly found in UPEC strains. Intriguingly, ST131 strains were associated with fewer sepsis cases compared to non-ST131 strains (8 of 38 cases by ST131 and 5 of 8 cases by non-ST131 [OR, 0.16; 95% CI, 0.038-0.873; p = 0.031]). In silico analysis of 23 clinical isolates revealed that the genes detected in all strains may play a significant role in the pathogenesis of invasive UTIs. Clustering and gene locus analysis highlighted the genotype-MLST dependence of UPEC-specific virulence-associated genes. ST38-specific strains were atypical, characterized by the absence of several UPEC-specific genes, including pap loci, pathogenicity island marker (malX), and ompT, as well as the presence of genes encoding Ycb fimbriae and a Type 3 secretion system, which are typically found in enteropathogenic E. coli (EPEC). These results suggest that the virulence of clinical isolates causing invasive infections can vary, and that the pathogenicity of UPEC should be considered when analyzing the correlation between MLST and the repertoire of virulence-associated genes.
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Affiliation(s)
- Mayuko Tanaka
- Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Tomoko Hanawa
- Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Tomoya Suda
- Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Yasunori Tanji
- Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Le Nhat Minh
- Department of Traumatology and Critical Care Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Kohei Kondo
- Antimicrobial Resistance Research Center, National Institute of Infectious Disease, Tokyo, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aa Haeruman Azam
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kotaro Kiga
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shota Yonetani
- Department of Medical Technology, Faculty of Health Sciences, Kyorin University, Tokyo, Japan
| | - Ryu Yashiro
- Department of Traumatology and Critical Care Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Takuya Ohmori
- Center for Data Science Education and Research, Kyorin University, Tokyo, Japan
| | - Takeaki Matsuda
- Department of General Medicine, Kyorin University School of Medicine, Tokyo, Japan
- Department of Traumatology and Critical Care Medicine, Kyorin University School of Medicine, Tokyo, Japan
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Reid CJ, Cummins ML, Djordjevic SP. Major F plasmid clusters are linked with ColV and pUTI89-like marker genes in bloodstream isolates of Escherichia coli. BMC Genomics 2025; 26:57. [PMID: 39838323 PMCID: PMC11748317 DOI: 10.1186/s12864-025-11226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 01/08/2025] [Indexed: 01/23/2025] Open
Abstract
BACKGROUND F plasmids are abundant in E. coli, carrying a variety of genetic cargo involved in fitness, pathogenicity, and antimicrobial resistance. ColV and pUTI89-like plasmids have drawn attention for their potential roles in various forms of extra-intestinal pathogenicity. However, the rates of their carriage and the overall diversity of F plasmids in E. coli bloodstream infections (BSI E. coli) remain unknown. METHODS We performed a t-SNE-based cluster analysis of predicted F plasmids from a collection of 4711 BSI E. coli draft genomes to describe their diversity and abundance. We also screened them for markers of ColV and pUTI89-like plasmids, F plasmid replicon sequence types (RST) and E. coli sequence types (ST) to understand how genetic features were related to plasmid clusters. RESULTS Predicted F plasmids in BSI E. coli draft genomes were embedded within five major clusters based on a model of complete F plasmid sequences. Nearly half of the clustered sequences belonged to two major clusters, which were associated with ColV and pUTI89-like marker genes, respectively. Genomes from the ColV cluster featured F2:A-:B1 and F24:A-B1 RSTs in association with ST95, ST58 and ST88, whilst the pUTI89-like cluster was mostly F29:A-:B10 linked to ST73, ST69, ST95 and ST131. Plasmids associated with different lineages of ST131 formed additional major clusters, whilst F51:A-:B10 plasmids in ST73 were also common. CONCLUSIONS ColV and pUTI89-like plasmid markers are predominant in BSI E. coli that carry F plasmids. These markers are associated with distinct clusters of plasmids across diverse sequence types of E. coli. We hypothesise that their abundance in BSI E. coli is partially driven by carriage of backbone genes previously shown to contribute to virulence in models of bloodstream infection. Their carriage by pandemic E. coli STs suggests clonal expansion also plays a role in their success in BSI. Ecological pathways via which these plasmids evolve, and spread are likely to be distinct as other studies show ColV is strongly associated with poultry and food animal production, whereas pUTI89-like plasmids appear to be mostly human-restricted.
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Affiliation(s)
- Cameron J Reid
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Environment Research Unit, Urrbrae, SA, Australia
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
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Ha JH, Shin JI, Kim KM, Choi JG, Trinh MP, Anh WJ, Kang KM, Kang HL, Byun JH, Boonyanugomol W, Kwon KW, Jung MH, Baik SC, Lee WK, Shin MK. Prevalence and virulence profiles of ESBL-producing Escherichia coli in urinary and blood infections in South Korea. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01205-9. [PMID: 39433645 DOI: 10.1007/s12223-024-01205-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 09/30/2024] [Indexed: 10/23/2024]
Abstract
Escherichia coli is a significant pathogen in extraintestinal infections, and ESBL-producing E. coli poses a major clinical challenge due to its antibiotic resistance. This study comprehensively analyzed E. coli isolates from urine and blood samples of patients with urinary tract and bloodstream infections at three major tertiary hospitals in South Korea. The goal was to provide insights into the distribution, antibiotic resistance, and virulence factors of these strains. Our analysis identified CTX-M and TEM as the dominant ESBL types, found in 71.7% and 61.7% of isolates, respectively, with 46.7% showing co-occurrence. Multilocus sequence typing (MLST) revealed the predominance of high-risk clones such as ST131, ST69, ST73, and ST95, with rare sequence types like ST410 and ST405 also identified. The high prevalence of virulence factors, including iutA (80.8%) and kpsMII (74.2%), further highlights the complexity of these strains. In addition, 38.3% of clinical isolates contained a combination of siderophore, adhesin, protectin, and toxin-related genes. There was no significant difference between urinary tract and bloodstream infections or regional differentiation in Korea. This study highlights the importance of controlling ESBL-producing E. coli infections, especially given the increasing incidence among patients with underlying medical conditions and older adults who are more susceptible to urinary tract infections. These findings serve as valuable indicators for pathogen analysis, especially those harboring antibiotic resistance and toxin genes. The insights gained are expected to contribute significantly to the development of infectious disease prevention and control strategies.
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Affiliation(s)
- Jong-Hun Ha
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Ih Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Biomedicine & Health Sciences and Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jeong-Gyu Choi
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Won Jun Anh
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyung-Min Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyung-Lyun Kang
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Hyun Byun
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Wongwarut Boonyanugomol
- Department of Sciences and Liberal Arts, Mahidol University, Amnatcharoen Campus, Amnatcharoen, Thailand
| | - Kee Woong Kwon
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Myung Hwan Jung
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seung Chul Baik
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea.
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea.
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea.
- Department of Convergence Medical Science, Gyeongsang National University, Jinju, Republic of Korea.
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Saidenberg ABS, Edslev SM, Hallstrøm S, Rasmussen A, Park DE, Aziz M, Dos Santos Queiroz B, Baptista AAS, Barbosa F, Rocha VGP, van Vliet AHM, Dalsgaard A, Price LB, Knöbl T, Stegger M. Escherichia coli ST117: exploring the zoonotic hypothesis. Microbiol Spectr 2024; 12:e0046624. [PMID: 39235965 PMCID: PMC11448156 DOI: 10.1128/spectrum.00466-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 08/04/2024] [Indexed: 09/07/2024] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) can lead to severe infections, with additional risks of increasing antimicrobial resistance rates. Genotypic similarities between ExPEC and avian pathogenic E. coli (APEC) support a possible role for a poultry meat reservoir in human disease. Some genomic studies have been done on the ST117 lineage which contaminates poultry meat, carries multidrug resistance, can be found in the human intestinal microbiota, and causes human extraintestinal disease. This study analyzed the genomes of 61 E. coli from Brazilian poultry outbreaks focusing on ST117, to further define its possible zoonotic characteristics by genotypic and phylogenomic analyses, along with 1,699 worldwide ST117 isolates originating from human, animal, and environment sources. A predominance of ST117 was detected in the Brazilian isolates (n = 20/61) frequently carrying resistance to critical antibiotics (>86%) linked to IncFII, IncI1, or IncX4 replicons. High similarities were found between IncX4 from Brazilian outbreaks and those from E. coli recovered from imported Brazilian poultry meat and human clinical cases. The ST117 phylogeny showed non-specificity according to host and continent and an AMR index score indicated the highest resistance in Asia and South America, with the latter statistically more resistant and overrepresented with resistance to extended-spectrum beta-lactamases (ESBL). Most ST117 human isolates were predicted to have a poultry origin (93%, 138/148). In conclusion, poultry is a likely source for zoonotic ExPEC strains, particularly the ST117 lineage which can also serve as a reservoir for resistance determinants against critical antibiotics encoded on highly transmissible plasmids. IMPORTANCE Certain extraintestinal pathogenic Escherichia coli (ExPEC) are particularly important as they affect humans and animals. Lineages, such as ST117, are predominant in poultry and frequent carriers of antibiotic resistance, presenting a risk to humans handling or ingesting poultry products. We analyzed ExPEC isolates causing outbreaks in Brazilian poultry, focusing on the ST117 as the most detected lineage. Genomic comparisons with international isolates from humans and animals were performed describing the potential zoonotic profile. The Brazilian ST117 isolates carried resistance determinants against critical antibiotics, mainly on plasmids, in some cases identical to those carried by international isolates. South American ST117 isolates from all sources generally exhibit more resistance, including to critical antibiotics, and worldwide, the vast majority of human isolates belonging to this lineage have a predicted poultry origin. As the world's largest poultry exporter, Brazil has an important role in developing strategies to prevent the dissemination of multidrug-resistant zoonotic ExPEC strains.
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Affiliation(s)
- A B S Saidenberg
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- School of Veterinary Medicine and Animal Science, São Paulo, Brazil
- Section for Food Safety and Zoonoses, Institute for Veterinary and Companion Animal Science, Københavns Universitet, Copenhagen, Denmark
| | - S M Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - S Hallstrøm
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - A Rasmussen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - D E Park
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - M Aziz
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | | | - A A S Baptista
- Preventive Veterinary Medicine Department, State University of Londrina, Parana, Brazil
| | - F Barbosa
- School of Veterinary Medicine and Animal Science, São Paulo, Brazil
| | - V G P Rocha
- School of Veterinary Medicine and Animal Science, São Paulo, Brazil
| | - Arnoud H M van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - A Dalsgaard
- Section for Food Safety and Zoonoses, Institute for Veterinary and Companion Animal Science, Københavns Universitet, Copenhagen, Denmark
| | - L B Price
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - T Knöbl
- School of Veterinary Medicine and Animal Science, São Paulo, Brazil
| | - M Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
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