351
|
Extensive dissemination of extended spectrum β-lactamase-producing Enterobacteriaceae in a Dutch nursing home. Infect Control Hosp Epidemiol 2016; 36:394-400. [PMID: 25782893 DOI: 10.1017/ice.2014.76] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Risk factors for rectal carriage of ESBL-E and transmission were investigated in an outbreak of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E). DESIGN Rectal carriage of ESBL-E was determined in a cross-sectional survey by culture of perianal swabs or fecal samples. Both phenotypical and genotypical methods were used to detect the production of ESBL. Nosocomial transmission was defined as the presence of genotypically related strains in ≥2 residents within the NH. Patient characteristics and variables in infection control practices were registered to investigate risk factors for transmission. SETTING A nursing home (NH) in the southern Netherlands. PARTICIPANTS Of 189 residents, 160 residents (84.7%) were screened for ESBL-E carriage. Of these 160 residents, 33 (20.6%) were ESBL-E positive. ESBL carriage rates varied substantially between wards (range, 0-47%). Four different ESBL-E clusters were observed. A bla CTX-M1-15 positive E. coli ST131 constituted the largest cluster (n=21) and was found in multiple wards (n=7). RESULTS Our investigation revealed extensive clonal dissemination of bla CTX-M1-15-positive E. coli ST131 in a nursing home. Unexplained differences in ESBL prevalence were detected among the wards. CONCLUSIONS As NHs constitute potential sources of multidrug-resistant bacteria, it is important to gain a better understanding of the risks factors and routes of transmission of ESBL-E.
Collapse
|
352
|
Millar MR, Seale J, Turton J, Wilks M, Costeloe K, Woodford N, Juszczak E, Whiley A, Panton N, Wareham DW. ESBL-producing Enterobacteriaceae in 24 neonatal units and associated networks in the south of England: no clustering of ESBL-producing Escherichia coli in units or networks. J Antimicrob Chemother 2016; 71:1174-7. [PMID: 26755494 DOI: 10.1093/jac/dkv459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/03/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objectives of this study were to characterize ESBL-producing Enterobacteriaceae present in 24 neonatal units (NNUs) in eight networks participating in a multicentre probiotic study and to test the hypothesis that specific strains would cluster within individual units and networks. METHODS We performed analysis of stool samples for the presence of ESBL-producing Enterobacteriaceae at 2 weeks post-natal age and 36 weeks post-menstrual age. ESBL-producing Enterobacteriaceae were characterized and typed using molecular methods. RESULTS ESBL-producing Enterobacteriaceae (n = 71) were isolated from 67/1229 (5.5%) infants from whom we received a sample at either sampling time or both sampling times, and from infants in 18 (75%) of the 24 recruiting NNUs. Thirty-three Escherichia coli, 23 Klebsiella spp. and 6 Enterobacter spp. strains were characterized. ESBL-producing E. coli were all distinguishable within individual NNUs by antibiotic resistance genotype, serogroup (O25b), phenotype, phylotype or ST. Ten of the 33 were ST131 and 9 of the 10 ST131 isolates were ciprofloxacin resistant. Seven of the 10 ST131 isolates carried genes encoding CTX-M group 1 enzymes. ST131 isolates were isolated from centres within five of the eight NNU networks. There were clusters of indistinguishable ESBL-producing Klebsiella and Enterobacter isolates associated with specific NNUs. CONCLUSIONS Strains of E. coli ST131 were distributed across neonatal networks in the south of England. There was no evidence of clustering of clonally related ESBL-producing E. coli strains, by contrast with Klebsiella spp. and Enterobacter spp., which did cluster within units. The possibility that ESBL-producing E. coli strains are spread by vertical transmission requires further investigation.
Collapse
Affiliation(s)
- Michael R Millar
- Department of Infection, Barts Health NHS Trust, 3rd Floor, Pathology and Pharmacy Building, 80 Newark Street, Whitechapel, London E1 2ES, UK
| | - Jo Seale
- Department of Infection, Barts Health NHS Trust, 3rd Floor, Pathology and Pharmacy Building, 80 Newark Street, Whitechapel, London E1 2ES, UK
| | - Jane Turton
- Public Health England, 61 Colindale Avenue, London NW9 5HT, UK
| | - Mark Wilks
- Department of Infection, Barts Health NHS Trust, 3rd Floor, Pathology and Pharmacy Building, 80 Newark Street, Whitechapel, London E1 2ES, UK
| | - Kate Costeloe
- Blizard Institute, Queen Mary, University of London, London, UK
| | - Neil Woodford
- Public Health England, 61 Colindale Avenue, London NW9 5HT, UK
| | - Ed Juszczak
- National Perinatal Epidemiology Unit, Oxford, UK
| | - Angela Whiley
- Department of Infection, Barts Health NHS Trust, 3rd Floor, Pathology and Pharmacy Building, 80 Newark Street, Whitechapel, London E1 2ES, UK
| | - Nicola Panton
- Department of Infection, Barts Health NHS Trust, 3rd Floor, Pathology and Pharmacy Building, 80 Newark Street, Whitechapel, London E1 2ES, UK
| | - David W Wareham
- Blizard Institute, Queen Mary, University of London, London, UK
| |
Collapse
|
353
|
Strain- and host species-specific inflammasome activation, IL-1β release, and cell death in macrophages infected with uropathogenic Escherichia coli. Mucosal Immunol 2016; 9:124-36. [PMID: 25993444 DOI: 10.1038/mi.2015.44] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/07/2015] [Indexed: 02/04/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). Little is known about interactions between UPEC and the inflammasome, a key innate immune pathway. Here we show that UPEC strains CFT073 and UTI89 trigger inflammasome activation and lytic cell death in human macrophages. Several other UPEC strains, including two multidrug-resistant ST131 isolates, did not kill macrophages. In mouse macrophages, UTI89 triggered cell death only at a high multiplicity of infection, and CFT073-mediated inflammasome responses were completely NLRP3-dependent. Surprisingly, CFT073- and UTI89-mediated responses only partially depended on NLRP3 in human macrophages. In these cells, NLRP3 was required for interleukin-1β (IL-1β) maturation, but contributed only marginally to cell death. Similarly, caspase-1 inhibition did not block cell death in human macrophages. In keeping with such differences, the pore-forming toxin α-hemolysin mediated a substantial proportion of CFT073-triggered IL-1β secretion in mouse but not human macrophages. There was also a more substantial α-hemolysin-independent cell death response in human vs. mouse macrophages. Thus, in mouse macrophages, CFT073-triggered inflammasome responses are completely NLRP3-dependent, and largely α-hemolysin-dependent. In contrast, UPEC activates an NLRP3-independent cell death pathway and an α-hemolysin-independent IL-1β secretion pathway in human macrophages. This has important implications for understanding UTI in humans.
Collapse
|
354
|
Pesesky MW, Hussain T, Wallace M, Wang B, Andleeb S, Burnham CAD, Dantas G. KPC and NDM-1 genes in related Enterobacteriaceae strains and plasmids from Pakistan and the United States. Emerg Infect Dis 2015; 21:1034-7. [PMID: 25988236 PMCID: PMC4451916 DOI: 10.3201/eid2106.141504] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To characterize the genomic context of New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemase (KPC), we sequenced 78 Enterobacteriaceae isolates from Pakistan and the United States encoding KPC, NDM-1, or no carbapenemase. High similarities of the results indicate rapid spread of carbapenem resistance between strains, including globally disseminated pathogens.
Collapse
|
355
|
Schaufler K, Semmler T, Wieler LH, Wöhrmann M, Baddam R, Ahmed N, Müller K, Kola A, Fruth A, Ewers C, Guenther S. Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410--another successful pandemic clone? FEMS Microbiol Ecol 2015; 92:fiv155. [PMID: 26656065 DOI: 10.1093/femsec/fiv155] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 12/23/2022] Open
Abstract
Clinically relevant extended-spectrum beta-lactamase (ESBL)-producing multi-resistant Escherichia coli have been on the rise for years. Initially restricted to mostly a clinical context, recent findings prove their prevalence in extraclinical settings independent of the original occurrence of antimicrobial resistance in the environment. To get further insights into the complex ecology of potentially clinically relevant ESBL-producing E. coli, 24 isolates from wild birds in Berlin, Germany, and 40 ESBL-producing human clinical E. coli isolates were comparatively analyzed. Isolates of ST410 occurred in both sample groups (six). In addition, three ESBL-producing E. coli isolates of ST410 from environmental dog feces and one clinical dog isolate were included. All 10 isolates were clonally analyzed showing almost identical macrorestriction patterns. They were chosen for whole-genome sequencing revealing that the whole-genome content of these 10 E. coli isolates showed a very high genetic similarity, differing by low numbers of single nucleotide polymorphisms only. This study gives initial evidence for a recent interspecies transmission of a new successful clone of ST410 E. coli between wildlife, humans, companion animals and the environment. The results underline the zoonotic potential of clinically relevant multi-resistant bacteria found in the environment as well as the mandatory nature of the 'One Health' approach.
Collapse
Affiliation(s)
- Katharina Schaufler
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Torsten Semmler
- NG 1 - Microbial Genomics, Robert Koch Institute, 13302 Berlin, Germany
| | | | - Michael Wöhrmann
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Ramani Baddam
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, 500046 Hyderabad, India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, 500046 Hyderabad, India
| | - Kerstin Müller
- Clinic of Small Animals, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité Universitätsklinikum, 12203 Berlin, Germany
| | - Angelika Fruth
- Department for Infectious Diseases, Division of Bacterial Infections and National Reference, Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Veterinary Faculty, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| |
Collapse
|
356
|
Abstract
SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.
Collapse
|
357
|
Ciesielczuk H, Doumith M, Hope R, Woodford N, Wareham DW. Characterization of the extra-intestinal pathogenic Escherichia coli ST131 clone among isolates recovered from urinary and bloodstream infections in the United Kingdom. J Med Microbiol 2015; 64:1496-1503. [DOI: 10.1099/jmm.0.000179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H. Ciesielczuk
- Antimicrobial Research Group, Centre for Immunology and Infectious Disease, Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale, UK
- Department of Clinical Microbiology, Royal Free Hospital, Pond Street, London, UK
| | - M. Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale, UK
| | - R. Hope
- Centre for Infectious Disease Surveillance and Control, Healthcare Associated Infection and Antimicrobial Resistance Department, Public Health England, Colindale, UK
| | - N. Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale, UK
| | - D. W. Wareham
- Antimicrobial Research Group, Centre for Immunology and Infectious Disease, Blizard Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, UK
| |
Collapse
|
358
|
Jahandeh N, Ranjbar R, Behzadi P, Behzadi E. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes. Cent European J Urol 2015; 68:452-8. [PMID: 26855801 PMCID: PMC4742438 DOI: 10.5173/ceju.2015.625] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/20/2015] [Accepted: 09/15/2015] [Indexed: 12/26/2022] Open
Abstract
Introduction The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Material and methods Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. Results There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. Conclusions The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.
Collapse
Affiliation(s)
- Nadia Jahandeh
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Payam Behzadi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Elham Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
359
|
Multilocus Sequence Typing and Virulence Profiles in Uropathogenic Escherichia coli Isolated from Cats in the United States. PLoS One 2015; 10:e0143335. [PMID: 26587840 PMCID: PMC4654559 DOI: 10.1371/journal.pone.0143335] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
The population structure, virulence, and antimicrobial resistance of uropathogenic E. coli (UPEC) from cats are rarely characterized. The aim of this study was to compare and characterize the UPEC isolated from cats in four geographic regions of USA in terms of their multilocus sequence typing (MLST), virulence profiles, clinical signs, antimicrobial resistance and phylogenetic grouping. The results showed that a total of 74 E. coli isolates were typed to 40 sequence types with 10 being novel. The most frequent phylogenetic group was B2 (n = 57). The most frequent sequence types were ST73 (n = 12) and ST83 (n = 6), ST73 was represented by four multidrug resistant (MDR) and eight non-multidrug resistant (SDR) isolates, and ST83 were significantly more likely to exhibit no drug resistant (NDR) isolates carrying the highest number of virulence genes. Additionally, MDR isolates were more diverse, and followed by SDR and NDR isolates in regards to the distribution of the STs. afa/draBC was the most prevalent among the 29 virulence-associated genes. Linking virulence profile and antimicrobial resistance, the majority of virulence-associated genes tested were more prevalent in NDR isolates, and followed by SDR and MDR isolates. Twenty (50%) MLST types in this study have previously been associated with human isolates, suggesting that these STs are potentially zoonotic. Our data enhanced the understanding of E. coli population structure and virulence association from cats. The diverse and various combinations of virulence-associated genes implied that the infection control may be challenging.
Collapse
|
360
|
Lineage-Specific Methyltransferases Define the Methylome of the Globally Disseminated Escherichia coli ST131 Clone. mBio 2015; 6:e01602-15. [PMID: 26578678 PMCID: PMC4659465 DOI: 10.1128/mbio.01602-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Escherichia coli sequence type 131 (ST131) is a clone of uropathogenic E. coli that has emerged rapidly and disseminated globally in both clinical and community settings. Members of the ST131 lineage from across the globe have been comprehensively characterized in terms of antibiotic resistance, virulence potential, and pathogenicity, but to date nothing is known about the methylome of these important human pathogens. Here we used single-molecule real-time (SMRT) PacBio sequencing to determine the methylome of E. coli EC958, the most-well-characterized completely sequenced ST131 strain. Our analysis of 52,081 methylated adenines in the genome of EC958 discovered three (m6)A methylation motifs that have not been described previously. Subsequent SMRT sequencing of isogenic knockout mutants identified the two type I methyltransferases (MTases) and one type IIG MTase responsible for (m6)A methylation of novel recognition sites. Although both type I sites were rare, the type IIG sites accounted for more than 12% of all methylated adenines in EC958. Analysis of the distribution of MTase genes across 95 ST131 genomes revealed their prevalence is highly conserved within the ST131 lineage, with most variation due to the presence or absence of mobile genetic elements on which individual MTase genes are located. IMPORTANCE DNA modification plays a crucial role in bacterial regulation. Despite several examples demonstrating the role of methyltransferase (MTase) enzymes in bacterial virulence, investigation of this phenomenon on a whole-genome scale has remained elusive until now. Here we used single-molecule real-time (SMRT) sequencing to determine the first complete methylome of a strain from the multidrug-resistant E. coli sequence type 131 (ST131) lineage. By interrogating the methylome computationally and with further SMRT sequencing of isogenic mutants representing previously uncharacterized MTase genes, we defined the target sequences of three novel ST131-specific MTases and determined the genomic distribution of all MTase target sequences. Using a large collection of 95 previously sequenced ST131 genomes, we identified mobile genetic elements as a major factor driving diversity in DNA methylation patterns. Overall, our analysis highlights the potential for DNA methylation to dramatically influence gene regulation at the transcriptional level within a well-defined E. coli clone.
Collapse
|
361
|
Kakkanat A, Totsika M, Schaale K, Duell BL, Lo AW, Phan MD, Moriel DG, Beatson SA, Sweet MJ, Ulett GC, Schembri MA. The role of H4 flagella in Escherichia coli ST131 virulence. Sci Rep 2015; 5:16149. [PMID: 26548325 PMCID: PMC4637896 DOI: 10.1038/srep16149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/02/2015] [Indexed: 01/04/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug resistant clone associated with urinary tract and bloodstream infections. Most ST131 strains exhibit resistance to multiple antibiotics and cause infections associated with limited treatment options. The largest sub-clonal ST131 lineage is resistant to fluoroquinolones, contains the type 1 fimbriae fimH30 allele and expresses an H4 flagella antigen. Flagella are motility organelles that contribute to UPEC colonisation of the upper urinary tract. In this study, we examined the specific role of H4 flagella in ST131 motility and interaction with host epithelial and immune cells. We show that the majority of H4-positive ST131 strains are motile and are enriched for flagella expression during static pellicle growth. We also tested the role of H4 flagella in ST131 through the construction of specific mutants, over-expression strains and isogenic mutants that expressed alternative H1 and H7 flagellar subtypes. Overall, our results revealed that H4, H1 and H7 flagella possess conserved phenotypes with regards to motility, epithelial cell adhesion, invasion and uptake by macrophages. In contrast, H4 flagella trigger enhanced induction of the anti-inflammatory cytokine IL-10 compared to H1 and H7 flagella, a property that may contribute to ST131 fitness in the urinary tract.
Collapse
Affiliation(s)
- Asha Kakkanat
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kolja Schaale
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Duell
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Danilo G Moriel
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Matthew J Sweet
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Glen C Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
362
|
Wurpel DJ, Totsika M, Allsopp LP, Webb RI, Moriel DG, Schembri MA. Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells. J Proteomics 2015; 131:177-189. [PMID: 26546558 DOI: 10.1016/j.jprot.2015.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 01/15/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infection (UTI) in humans. For the successful colonisation of the human urinary tract, UPEC employ a diverse collection of secreted or surface-exposed virulence factors including toxins, iron acquisition systems and adhesins. In this study, a comparative proteomic approach was utilised to define the UPEC pan and core surface proteome following growth in pooled human urine. Identified proteins were investigated for subcellular origin, prevalence and homology to characterised virulence factors. Fourteen core surface proteins were identified, as well as eleven iron uptake receptor proteins and four distinct fimbrial types, including type 1, P, F1C/S and a previously uncharacterised fimbrial type, designated UCA-like (UCL) fimbriae in this study. These pathogenicity island (PAI)-associated fimbriae are related to UCA fimbriae of Proteus mirabilis, associated with UPEC and exclusively found in members of the E. coli B2 and D phylogroup. We further demonstrated that UCL fimbriae promote significant biofilm formation on abiotic surfaces and mediate specific attachment to exfoliated human uroepithelial cells. Combined, this study has defined the surface proteomic profiles and core surface proteome of UPEC during growth in human urine and identified a new type of fimbriae that may contribute to UTI.
Collapse
Affiliation(s)
- Daniël J Wurpel
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Luke P Allsopp
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Richard I Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Australia
| | - Danilo G Moriel
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Mark A Schembri
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| |
Collapse
|
363
|
Alhashash F, Wang X, Paszkiewicz K, Diggle M, Zong Z, McNally A. Increase in bacteraemia cases in the East Midlands region of the UK due to MDREscherichia coliST73: high levels of genomic and plasmid diversity in causative isolates. J Antimicrob Chemother 2015; 71:339-43. [DOI: 10.1093/jac/dkv365] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/08/2015] [Indexed: 12/25/2022] Open
|
364
|
Bartley PB, Ben Zakour NL, Stanton-Cook M, Muguli R, Prado L, Garnys V, Taylor K, Barnett TC, Pinna G, Robson J, Paterson DL, Walker MJ, Schembri MA, Beatson SA. Hospital-wide Eradication of a NosocomialLegionella pneumophilaSerogroup 1 Outbreak. Clin Infect Dis 2015; 62:273-279. [DOI: 10.1093/cid/civ870] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022] Open
|
365
|
Dale AP, Woodford N. Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones. J Infect 2015; 71:615-26. [PMID: 26409905 DOI: 10.1016/j.jinf.2015.09.009] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) have a complex phylogeny, broad virulence factor (VF) armament and significant genomic plasticity, and are associated with a spectrum of host infective syndromes ranging from simple urinary tract infection to life-threatening bacteraemia. Their importance as pathogens has come to the fore in recent years, particularly in the context of the global emergence of hyper-virulent and antibiotic resistant strains. Despite this, the mechanisms underlying ExPEC transmission dynamics and clonal selection remain poorly understood. Large-scale epidemiological and clinical studies are urgently required to ascertain the mechanisms underlying these processes to enable the development of novel evidence-based preventative and therapeutic strategies. In the current review, we provide a concise summary of the methods utilised for ExPEC phylogenetic delineation before exploring in detail the associations between ExPEC VFs and site-specific disease. We then consider the role of ExPEC as an intestinal colonist and outline known associations between ExPEC clonal variation, specific disease syndromes and antibiotic resistance.
Collapse
Affiliation(s)
- Adam P Dale
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, South Academic Block, Tremona Road, Southampton SO16 6YD, UK.
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, London NW9 5EQ, UK; The NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0HS, UK
| |
Collapse
|
366
|
Franz E, Veenman C, van Hoek AHAM, de Roda Husman A, Blaak H. Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater. Sci Rep 2015; 5:14372. [PMID: 26399418 PMCID: PMC4585870 DOI: 10.1038/srep14372] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/17/2015] [Indexed: 11/10/2022] Open
Abstract
To assess public health risks from environmental exposure to Extended-Spectrum β-Lactamases (ESBL)-producing bacteria, it is necessary to have insight in the proportion of relative harmless commensal variants and potentially pathogenic ones (which may directly cause disease). In the current study, 170 ESBL-producing E. coli from Dutch wastewater (n = 82) and surface water (n = 88) were characterized with respect to ESBL-genotype, phylogenetic group, resistance phenotype and virulence markers associated with enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), extraintesinal E. coli (ExPEC), and Shiga toxin-producing E. coli (STEC). Overall, 17.1% of all ESBL-producing E. coli were suspected pathogenic variants. Suspected ExPECs constituted 8.8% of all ESBL-producing variants and 8.3% were potential gastrointestinal pathogens (4.1% EAEC, 1.8% EPEC, 1.2% EIEC, 1.2% ETEC, no STEC). Suspected pathogens were significantly associated with ESBL-genotype CTX-M-15 (X2 = 14.7, P < 0.001) and phylogenetic group B2 (X2 = 23.5, P < 0.001). Finally, 84% of the pathogenic ESBL-producing E. coli isolates were resistant to three or more different classes of antibiotics. In conclusion, this study demonstrates that the aquatic environment is a potential reservoir of E. coli variants that combine ESBL-genes, a high level of multi-drug resistance and virulence factors, and therewith pose a health risk to humans upon exposure.
Collapse
Affiliation(s)
- Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Christiaan Veenman
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Angela H A M van Hoek
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Ana de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Hetty Blaak
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, The Netherlands
| |
Collapse
|
367
|
Zowawi HM, Harris PNA, Roberts MJ, Tambyah PA, Schembri MA, Pezzani MD, Williamson DA, Paterson DL. The emerging threat of multidrug-resistant Gram-negative bacteria in urology. Nat Rev Urol 2015; 12:570-84. [PMID: 26334085 DOI: 10.1038/nrurol.2015.199] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Antibiotic resistance in Gram-negative uropathogens is a major global concern. Worldwide, the prevalence of Enterobacteriaceae that produce extended-spectrum β-lactamase or carbapenemase enzymes continues to increase at alarming rates. Likewise, resistance to other antimicrobial agents including aminoglycosides, sulphonamides and fluoroquinolones is also escalating rapidly. Bacterial resistance has major implications for urological practice, particularly in relation to catheter-associated urinary tract infections (UTIs) and infectious complications following transrectal-ultrasonography-guided biopsy of the prostate or urological surgery. Although some new drugs with activity against Gram-negative bacteria with highly resistant phenotypes will become available in the near future, the existence of a single agent with activity against the great diversity of resistance is unlikely. Responding to the challenges of Gram-negative resistance will require a multifaceted approach including considered use of current antimicrobial agents, improved diagnostics (including the rapid detection of resistance) and surveillance, better adherence to basic measures of infection prevention, development of new antibiotics and research into non-antibiotic treatment and preventive strategies.
Collapse
Affiliation(s)
- Hosam M Zowawi
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Royal Brisbane Hospital, Herston, QLD 4006, Australia
| | - Patrick N A Harris
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Royal Brisbane Hospital, Herston, QLD 4006, Australia
| | - Matthew J Roberts
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Royal Brisbane Hospital, Herston, QLD 4006, Australia
| | - Paul A Tambyah
- Division of Infectious Diseases, National University Health System, 1E Kent Ridge Road, 119228, Singapore
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - M Diletta Pezzani
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, G. B. Grassi 74, 20157 Milan, Italy
| | - Deborah A Williamson
- Department of Pathology, University of Otago, 23A Mein Street, Newtown, Wellington 6242, New Zealand
| | - David L Paterson
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Royal Brisbane Hospital, Herston, QLD 4006, Australia
| |
Collapse
|
368
|
Greater ciprofloxacin tolerance as a possible selectable phenotype underlying the pandemic spread of the H30 subclone of Escherichia coli sequence type 131. Antimicrob Agents Chemother 2015; 59:7132-5. [PMID: 26324269 DOI: 10.1128/aac.01687-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/25/2015] [Indexed: 01/15/2023] Open
Abstract
Minimum bactericidal concentrations (MBCs) for ciprofloxacin were significantly higher among 41 members of the H30 subclone within Escherichia coli sequence type 131 than among 48 other fluoroquinolone-resistant E. coli isolates. This MBC difference, which was not explained by ciprofloxacin MICs, gyrA, parC, and parE mutations, the presence of aac(6')-Ib-cr, or organic solvent tolerance (a surrogate for efflux pump activity), conceivably could have promoted the pandemic emergence of the H30 sequence type 131 subclone.
Collapse
|
369
|
Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
Collapse
Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
| |
Collapse
|
370
|
The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 2015; 28:565-91. [PMID: 25926236 DOI: 10.1128/cmr.00116-14] [Citation(s) in RCA: 551] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains, respectively. E. coli ST131 causes extraintestinal infections and is often fluoroquinolone resistant and associated with extended-spectrum β-lactamase production, especially CTX-M-15. K. pneumoniae ST258 causes urinary and respiratory tract infections and is associated with carbapenemases, most often KPC-2 and KPC-3. The most prevalent lineage within ST131 is named fimH30 because it contains the H30 variant of the type 1 fimbrial adhesin gene, and recent molecular studies have demonstrated that this lineage emerged in the early 2000s and was then followed by the rapid expansion of its sublineages H30-R and H30-Rx. K. pneumoniae ST258 comprises 2 distinct lineages, namely clade I and clade II. Moreover, it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Epidemic plasmids with blaCTX-M and blaKPC belonging to incompatibility group F have contributed significantly to the success of these clones. E. coli ST131 and K. pneumoniae ST258 are the quintessential examples of international multidrug-resistant high-risk clones.
Collapse
|
371
|
Mehrad B, Clark NM, Zhanel GG, Lynch JP. Antimicrobial resistance in hospital-acquired gram-negative bacterial infections. Chest 2015; 147:1413-1421. [PMID: 25940252 DOI: 10.1378/chest.14-2171] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Aerobic gram-negative bacilli, including the family of Enterobacteriaceae and non-lactose fermenting bacteria such as Pseudomonas and Acinetobacter species, are major causes of hospital-acquired infections. The rate of antibiotic resistance among these pathogens has accelerated dramatically in recent years and has reached pandemic scale. It is no longer uncommon to encounter gram-negative infections that are untreatable using conventional antibiotics in hospitalized patients. In this review, we provide a summary of the major classes of gram-negative bacilli and their key mechanisms of antimicrobial resistance, discuss approaches to the treatment of these difficult infections, and outline methods to slow the further spread of resistance mechanisms.
Collapse
Affiliation(s)
- Borna Mehrad
- Division of Pulmonary and Critical Care Medicine and The Carter Center for Immunology, University of Virginia, Charlottesville, VA
| | - Nina M Clark
- Division of Infectious Diseases, Department of Medicine, Loyola University, Maywood, IL
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Joseph P Lynch
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA.
| |
Collapse
|
372
|
Manges AR. Editorial Commentary: Genomic Epidemiology: Revealing Hidden Reservoirs for Klebsiella pneumoniae. Clin Infect Dis 2015. [PMID: 26206846 PMCID: PMC4551006 DOI: 10.1093/cid/civ433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Amee R Manges
- Faculty of Medicine, School of Population and Public Health, University of British Columbia, Vancouver, Canada
| |
Collapse
|
373
|
Genomic and Functional Portrait of a Highly Virulent, CTX-M-15-Producing H30-Rx Subclone of Escherichia coli Sequence Type 131. Antimicrob Agents Chemother 2015. [PMID: 26195517 DOI: 10.1128/aac.01447-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a pandemic clone associated with multidrug-resistant, extraintestinal infections, attributable to the presence of the CTX-M-15 extended-spectrum β-lactamase gene and mutations entailing fluoroquinolone resistance. Studies on subclones within E. coli ST131 are critically required for targeting and implementation of successful control efforts. Our study comprehensively analyzed the genomic and functional attributes of the H30-Rx subclonal strains NA097 and NA114, belonging to the ST131 lineage. We carried out whole-genome sequencing, comparative analysis, phenotypic virulence assays, and profiling of the antibacterial responses of THP1 cells infected with these subclones. Phylogenomic analysis suggested that the strains were clonal in nature and confined entirely to a single clade. Comparative genomic analysis revealed that the virulence and resistance repertoires were comparable among the H30-Rx ST131 strains except for the commensal ST131 strain SE15. Similarly, seven phage-specific regions were found to be strongly associated with the H30-Rx strains but were largely absent in the genome of SE15. Phenotypic analysis confirmed the virulence and resistance similarities between the two strains. However, NA097 was found to be more robust than NA114 in terms of virulence gene carriage (dra operon), invasion ability (P < 0.05), and antimicrobial resistance (streptomycin resistance). RT(2) gene expression profiling revealed generic upregulation of key proinflammatory responses in THP1 cells, irrespective of ST131 lineage status. In conclusion, our study provides comprehensive, genome-inferred insights into the biology and immunological properties of ST131 strains and suggests clonal diversification of genomic and phenotypic features within the H30-Rx subclone of E. coli ST131.
Collapse
|
374
|
Mora-Bau G, Platt AM, van Rooijen N, Randolph GJ, Albert ML, Ingersoll MA. Macrophages Subvert Adaptive Immunity to Urinary Tract Infection. PLoS Pathog 2015; 11:e1005044. [PMID: 26182347 PMCID: PMC4504509 DOI: 10.1371/journal.ppat.1005044] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/23/2015] [Indexed: 12/24/2022] Open
Abstract
Urinary tract infection (UTI) is one of the most common bacterial infections with frequent recurrence being a major medical challenge. Development of effective therapies has been impeded by the lack of knowledge of events leading to adaptive immunity. Here, we establish conclusive evidence that an adaptive immune response is generated during UTI, yet this response does not establish sterilizing immunity. To investigate the underlying deficiency, we delineated the naïve bladder immune cell compartment, identifying resident macrophages as the most populous immune cell. To evaluate their impact on the establishment of adaptive immune responses following infection, we measured bacterial clearance in mice depleted of either circulating monocytes, which give rise to macrophages, or bladder resident macrophages. Surprisingly, mice depleted of resident macrophages, prior to primary infection, exhibited a nearly 2-log reduction in bacterial burden following secondary challenge compared to untreated animals. This increased bacterial clearance, in the context of a challenge infection, was dependent on lymphocytes. Macrophages were the predominant antigen presenting cell to acquire bacteria post-infection and in their absence, bacterial uptake by dendritic cells was increased almost 2-fold. These data suggest that bacterial uptake by tissue macrophages impedes development of adaptive immune responses during UTI, revealing a novel target for enhancing host responses to bacterial infection of the bladder. Urinary tract infection is a common infection with a high propensity for recurrence. The majority of infections are caused by uropathogenic E. coli, a growing public health concern with increasing prevalence of antibiotic resistant strains. Finding therapeutic options that circumvent the need for antibiotics, while boosting patients’ immune response to infection is desirable to counteract further increases in antibiotic resistance and to provide long-lasting resistance to infection. Currently, little is known about how adaptive immune responses, which typically prevent recurrent infection in other organs, arise from the bladder during urinary tract infection. Here, we investigated the initial interactions between immune cell populations of the bladder and uropathogenic E. coli, finding that macrophages are the principal cell population to engulf bacteria. Interestingly, these same cells appear to inhibit the development of adaptive immunity to the bacteria, as their depletion, prior to primary infection, results in a stronger immune response during bacterial challenge. We found that in the absence of macrophages, dendritic cells, which are the most potent initiators of adaptive immunity, are able to take up more bacteria for presentation. Our study has revealed a mechanism in which specific immune cells may act in a manner detrimental to host immunity.
Collapse
Affiliation(s)
- Gabriela Mora-Bau
- Unité d'Immunobiologie des Cellules Dendritiques, Department of Immunology, Institut Pasteur and INSERM U818, Paris, France
| | - Andrew M Platt
- Department of Gene and Cell Medicine and the Immunology Institute, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Nico van Rooijen
- Department of Molecular Cell Biology, Free University Medical Center, Amsterdam, The Netherlands
| | - Gwendalyn J Randolph
- Department of Gene and Cell Medicine and the Immunology Institute, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Matthew L Albert
- Unité d'Immunobiologie des Cellules Dendritiques, Department of Immunology, Institut Pasteur and INSERM U818, Paris, France
| | - Molly A Ingersoll
- Unité d'Immunobiologie des Cellules Dendritiques, Department of Immunology, Institut Pasteur and INSERM U818, Paris, France
| |
Collapse
|
375
|
Alghoribi MF, Gibreel TM, Farnham G, Al Johani SM, Balkhy HH, Upton M. Antibiotic-resistant ST38, ST131 and ST405 strains are the leading uropathogenic Escherichia coli clones in Riyadh, Saudi Arabia. J Antimicrob Chemother 2015; 70:2757-62. [PMID: 26183183 DOI: 10.1093/jac/dkv188] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 06/11/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES We investigated the molecular epidemiology of uropathogenic Escherichia coli (UPEC) from a tertiary care hospital in Riyadh, Saudi Arabia, revealing, for the first time, the population structure of UPEC in the region. METHODS A total of 202 UPEC isolates were recovered from hospital and community patients with urinary tract infection in December 2012 and January 2013. Strains were characterized by MLST, antibiotic susceptibility determination and virulence gene detection. RESULTS The most common lineages were ST131 (17.3%), ST73 (11.4%), ST38 (7.4%), ST69 (7.4%), ST10 (6.4%), ST127 (5.9%), ST95 (5.4%), ST12 (3.5%), ST998 (3.5%) and ST405 (3%). ST131 and ST405 isolates were significantly associated with high levels of antibiotic resistance (60% of ST131 carried CTX-M-14 or CTX-M-15 and 66.7% of ST405 isolates carried CTX-M-15). ST131, CTX-M-15-positive isolates were predominantly of the fimH30/clade C group, resistant to fluoroquinolones; members of this sub-group were more likely to carry a high number of genes encoding selected virulence determinants. The relatively high proportion of ST38 was notable and four of these isolates harboured aggR. CONCLUSIONS Our findings highlight the presence of MDR, CTX-M-positive ST38, ST131 and ST405 UPEC in Saudi Arabia. The high proportion of isolates with CTX-M is a particular concern. We suggest that ST38 UPEC warrant further study.
Collapse
Affiliation(s)
- Majed F Alghoribi
- School of Medicine, University of Manchester, Manchester, UK King Abdullah International Medical Research Center, Riyadh, Saudi Arabia King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Garry Farnham
- Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - Sameera M Al Johani
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia Microbiology, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia Infection Prevention and Control Department, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Mathew Upton
- Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| |
Collapse
|
376
|
Nordahl Petersen T, Rasmussen S, Hasman H, Carøe C, Bælum J, Schultz AC, Bergmark L, Svendsen CA, Lund O, Sicheritz-Pontén T, Aarestrup FM. Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci Rep 2015; 5:11444. [PMID: 26161690 PMCID: PMC4498435 DOI: 10.1038/srep11444] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/17/2015] [Indexed: 11/09/2022] Open
Abstract
Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions. An average of 18.6 Gb (14.8 to 25.7 Gb) of raw Illumina paired end sequence data was generated, cleaned, trimmed and mapped against reference sequence databases for bacteria and antimicrobial resistance genes. An average of 106,839 (0.06%) reads were assigned to resistance genes with genes encoding resistance to tetracycline, macrolide and beta-lactam resistance genes as the most abundant in all samples. We found significantly higher abundance and diversity of genes encoding antimicrobial resistance, including critical important resistance (e.g. blaCTX-M) carried on airplanes from South Asia compared to North America. Presence of Salmonella enterica and norovirus were also detected in higher amounts from South Asia, whereas Clostridium difficile was most abundant in samples from North America. Our study provides a first step towards a potential novel strategy for global surveillance enabling simultaneous detection of multiple human health threatening genetic elements, infectious agents and resistance genes.
Collapse
Affiliation(s)
| | - Simon Rasmussen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henrik Hasman
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Carøe
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jacob Bælum
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Lasse Bergmark
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Ole Lund
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
377
|
Schembri MA, Zakour NLB, Phan MD, Forde BM, Stanton-Cook M, Beatson SA. Molecular Characterization of the Multidrug Resistant Escherichia coli ST131 Clone. Pathogens 2015; 4:422-30. [PMID: 26131613 PMCID: PMC4584265 DOI: 10.3390/pathogens4030422] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 06/08/2015] [Accepted: 06/23/2015] [Indexed: 01/20/2023] Open
Abstract
Escherichia coli ST131 is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections in both community and clinical settings. The most common group of ST131 strains are defined by resistance to fluoroquinolones and possession of the type 1 fimbriae fimH30 allele. Here we provide an update on our recent work describing the globally epidemiology of ST131. We review the phylogeny of ST131 based on whole genome sequence data and highlight the important role of recombination in the evolution of this clonal lineage. We also summarize our findings on the virulence of the ST131 reference strain EC958, and highlight the use of transposon directed insertion-site sequencing to define genes associated with serum resistance and essential features of its large antibiotic resistance plasmid pEC958.
Collapse
Affiliation(s)
- Mark A Schembri
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Nouri L Ben Zakour
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Minh-Duy Phan
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Brian M Forde
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Mitchell Stanton-Cook
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Scott A Beatson
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| |
Collapse
|
378
|
Variation in resistance traits, phylogenetic backgrounds, and virulence genotypes among Escherichia coli clinical isolates from adjacent hospital campuses serving distinct patient populations. Antimicrob Agents Chemother 2015; 59:5331-9. [PMID: 26100703 DOI: 10.1128/aac.00048-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/10/2015] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the H30 and H30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive E. coli clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The H30 and H30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131 per se, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131, bla CTX-M-15 was confined to H30Rx isolates and other bla CTX-M variants to non-Rx H30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the H30 and H30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive virulence gene associations that may confer fitness advantages over other resistant E. coli.
Collapse
|
379
|
Skalweit MJ. Profile of ceftolozane/tazobactam and its potential in the treatment of complicated intra-abdominal infections. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:2919-25. [PMID: 26082619 PMCID: PMC4461093 DOI: 10.2147/dddt.s61436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-resistant pathogens have gained a foothold especially in the most vulnerable patient populations, hospitalized and immunocompromised individuals. Furthermore, extended-spectrum β-lactamase and carbapenemase-producing organisms are finding their way even into the community, with patients presenting to the hospital with established colonization and infection with resistant Enterobacteriaceae in particular. Recently, a novel antipseudomonal cephalosporin in combination with an established Class A β-lactamase inhibitor, ceftolozane/tazobactam has been approved by the FDA for use in the treatment of complicated urinary tract infections and complicated intra-abdominal infections. Ceftolozane is a uniquely potent antipseudomonal cephalosporin because of its high affinity for the penicillin-binding proteins of Pseudomonas aeruginosa, its low affinity for the intrinsic Class C β-lactamases of P. aeruginosa, its ability to enter P. aeruginosa through the outer membrane without the utilization of OprD protein, and the fact that it is not a substrate of the often upregulated MexAB/OprM efflux system of P. aeruginosa. The biological chemistry, pharmacokinetics/pharmacodynamics, microbiologic spectrum, and clinical trials that led to the approval of ceftolozane is reviewed. A discussion regarding its potential role in the treatment of complicated intra-abdominal infections and other infectious disease syndromes associated with drug-resistant pathogens follows.
Collapse
Affiliation(s)
- Marion J Skalweit
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs and Case Western Reserve University School of Medicine, Cleveland, OH, USA ; Department of Biochemistry, Louis Stokes Cleveland Department of Veterans Affairs and Case Western Reserve University School of Medicine, Cleveland, OH, USA
| |
Collapse
|
380
|
Downing T. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms 2015; 3:236-67. [PMID: 27682088 PMCID: PMC5023239 DOI: 10.3390/microorganisms3020236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 11/16/2022] Open
Abstract
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.
Collapse
Affiliation(s)
- Tim Downing
- School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland.
| |
Collapse
|
381
|
Intensity and Mechanisms of Fluoroquinolone Resistance within the H30 and H30Rx Subclones of Escherichia coli Sequence Type 131 Compared with Other Fluoroquinolone-Resistant E. coli. Antimicrob Agents Chemother 2015; 59:4471-80. [PMID: 25987621 DOI: 10.1128/aac.00673-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/08/2015] [Indexed: 12/23/2022] Open
Abstract
The recent expansion of the H30 subclone of Escherichia coli sequence type 131 (ST131) and its CTX-M-15-associated H30Rx subset remains unexplained. Although ST131 H30 typically exhibits fluoroquinolone resistance, so do multiple other E. coli lineages that have not expanded similarly. To determine whether H30 isolates have more intense fluoroquinolone resistance than other fluoroquinolone-resistant E. coli isolates and to identify possible mechanisms, we determined the MICs for four fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin, and norfloxacin) among 89 well-characterized, genetically diverse fluoroquinolone-resistant E. coli isolates (48 non-H30 and 41 H30 [23 H30Rx and 18 H30 non-Rx]). We compared the MICs with the H30 and H30Rx status, the presence/number of nonsynonymous mutations in gyrA, parC, and parE, the presence of aac(6')-1b-cr (an aminoglycoside/fluoroquinolone agent-modifying enzyme), and the efflux pump activity (measured as organic solvent tolerance [OST]). Among 1,518 recent E. coli clinical isolates, ST131 H30 predominated clonally, both overall and among the fluoroquinolone-resistant isolates. Among the 89 study isolates, compared with non-H30 isolates, H30 isolates exhibited categorically higher MICs for all four fluoroquinolone agents, higher absolute ciprofloxacin and norfloxacin MICs, more nonsynonymous mutations in gyrA, parC, and parE (specifically gyrA D87N, parC E84V, and parE I529L), and a numerically higher prevalence of (H30Rx-associated) aac(6')-1b-cr but lower OST scores. All putative resistance mechanisms were significantly associated with the MICs [for aac(6')-1b-cr: ciprofloxacin and norfloxacin only]. parC D87N corresponded with ST131 H30 and parE I529L with ST131 generally. Thus, more intense fluoroquinolone resistance may provide ST131 H30, especially H30Rx [if aac(6')-1b-cr positive], with subtle fitness advantages over other fluoroquinolone-resistant E. coli strains. This urges both parsimonious fluoroquinolone use and a search for other fitness-enhancing traits within ST131 H30.
Collapse
|
382
|
Tal Jasper R, Coyle JR, Katz DE, Marchaim D. The complex epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae. Future Microbiol 2015; 10:819-39. [DOI: 10.2217/fmb.15.16] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
ABSTRACT Antimicrobial resistance is a growing worldwide iatrogenic complication of modern medical care. Extended-spectrum β-lactamases have emerged as one of the most successful resistance mechanisms, limiting our therapeutic options to treat various human infections. The dissemination of these enzymes to the community probably signifies an irreversible step. This paper will review the evolution of human infections associated with extended-spectrum β-lactamase-producing organisms in the past 20 years, and will present and discuss the current challenges, controversies, debates and knowledge gaps in this research field.
Collapse
Affiliation(s)
- Ruthy Tal Jasper
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Joseph R Coyle
- Division of Communicable Diseases, Bureau of Disease Control, Prevention & Epidemiology, Michigan Department of Community Health, 201 Townsend St, Lansing, MI, USA, 48909
| | - David E Katz
- Department of Internal Medicine D, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Dror Marchaim
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Division of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| |
Collapse
|
383
|
Markland SM, LeStrange KJ, Sharma M, Kniel KE. Old Friends in New Places: Exploring the Role of ExtraintestinalE. coliin Intestinal Disease and Foodborne Illness. Zoonoses Public Health 2015; 62:491-6. [DOI: 10.1111/zph.12194] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/13/2022]
Affiliation(s)
- S. M. Markland
- Department of Animal and Food Sciences; University of Delaware; Newark DE USA
| | - K. J. LeStrange
- Department of Animal and Food Sciences; University of Delaware; Newark DE USA
| | - M. Sharma
- Environmental Microbial and Food Safety Laboratory; USDA-Agricultural Research Service; Beltsville MD USA
| | - K. E. Kniel
- Department of Animal and Food Sciences; University of Delaware; Newark DE USA
| |
Collapse
|
384
|
Phan MD, Forde BM, Peters KM, Sarkar S, Hancock S, Stanton-Cook M, Ben Zakour NL, Upton M, Beatson SA, Schembri MA. Molecular characterization of a multidrug resistance IncF plasmid from the globally disseminated Escherichia coli ST131 clone. PLoS One 2015; 10:e0122369. [PMID: 25875675 PMCID: PMC4398462 DOI: 10.1371/journal.pone.0122369] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli sequence type 131 (E. coli ST131) is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections. Plasmids represent a major vehicle for the carriage of antibiotic resistance genes in E. coli ST131. In this study, we determined the complete sequence and performed a comprehensive annotation of pEC958, an IncF plasmid from the E. coli ST131 reference strain EC958. Plasmid pEC958 is 135.6 kb in size, harbours two replicons (RepFIA and RepFII) and contains 12 antibiotic resistance genes (including the blaCTX-M-15 gene). We also carried out hyper-saturated transposon mutagenesis and multiplexed transposon directed insertion-site sequencing (TraDIS) to investigate the biology of pEC958. TraDIS data showed that while only the RepFII replicon was required for pEC958 replication, the RepFIA replicon contains genes essential for its partitioning. Thus, our data provides direct evidence that the RepFIA and RepFII replicons in pEC958 cooperate to ensure their stable inheritance. The gene encoding the antitoxin component (ccdA) of the post-segregational killing system CcdAB was also protected from mutagenesis, demonstrating this system is active. Sequence comparison with a global collection of ST131 strains suggest that IncF represents the most common type of plasmid in this clone, and underscores the need to understand its evolution and contribution to the spread of antibiotic resistance genes in E. coli ST131.
Collapse
Affiliation(s)
- Minh Duy Phan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brian M. Forde
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kate M. Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohinee Sarkar
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Steven Hancock
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mitchell Stanton-Cook
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nouri L. Ben Zakour
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mathew Upton
- Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, United Kingdom
| | - Scott A. Beatson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A. Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- * E-mail:
| |
Collapse
|
385
|
Phan MD, Peters KM, Sarkar S, Forde BM, Lo AW, Stanton-Cook M, Roberts LW, Upton M, Beatson SA, Schembri MA. Third-generation cephalosporin resistance conferred by a chromosomally encoded blaCMY-23 gene in the Escherichia coli ST131 reference strain EC958. J Antimicrob Chemother 2015; 70:1969-72. [PMID: 25786480 DOI: 10.1093/jac/dkv066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/23/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Escherichia coli ST131 is a globally disseminated MDR clone originally identified due to its association with the blaCTX-M-15 gene encoding an ESBL. It is thus assumed that blaCTX-M-15 is the major determinant for resistance to β-lactam antibiotics in this clone. The complete sequence of EC958, a reference strain for E. coli ST131, revealed that it contains a chromosomally located blaCMY-23 gene with an upstream ISEcp1 element as well as several additional plasmid-encoded β-lactamase genes. Here, we examined the genetic context of the blaCMY-23 element in EC958 and other E. coli ST131 strains and investigated the contribution of blaCMY-23 to EC958 resistance to a range of β-lactam antibiotics. METHODS The genetic context of blaCMY-23 and its associated mobile elements was determined by PCR and sequencing. Antibiotic susceptibility testing was performed using Etests. The activity of the blaCMY-23 promoter was assessed using lacZ reporter assays. Mutations were generated using λ-Red-recombination. RESULTS The genetic structure of the ISEcp1-IS5-blaCMY-23 mobile element was determined and localized within the betU gene on the chromosome of EC958 and five other E. coli ST131 strains. The transcription of blaCMY-23, driven by a previously defined promoter within ISEcp1, was significantly higher than other β-lactamase genes and could be induced by cefotaxime. Deletion of the blaCMY-23 gene resulted in enhanced susceptibility to cefoxitin, cefotaxime and ceftazidime. CONCLUSIONS This is the first known report to demonstrate the chromosomal location of blaCMY-23 in E. coli ST131. In EC958, CMY-23 plays a major role in resistance to third-generation cephalosporins and cephamycins.
Collapse
Affiliation(s)
- Minh-Duy Phan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kate M Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohinee Sarkar
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alvin W Lo
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mitchell Stanton-Cook
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Leah W Roberts
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mathew Upton
- Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL4 8AA, UK
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
386
|
Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing. mBio 2015; 6:e00054. [PMID: 25759497 PMCID: PMC4453535 DOI: 10.1128/mbio.00054-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Methicillin-resistant Staphylococcus aureus (MRSA) USA300 is a successful S. aureus clone in the United States and a common cause of skin and soft tissue infections (SSTIs). We performed whole-genome sequencing (WGS) of 146 USA300 MRSA isolates from SSTIs and colonization cultures obtained from an investigation conducted from 2008 to 2010 in Chicago and Los Angeles households that included an index case with an S. aureus SSTI. Identifying unique single nucleotide polymorphisms (SNPs) and analyzing whole-genome phylogeny, we characterized isolates to understand transmission dynamics, genetic relatedness, and microevolution of USA300 MRSA within the households. We also compared the 146 USA300 MRSA isolates from our study with the previously published genome sequences of the USA300 MRSA isolates from San Diego (n = 35) and New York City (n = 277). We found little genetic variation within the USA300 MRSA household isolates from Los Angeles (mean number of SNPs ± standard deviation, 17.6 ± 35; π nucleotide diversity, 3.1 × 10(-5)) or from Chicago (mean number of SNPs ± standard deviation, 12 ± 19; π nucleotide diversity, 3.1 × 10(-5)). The isolates within a household clustered into closely related monophyletic groups, suggesting the introduction into and transmission within each household of a single common USA300 ancestral strain. From a Bayesian evolutionary reconstruction, we inferred that USA300 persisted within households for 2.33 to 8.35 years prior to sampling. We also noted that fluoroquinolone-resistant USA300 clones emerged around 1995 and were more widespread in Los Angeles and New York City than in Chicago. Our findings strongly suggest that unique USA300 MRSA isolates are transmitted within households that contain an individual with an SSTI. Decolonization of household members may be a critical component of prevention programs to control USA300 MRSA spread in the United States. IMPORTANCE USA300, a virulent and easily transmissible strain of methicillin-resistant Staphylococcus aureus (MRSA), is the predominant community-associated MRSA clone in the United States. It most commonly causes skin infections but also causes necrotizing pneumonia and endocarditis. Strategies to limit the spread of MRSA in the community can only be effective if we understand the most common sources of transmission and the microevolutionary processes that provide a fitness advantage to MRSA. We performed a whole-genome sequence comparison of 146 USA300 MRSA isolates from Chicago and Los Angeles. We show that households represent a frequent site of transmission and a long-term reservoir of USA300 strains; individuals within households transmit the same USA300 strain among themselves. Our study also reveals that a large proportion of the USA300 isolates sequenced are resistant to fluoroquinolone antibiotics. The significance of this study is that if households serve as long-term reservoirs of USA300, household MRSA eradication programs may result in a uniquely effective control method.
Collapse
|
387
|
Clermont O, Gordon D, Denamur E. Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. MICROBIOLOGY-SGM 2015; 161:980-988. [PMID: 25714816 DOI: 10.1099/mic.0.000063] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/19/2015] [Indexed: 02/02/2023]
Abstract
Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.
Collapse
Affiliation(s)
- Olivier Clermont
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France
| | - David Gordon
- Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia
| | - Erick Denamur
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France
| |
Collapse
|
388
|
Antibiotic-resistant Klebsiella pneumoniae and Escherichia coli high-risk clones and an IncFII(k) mosaic plasmid hosting Tn1 (blaTEM-4) in isolates from 1990 to 2004. Antimicrob Agents Chemother 2015; 59:2904-8. [PMID: 25691645 DOI: 10.1128/aac.00296-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 12/11/2022] Open
Abstract
We describe the genetic background of bla(TEM-4) and the complete sequence of pRYC11::bla(TEM-4), a mosaic plasmid that is highly similar to pKpQIL-like variants, predominant among TEM-4 producers in a Spanish hospital (1990 to 2004), which belong to Klebsiella pneumoniae and Escherichia coli high-risk clones responsible for the current spread of different antibiotic resistance genes. Predominant populations of plasmids and host adapted clonal lineages seem to have greatly contributed to the spread of resistance to extended-spectrum cephalosporins.
Collapse
|
389
|
Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition. Infect Immun 2015; 83:1749-64. [PMID: 25667270 DOI: 10.1128/iai.02810-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/09/2015] [Indexed: 12/21/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.
Collapse
|
390
|
Ruer S, Pinotsis N, Steadman D, Waksman G, Remaut H. Virulence-targeted Antibacterials: Concept, Promise, and Susceptibility to Resistance Mechanisms. Chem Biol Drug Des 2015; 86:379-99. [DOI: 10.1111/cbdd.12517] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/23/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ségolène Ruer
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - David Steadman
- Wolfson Institute for Biomedical Research (WIBR); UCL; London WC1E 6BT UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology (ISMB); UCL and Birkbeck College; London WC1E 7HX UK
| | - Han Remaut
- Structural and Molecular Microbiology; Structural Biology Research Center; VIB; Pleinlaan 2 Brussels 1050 Belgium
- Structural Biology Brussels; Vrije Universiteit Brussel; Pleinlaan 2 Brussels 1050 Belgium
| |
Collapse
|
391
|
Singer RS. Urinary tract infections attributed to diverse ExPEC strains in food animals: evidence and data gaps. Front Microbiol 2015; 6:28. [PMID: 25699025 PMCID: PMC4316786 DOI: 10.3389/fmicb.2015.00028] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 01/08/2015] [Indexed: 12/28/2022] Open
Abstract
Between 70 and 95% of urinary tract infections (UTI) are caused by strains of Escherichia coli. These strains, often termed Extraintestinal Pathogenic E. coli (ExPEC), possess specific virulence traits allowing them to colonize more inhospitable environments, such as the urogenital tract. Some ExPEC isolates from humans have similar virulence factor profiles to ExPEC isolates from animals, and because of the potential for these strains to cause UTI in people, these infections have been referred to as foodborne UTI, or FUTI. Finding similarities in ExPEC in animals and humans is not necessarily proof of transmission, particularly a unidirectional pathway from animals to humans; similarities in virulence factor profiles should be expected given the specific bacterial requirements for colonizing physiological compartments with similar characteristics in all animals. Many of the most important strains of human ExPEC globally, such as ST131, are highly virulent and clonal implying routes of transmission other than food. Documenting routes of transmission is particularly difficult due to the wide range of potential ExPEC sources, including the human intestinal tract, and non-human reservoirs such as food animals and retail meat products, sewage and other environmental sources, and companion animals. The significant environmental reservoir of ExPEC, including strains such as ST131, could potentially explain much more completely the global dissemination of virulent ExPEC clones and the rapid dissemination of new strains within the community. Taken in its totality, the link between ExPEC in animals and UTI in humans might exist, but studies conducted to date do not enable an estimation of the relative importance of this route of transmission. To reduce the burden of illness associated with ExPEC, the scientific community needs to push forward with ecologically-based, scientifically-sound study designs that can address the plethora of ways in which E. coli can spread.
Collapse
Affiliation(s)
- Randall S Singer
- Department of Veterinary and Biomedical Sciences, University of Minnesota , Saint Paul, MN, USA ; Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile , Valdivia, Chile
| |
Collapse
|
392
|
Increasing burden of urinary tract infections due to intrinsic colistin-resistant bacteria in hospitals in Marseille, France. Int J Antimicrob Agents 2015; 45:144-50. [DOI: 10.1016/j.ijantimicag.2014.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/23/2022]
|
393
|
Blocking yersiniabactin import attenuates extraintestinal pathogenic Escherichia coli in cystitis and pyelonephritis and represents a novel target to prevent urinary tract infection. Infect Immun 2015; 83:1443-50. [PMID: 25624354 DOI: 10.1128/iai.02904-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The emergence and spread of extended-spectrum beta-lactamases and carbapenemases among common bacterial pathogens are threatening our ability to treat routine hospital- and community-acquired infections. With the pipeline for new antibiotics virtually empty, there is an urgent need to develop novel therapeutics. Bacteria require iron to establish infection, and specialized pathogen-associated iron acquisition systems like yersiniabactin, common among pathogenic species in the family Enterobacteriaceae, including multidrug-resistant Klebsiella pneumoniae and pathogenic Escherichia coli, represent potentially novel therapeutic targets. Although the yersiniabactin system was recently identified as a vaccine target for uropathogenic E. coli (UPEC)-mediated urinary tract infection (UTI), its contribution to UPEC pathogenesis is unknown. Using an E. coli mutant (strain 536ΔfyuA) unable to acquire yersiniabactin during infection, we established the yersiniabactin receptor as a UPEC virulence factor during cystitis and pyelonephritis, a fitness factor during bacteremia, and a surface-accessible target of the experimental FyuA vaccine. In addition, we determined through transcriptome sequencing (RNA-seq) analyses of RNA from E. coli causing cystitis in women that iron acquisition systems, including the yersiniabactin system, are highly expressed by bacteria during natural uncomplicated UTI. Given that yersiniabactin contributes to the virulence of several pathogenic species in the family Enterobacteriaceae, including UPEC, and is frequently associated with multidrug-resistant strains, it represents a promising novel target to combat antibiotic-resistant infections.
Collapse
|
394
|
Ho PL, Chu YPS, Lo WU, Chow KH, Law PY, Tse CWS, Ng TK, Cheng VCC, Que TL. High prevalence of Escherichia coli sequence type 131 among antimicrobial-resistant E. coli isolates from geriatric patients. J Med Microbiol 2015; 64:243-247. [PMID: 25587081 DOI: 10.1099/jmm.0.000012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous work on the subclones within Escherichia coli ST131 predominantly involved isolates from Western countries. This study assessed the prevalence and antimicrobial resistance attributed to this clonal group. A total of 340 consecutive, non-duplicated urinary E. coli isolates originating from four clinical laboratories in Hong Kong in 2013 were tested. ST131 prevalence among the total isolates was 18.5 % (63/340) and was higher among inpatient isolates (23.0 %) than outpatient isolates (11.8 %, P<0.001), and higher among isolates from patients aged ≥65 years than from patients aged 18-50 years and 51-64 years (25.4 vs 3.4 and 4.0 %, respectively, P<0.001). Of the 63 ST131 isolates, 43 (68.3 %) isolates belonged to the H30 subclone, whereas the remaining isolates belonged to H41 (n = 17), H54 (n = 2) and H22 (n = 1). All H30 isolates were ciprofloxacin-resistant, of which 18.6 % (8/43) belonged to the H30-Rx subclone. Twenty-six (41.3 %) ST131 isolates were ESBL-producers, of which 19 had blaCTX-M-14 (12 non-H30-Rx, two H30-Rx and five H41), six had blaCTX-M-15 (five non-H30-Rx and one H30-Rx) and one was blaCTX-M-negative (H30). In conclusion, ST131 accounts for a large share of the antimicrobial-resistant E. coli isolates from geriatric patients. Unlike previous reports, ESBL-producing ST131 strains mainly belonged to non-H30-Rx rather than the H30-Rx subclone, with blaCTX-M-14 as the dominant enzyme type.
Collapse
Affiliation(s)
- Pak-Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, University of Hong Kong, Hong Kong SAR, PR China
| | - Yuki Pui-Shan Chu
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong SAR, PR China
| | - Wai-U Lo
- Department of Microbiology and Carol Yu Centre for Infection, University of Hong Kong, Hong Kong SAR, PR China
| | - Kin-Hung Chow
- Department of Microbiology and Carol Yu Centre for Infection, University of Hong Kong, Hong Kong SAR, PR China
| | - Pierra Y Law
- Department of Microbiology and Carol Yu Centre for Infection, University of Hong Kong, Hong Kong SAR, PR China
| | - Cindy Wing-Sze Tse
- Department of Clinical Pathology, Kwong Wah Hospital, Hong Kong SAR, PR China
| | - Tak-Keung Ng
- Department of Clinical Pathology, Princess Margaret Hospital, Hong Kong SAR, PR China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology and Carol Yu Centre for Infection, University of Hong Kong, Hong Kong SAR, PR China
| | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong SAR, PR China
| |
Collapse
|
395
|
Perez F, Bonomo RA. Editorial commentary: Bloodstream infection caused by extended-spectrum β-lactamase-producing Gram-negative bacteria: how to define the best treatment regimen? Clin Infect Dis 2015; 60:1326-9. [PMID: 25586684 DOI: 10.1093/cid/civ007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/25/2014] [Indexed: 01/25/2023] Open
Affiliation(s)
- Federico Perez
- Medicine Research Services, Louis Stokes Cleveland Department of Vetarans Affairs Medical Center Department of Medicine
| | - Robert A Bonomo
- Medicine Research Services, Louis Stokes Cleveland Department of Vetarans Affairs Medical Center Department of Medicine Department of Pharmacology Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| |
Collapse
|
396
|
Sequence type 131 fimH30 and fimH41 subclones amongst Escherichia coli isolates in Australia and New Zealand. Int J Antimicrob Agents 2015; 45:351-8. [PMID: 25707371 DOI: 10.1016/j.ijantimicag.2014.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 11/24/2014] [Indexed: 11/20/2022]
Abstract
The clonal composition of Escherichia coli causing extra-intestinal infections includes ST131 and other common uropathogenic clones. Drivers for the spread of these clones and risks for their acquisition have been difficult to define. In this study, molecular epidemiology was combined with clinical data from 182 patients enrolled in a case-control study of community-onset expanded-spectrum cephalosporin-resistant E. coli (ESC-R-EC) in Australia and New Zealand. Genetic analysis included antimicrobial resistance mechanisms, clonality by DiversiLab (rep-PCR) and multilocus sequence typing (MLST), and subtyping of ST131 by identification of polymorphisms in the fimH gene. The clonal composition of expanded-spectrum cephalosporin-susceptible E. coli and ESC-R-EC isolates differed, with six MLST clusters amongst susceptible isolates (median 7 isolates/cluster) and three clusters amongst resistant isolates, including 40 (45%) ST131 isolates. Population estimates indicate that ST131 comprises 8% of all E. coli within our population; the fluoroquinolone-susceptible H41 subclone comprised 4.5% and the H30 subclone comprised 3.5%. The H30 subclone comprised 39% of all ESC-R-EC and 41% of all fluoroquinolone-resistant E. coli within our population. Patients with ST131 were also more likely than those with non-ST131 isolates to present with an upper than lower urinary tract infection (RR=1.8, 95% CI 1.01-3.1). ST131 and the H30 subclone were predominant amongst ESC-R-EC but were infrequent amongst susceptible isolates where the H41 subclone was more prevalent. Within our population, the proportional contribution of ST131 to fluoroquinolone resistance is comparable with that of other regions. In contrast, the overall burden of ST131 is low by global standards.
Collapse
|
397
|
Fortini D, Fashae K, Villa L, Feudi C, García-Fernández A, Carattoli A. A novel plasmid carrying bla CTX-M-15 identified in commensal Escherichia coli from healthy pregnant women in Ibadan, Nigeria. J Glob Antimicrob Resist 2014; 3:9-12. [PMID: 27873656 DOI: 10.1016/j.jgar.2014.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/13/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022] Open
Abstract
The aim of this study was to investigate the molecular characteristics of commensal Escherichia coli producing extended-spectrum β-lactamases and showing fluoroquinolone resistance circulating in a healthy population in Ibadan, Nigeria. In total, 101 faecal samples from healthy pregnant women on the day of admission to hospital were collected and plated on eosin-methylene blue agar supplemented with cefotaxime. Genotyping demonstrated the presence of the blaCTX-M-15 gene in all of the cefotaxime-resistant isolates (n=32), and there was circulation of prevalent clones. The aac(6')-Ib-cr, qnrS1, qepA1 and qnrB1 genes were identified in several strains. A novel plasmid supporting the spread of the blaCTX-M-15, blaTEM-1 and qnrS1 genes was identified in these isolates by complete DNA sequencing.
Collapse
Affiliation(s)
- Daniela Fortini
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Kayode Fashae
- Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Laura Villa
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Claudia Feudi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Aurora García-Fernández
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alessandra Carattoli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| |
Collapse
|
398
|
Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences. PLoS Genet 2014; 10:e1004766. [PMID: 25522143 PMCID: PMC4270462 DOI: 10.1371/journal.pgen.1004766] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages. Plasmids are difficult to analyze in WGS datasets, due to the fragmented nature of the obtained sequences. We developed a method, called PLACNET, which greatly facilitates this analysis. As an example, we analyzed the plasmidome of E. coli ST131, an ExPEC clonal group involved in human urinary tract infections and septicemia. Relevant variation within this clone (e.g., antibiotic resistance and virulence) is frequently caused by the acquisition and loss of plasmids and other mobile genetic elements. Nevertheless, our knowledge of the ST131 plasmidome is limited to a few antibiotic resistance plasmids and to identification of replicons from known plasmid groups. PLACNET analysis extends the number of sequenced plasmids in ST131, which can be used for comparative genomics, from 11 to 50. The ST131 plasmidome is seemingly huge, encompassing roughly 50% of the main plasmid groups of γ–proteobacteria. MOBF12/IncF plasmids are apparently the most active players in the dissemination of relevant genetic information.
Collapse
Affiliation(s)
- Val F. Lanza
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - María de Toro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Teresa M. Coque
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública, (CIBER-ESP), Madrid, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
- * E-mail:
| |
Collapse
|
399
|
Baquero F, Lanza VF, Cantón R, Coque TM. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl 2014; 8:223-39. [PMID: 25861381 PMCID: PMC4380917 DOI: 10.1111/eva.12235] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/12/2014] [Indexed: 12/19/2022] Open
Abstract
The three main processes shaping the evolutionary ecology of antibiotic resistance (AbR) involve the emergence, invasion and occupation by antibiotic-resistant genes of significant environments for human health. The process of emergence in complex bacterial populations is a high-frequency, continuous swarming of ephemeral combinatory genetic and epigenetic explorations inside cells and among cells, populations and communities, expanding in different environments (migration), creating the stochastic variation required for evolutionary progress. Invasion refers to the process by which AbR significantly increases in frequency in a given (invaded) environment, led by external invaders local multiplication and spread, or by endogenous conversion. Conversion occurs because of the spread of AbR genes from an exogenous resistant clone into an established (endogenous) bacterial clone(s) colonizing the environment; and/or because of dissemination of particular resistant genetic variants that emerged within an endogenous clonal population. Occupation of a given environment by a resistant variant means a permanent establishment of this organism in this environment, even in the absence of antibiotic selection. Specific interventions on emergence influence invasion, those acting on invasion also influence occupation and interventions on occupation determine emergence. Such interventions should be simultaneously applied, as they are not simple solutions to the complex problem of AbR.
Collapse
Affiliation(s)
- Fernando Baquero
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Val F Lanza
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Rafael Cantón
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III Madrid, Spain
| | - Teresa M Coque
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| |
Collapse
|
400
|
Haubold B, Klötzl F, Pfaffelhuber P. andi: fast and accurate estimation of evolutionary distances between closely related genomes. ACTA ACUST UNITED AC 2014; 31:1169-75. [PMID: 25504847 DOI: 10.1093/bioinformatics/btu815] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/07/2014] [Indexed: 11/13/2022]
Abstract
MOTIVATION A standard approach to classifying sets of genomes is to calculate their pairwise distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly computing the evolutionary distances between closely related genomes. RESULTS Our distance measure is based on ungapped local alignments that we anchor through pairs of maximal unique matches of a minimum length. These exact matches can be looked up efficiently using enhanced suffix arrays and our implementation requires approximately only 1 s and 45 MB RAM/Mbase analysed. The pairing of matches distinguishes non-homologous from homologous regions leading to accurate distance estimation. We show this by analysing simulated data and genome samples ranging from 29 Escherichia coli/Shigella genomes to 3085 genomes of Streptococcus pneumoniae. AVAILABILITY AND IMPLEMENTATION We have implemented the computation of anchor distances in the multithreaded UNIX command-line program andi for ANchor DIstances. C sources and documentation are posted at http://github.com/evolbioinf/andi/ CONTACT haubold@evolbio.mpg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Bernhard Haubold
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany
| | - Fabian Klötzl
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany
| | - Peter Pfaffelhuber
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany, Institue for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck, Germany and Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany
| |
Collapse
|