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Fuzi M, Rodriguez Baño J, Toth A. Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents. Front Microbiol 2020; 11:271. [PMID: 32158437 PMCID: PMC7052298 DOI: 10.3389/fmicb.2020.00271] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum β-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Jesus Rodriguez Baño
- Unit of Infectious Diseases, Clinical Microbiology and Preventive Medicine, Department of Medicine, Hospital Universitario Virgen Macarena, University of Seville - Biomedicine Institute of Seville (IBiS), Seville, Spain
| | - Akos Toth
- Department of Bacteriology, Mycology and Parasitology, National Public Health Center, Budapest, Hungary
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van der Zwaluw K, Witteveen S, Wielders L, van Santen M, Landman F, de Haan A, Schouls LM, Bosch T. Molecular characteristics of carbapenemase-producing Enterobacterales in the Netherlands; results of the 2014-2018 national laboratory surveillance. Clin Microbiol Infect 2020; 26:1412.e7-1412.e12. [PMID: 32006688 DOI: 10.1016/j.cmi.2020.01.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/17/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Carbapenem resistance mediated by mobile genetic elements has emerged worldwide and has become a major public health threat. To gain insight into the molecular epidemiology of carbapenem resistance in The Netherlands, Dutch medical microbiology laboratories are requested to submit suspected carbapenemase-producing Enterobacterales (CPE) to the National Institute for Public Health and the Environment as part of a national surveillance system. METHODS Meropenem MICs and species identification were confirmed by E-test and MALDI-TOF and carbapenemase production was assessed by the Carbapenem Inactivation Method. Of all submitted CPE, one species/carbapenemase gene combination per person per year was subjected to next-generation sequencing (NGS). RESULTS In total, 1838 unique isolates were received between 2014 and 2018, of which 892 were unique CPE isolates with NGS data available. The predominant CPE species were Klebsiella pneumoniae (n = 388, 43%), Escherichia coli (n = 264, 30%) and Enterobacter cloacae complex (n = 116, 13%). Various carbapenemase alleles of the same carbapenemase gene resulted in different susceptibilities to meropenem and this effect varied between species. Analyses of NGS data showed variation of prevalence of carbapenemase alleles over time with blaOXA-48 being predominant (38%, 336/892), followed by blaNDM-1 (16%, 145/892). For the first time in the Netherlands, blaOXA-181, blaOXA-232 and blaVIM-4 were detected. The genetic background of K. pneumoniae and E. coli isolates was highly diverse. CONCLUSIONS The CPE population in the Netherlands is diverse, suggesting multiple introductions. The predominant carbapenemase alleles are blaOXA-48 and blaNDM-1. There was a clear association between species, carbapenemase allele and susceptibility to meropenem.
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Affiliation(s)
- K van der Zwaluw
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - S Witteveen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L Wielders
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M van Santen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - F Landman
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A de Haan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - L M Schouls
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - T Bosch
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations. Sci Rep 2020; 10:36. [PMID: 31913346 PMCID: PMC6949217 DOI: 10.1038/s41598-019-56763-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Extraintestinal multidrug resistant Escherichia coli sequence type (ST) 131 is a worldwide pandemic pathogen and a major cause of urinary tract and bloodstream infections. The role of this pandemic lineage in multidrug resistance plasmid dissemination is still scarce. We herein performed a meta-analysis on E. coli ST131 whole-genome sequence (WGS) databases to unravel ST131 plasmidome and specifically to decipher CTX-M encoding plasmids-clade associations. We mined 880 ST131 WGS data and proved that CTX-M-27-encoding IncF[F1:A2:B20] (Group1) plasmids are strictly found in clade C1, whereas CTX-M-15-encoding IncF[F2:A1:B-] (Group2) plasmids exist only in clade C2 suggesting strong plasmid-clade adaptations. Specific Col-like replicons (Col156, Col(MG828), and Col8282) were also found to be clade C1-associated. BLAST-based search revealed that Group1 and Group2 plasmids are narrow-host-range and restricted to E.coli. Among a collection of 20 newly sequenced Israeli ST131 CTX-M-encoding plasmids (2003–2016), Group1 and Group2 plasmids were dominant and associated with the expected clades. We found, for the first time in ST131, a CTX-M-15-encoding phage-like plasmid group (Group3) and followed its spread in the WGS data. This study offers a comprehensive way to decipher plasmid-bacterium associations and demonstrates that the CTX-M-encoding ST131 Group1 and Group2 plasmids are clade-restricted and presumably less transmissible, potentially contributing to ST131 clonal superiority.
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Zendri F, Maciuca IE, Moon S, Jones PH, Wattret A, Jenkins R, Baxter A, Timofte D. Occurrence of ESBL-Producing Escherichia coli ST131, Including the H30-Rx and C1-M27 Subclones, Among Urban Seagulls from the United Kingdom. Microb Drug Resist 2019; 26:697-708. [PMID: 32519936 DOI: 10.1089/mdr.2019.0351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial resistance is a public health concern. Understanding any role that urban seagulls may have as a reservoir of resistant bacteria could be important for reducing transmission. This study investigated fecal Escherichia coli isolates from seagulls (herring gulls and lesser black-backed gulls) to determine the prevalence of extended-spectrum cephalosporin-resistant (ESC-R) and fluoroquinolone-resistant E. coli among gull species from two cities (Taunton and Birmingham) in the United Kingdom (UK). We characterized the genetic background and carriage of plasmid-mediated resistance genes in extended-spectrum β-lactamase (ESBL)-producing E. coli obtained from these birds. Sixty ESC-R E. coli isolates were obtained from 39 seagulls (39/78, 50%), of which 28 (28/60, 46.7%) were positive for plasmid-mediated CTX-M and/or AmpC β-lactamase resistance genes. Among these, blaCTX-M-15, blaCTX-M-14, and blaCMY-2 predominated. Three isolates belonging to the B2-ST131 clone were detected, of which two harbored blaCTX-M-15 (typed to C2/H30Rx) and one harbored blaCTX-M-27 and was typed to C1/H30-R (recently described as the C1-M27 sublineage). The plasmid-mediated quinolone resistance (PMQR) gene carriage prevalence (11.7%) consisted of aac(6')-Ib-cr and qnrB genes. No carbapenem or colistin resistance genes were detected. Urban seagulls in the UK are colonized and can spread major antimicrobial-resistant E. coli isolates harboring ESBL and PMQR determinants, including clinically important strains such as the pandemic clone B2-ST131 and the C1-M27 subclade. This is the first report of ST131-C1-M27 subclade in wildlife in the UK and in seagulls worldwide.
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Affiliation(s)
- Flavia Zendri
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Iuliana E Maciuca
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Simon Moon
- Somerset West and Taunton Council, Environmental Health, Taunton, United Kingdom
| | - Philip H Jones
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston, United Kingdom
| | - Andy Wattret
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
| | - Richard Jenkins
- School of Allied Health Sciences, De Montfort University, Leicester, United Kingdom
| | - Andy Baxter
- Birdstrike Management Ltd., York, United Kingdom
| | - Dorina Timofte
- Department of Veterinary Pathology and Public Health, Faculty of Health and Life Sciences, Institute of Veterinary Science, University of Liverpool, Neston, United Kingdom
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da Cruz Campos AC, Cavallo FM, Andrade NL, van Dijl JM, Couto N, Zrimec J, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA. Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages. Microorganisms 2019; 7:E534. [PMID: 31698849 PMCID: PMC6920910 DOI: 10.3390/microorganisms7110534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/17/2023] Open
Abstract
Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short- and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.
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Affiliation(s)
- Ana Carolina da Cruz Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Francis M. Cavallo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Nathália L. Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Jan Zrimec
- Department of biology and Biological Engineering, Chalmers University of Technology, Chalmersplatsen 4, 412 96 Göteborg, Sweden;
| | - Jerome R. Lo Ten Foe
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Ana C. P. Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil; (A.C.d.C.C.); (N.L.A.); (A.C.P.R.)
| | - Paulo V. Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rua Voluntário da Patria, 21, Rio de Janeiro 941-901107, Brazil;
| | - Alex W. Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - Monika A. Chlebowicz-Flissikowska
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands; (F.M.C.); (J.M.v.D.); (N.C.); (J.R.L.T.F.); (A.W.F.); (M.A.C.-F.)
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Miles-Jay A, Weissman SJ, Adler AL, Tchesnokova V, Sokurenko EV, Baseman JG, Zerr DM. Epidemiology and Antimicrobial Resistance Characteristics of the Sequence Type 131-H30 Subclone Among Extraintestinal Escherichia coli Collected From US Children. Clin Infect Dis 2019; 66:411-419. [PMID: 29020219 DOI: 10.1093/cid/cix805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/14/2017] [Indexed: 11/14/2022] Open
Abstract
Background Escherichia coli sequence type (ST) 131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined. Methods We used clinical data and isolates from a case-control study of extended-spectrum cephalosporin-resistant E. coli conducted at 4 US children's hospitals to estimate the burden and identify host correlates of infection with H30. H30 isolates were identified using 2-locus genotyping; host correlates were examined using log-binomial regression models stratified by extended-spectrum cephalosporin resistance status. Results A total of 339 extended-spectrum cephalosporin-resistant and 1008 extended-spectrum cephalosporin-susceptible E. coli isolates were available for analyses. The estimated period prevalence of H30 was 5.3% among all extraintestinal E. coli isolates (95% confidence interval [CI], 4.6%-7.1%); H30 made up 43.3% (81/187) of extended-spectrum β-lactamase (ESBL)-producing isolates in this study. Host correlates of infection with H30 differed by extended-spectrum cephalosporin resistance status: Among resistant isolates, age ≤5 years was positively associated with H30 infection (relative risk [RR], 1.83 [95% CI, 1.19-2.83]); among susceptible isolates, age ≤5 years was negatively associated with H30 (RR, 0.48 [95% CI, .27-.87]), while presence of an underlying medical condition was positively associated (RR, 4.49 [95% CI, 2.43-8.31]). Conclusions ST131-H30 is less common among extraintestinal E. coli collected from children compared to reported estimates among adults, possibly reflecting infrequent fluoroquinolone use in pediatrics; however, it is similarly dominant among ESBL-producing isolates. The H30 subclone appears to disproportionately affect young children relative to other extended-spectrum cephalosporin-resistant E. coli.
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Affiliation(s)
- Arianna Miles-Jay
- Department of Epidemiology, University of Washington, Seattle.,Seattle Children's Research Institute, Seattle
| | - Scott J Weissman
- Seattle Children's Research Institute, Seattle.,Department of Pediatrics, University of Washington, Seattle
| | | | | | | | - Janet G Baseman
- Department of Epidemiology, University of Washington, Seattle
| | - Danielle M Zerr
- Seattle Children's Research Institute, Seattle.,Department of Pediatrics, University of Washington, Seattle
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Abstract
Uropathogenic E. coli (UPEC) is the major cause of urinary tract infections and a frequent cause of sepsis. Nearly half of all UPEC strains produce the potent cytotoxin hemolysin, and its expression is associated with enhanced virulence. In this study, we explored hemolysin variation within the globally dominant UPEC ST131 clone, finding that strains from the ST131 sublineage with the greatest multidrug resistance also possess the strongest hemolytic activity. We also employed an innovative forward genetic screen to define the set of genes required for hemolysin production. Using this approach, and subsequent targeted mutagenesis and complementation, we identified new hemolysin-controlling elements involved in LPS inner core biosynthesis and cytoplasmic chaperone activity, and we show that mechanistically they are required for hemolysin secretion. These original discoveries substantially enhance our understanding of hemolysin regulation, secretion and function. Uropathogenic Escherichia coli (UPEC) is the major cause of urinary tract infections. Nearly half of all UPEC strains secrete hemolysin, a cytotoxic pore-forming toxin. Here, we show that the prevalence of the hemolysin toxin gene (hlyA) is highly variable among the most common 83 E. coli sequence types (STs) represented on the EnteroBase genome database. To explore this diversity in the context of a defined monophyletic lineage, we contextualized sequence variation of the hlyCABD operon within the genealogy of the globally disseminated multidrug-resistant ST131 clone. We show that sequence changes in hlyCABD and its newly defined 1.616-kb-long leader sequence correspond to phylogenetic designation, and that ST131 strains with the strongest hemolytic activity belong to the most extensive multidrug-resistant sublineage (clade C2). To define the set of genes involved in hemolysin production, the clade C2 strain S65EC was completely sequenced and subjected to a genome-wide screen by combining saturated transposon mutagenesis and transposon-directed insertion site sequencing with the capacity to lyse red blood cells. Using this approach, and subsequent targeted mutagenesis and complementation, 13 genes were confirmed to be specifically required for production of active hemolysin. New hemolysin-controlling elements included discrete sets of genes involved in lipopolysaccharide (LPS) inner core biosynthesis (waaC, waaF, waaG, and rfaE) and cytoplasmic chaperone activity (dnaK and dnaJ), and we show these are required for hemolysin secretion. Overall, this work provides a unique description of hemolysin sequence diversity in a single clonal lineage and describes a complex multilevel system of regulatory control for this important toxin.
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Ny S, Sandegren L, Salemi M, Giske CG. Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference. Sci Rep 2019; 9:10291. [PMID: 31312006 PMCID: PMC6635401 DOI: 10.1038/s41598-019-46580-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/28/2019] [Indexed: 11/19/2022] Open
Abstract
Clonal lineages of ESBL (Extended-Spectrum β-Lactamase)-producing E. coli belonging to sequence type 131 (ST131) have disseminated globally during the last 30 years, leading to an increased prevalence of resistance to fluoroquinolones and extended-spectrum cephalosporins in clinical isolates of E. coli. We aimed to study if Swedish ESBL-producing ST131 isolates originated from single or multiple introductions to the population by assessing the amount of genetic variation, on chromosomal and plasmid level, between Swedish and international E. coli ST131. Bayesian inference of Swedish E. coli ST131 isolates (n = 29), sequenced using PacBio RSII, together with an international ST131 dataset showed that the Swedish isolates were part of the international ST131 A, C1 and C2 clades. Highly conserved plasmids were identified in three clusters although they were separated by several years, which indicates a strong co-evolution between some ST131 lineages and specific plasmids. In conclusion, the tight clonal relationship observed within the ST131 clades, together with highly conserved plasmids, challenges investigation of strain transmission events. A combination of few SNPs on a genome-wide scale and an epidemiological temporospatial link, are needed to track the spread of the ST131 subclones.
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Affiliation(s)
- Sofia Ny
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Alfred Nobels allé 10, 141 52, Huddinge, Stockholm, Sweden.
- Public Health Agency of Sweden, Nobels väg 18, 17182, Solna, Stockholm, Sweden.
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 75123, Uppsala, Sweden
| | - Marco Salemi
- Department of Pathology, University of Florida. Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, Florida, 32610-0009, USA
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Alfred Nobels allé 10, 141 52, Huddinge, Stockholm, Sweden
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Don't Get Wound Up: Revised Fluoroquinolone Breakpoints for Enterobacteriaceae and Pseudomonas aeruginosa. J Clin Microbiol 2019; 57:JCM.02072-18. [PMID: 31043468 DOI: 10.1128/jcm.02072-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluoroquinolones remain some of the more commonly prescribed antimicrobial agents in the United States, despite the wide array of reported side effects that are associated with their use. In 2019, the Clinical and Laboratory Standards Institute revised the fluoroquinolone antimicrobial susceptibility testing breakpoints for both Enterobacteriaceae and Pseudomonas aeruginosa This breakpoint revision was deemed necessary on the basis of pharmacokinetic and pharmacodynamic analyses suggesting that the previous breakpoints were too high, in addition to the inability of the previous breakpoints to detect low-level resistance to this antibiotic class. In this minireview, we review the published data in support of this revision, as well as the potential challenges that these breakpoint revisions are likely to pose for clinical laboratories.
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Comparative Activities of Ceftazidime-Avibactam and Ceftolozane-Tazobactam against Enterobacteriaceae Isolates Producing Extended-Spectrum β-Lactamases from U.S. Hospitals. Antimicrob Agents Chemother 2019; 63:AAC.00160-19. [PMID: 31085510 DOI: 10.1128/aac.00160-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/03/2019] [Indexed: 01/09/2023] Open
Abstract
The activities of ceftazidime-avibactam, ceftolozane-tazobactam, and comparators were evaluated for 733 isolates displaying resistance to broad-spectrum cephalosporins and carrying extended-spectrum β-lactamase (ESBL) genes detected by whole-genome sequencing analysis. Isolates were collected during 2017 in U.S. hospitals. The ESBL producers were 486 Escherichia coli, 190 Klebsiella pneumoniae, and 42 Enterobacter cloacae isolates and isolates from 3 other species. The most common groups of ESBL-encoding genes were bla CTX-M-15-like (n = 491 isolates) and bla CTX-M-15 alone (n = 168) or plus bla OXA-1 (n = 260), followed by bla CTX-M-14-like (n = 162), which included bla CTX-M-27 and bla CTX-M-14 (104 and 51 isolates, respectively), and bla SHV-12 and bla SHV-7 (48 and 22 isolates, respectively). ESBL producers carried other β-lactamases, including 1 E. cloacae harboring bla KPC-3 All ESBL-producing isolates were susceptible to ceftazidime-avibactam, and 90.2/83.9% (CLSI/EUCAST breakpoints) were susceptible to ceftolozane-tazobactam. Tigecycline (98.1/95.8% susceptible) and colistin (99.2%) were comparators that displayed the greatest activity against these isolates. Ceftolozane-tazobactam inhibited 91.4/83.9% of isolates carrying bla CTX-M-15-like and 97.5/95.1% of isolates carrying bla CTX-M-14-like, and its activity was more limited against the 91 isolates carrying bla SHV (66.7/61.1% susceptible). Ceftolozane-tazobactam inhibited 95.5% of the E. coli isolates but only 83.0%, 64.3%, and 80.0% of K. pneumoniae, E. cloacae, and other species harboring ESBL-encoding genes (CLSI breakpoints), respectively. Outer membrane protein sequences for ceftolozane-tazobactam-nonsusceptible isolates did not exhibit significant differences compared to those in genetically related ceftolozane-tazobactam-susceptible isolates. Ceftazidime-avibactam was more active than other agents tested, including ceftolozane-tazobactam, and the activity of this combination was stable regardless of species or ESBL gene carried.
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Frenck RW, Ervin J, Chu L, Abbanat D, Spiessens B, Go O, Haazen W, van den Dobbelsteen G, Poolman J, Thoelen S, Ibarra de Palacios P. Safety and immunogenicity of a vaccine for extra-intestinal pathogenic Escherichia coli (ESTELLA): a phase 2 randomised controlled trial. THE LANCET. INFECTIOUS DISEASES 2019; 19:631-640. [PMID: 31079947 DOI: 10.1016/s1473-3099(18)30803-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/20/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND ExPEC4V (JNJ-63871860) is a bioconjugate vaccine, containing O-antigens from Escherichia coli serotypes O1A, O2, O6A, and O25B, developed for the prevention of invasive extra-intestinal pathogenic E coli (ExPEC) disease. We aimed to assess safety, reactogenicity, and immunogenicity of ExPEC4V in healthy adults. METHODS In this phase 2 randomised, double-blind placebo-controlled study, we recruited healthy adults (≥18 years with a body-mass index of 35 kg/m2 or less) between Nov 16, 2015, and Aug 8, 2017, and randomly assigned them to receive a single dose of ExPEC4V (antigen O1A:O2:O6A:O25B content 4:4:4:4 μg [group 1]; 4:4:4:8 μg [group 2], 8:8:8:8 μg [group 3], 8:8:8:16 μg [group 4], or 16:16:16:16 μg [group 5]) or placebo. The primary objectives were evaluation of the safety, tolerability, and immunogenicity of ExPEC4V and determination of its dose-dependent immunogenicity 15 days after vaccination by ELISA in individuals who had received at least one vaccination dose. Antibody titres and safety evaluation were used to select two ExPEC4V doses for assessment up to day 360. This trial is registered at ClinicalTrials.gov, number NCT02546960. FINDINGS Of 848 enrolled participants, 843 (99%) received the ExPEC4V vaccine (757) or placebo (86) and were included in the safety analysis. Of 757 participants vaccinated with ExPEC4V, 222 (29%) had a solicited local adverse event and 325 (43%) had any solicited systemic adverse event, compared with 11 (13%) and 30 (35%) of 86 participants in the control group. Symptoms were mild-to-moderate. The most frequently reported solicited local adverse event was pain or tenderness (205 [27·1%] of 757 in combined ExPEC4V groups) and the most frequently reported solicited systemic adverse event was fatigue (208 [27·6%] of 757). Only 13 (2%) of 843 had a grade 3 event. At day 15, 80% or more of all participants achieved a two times or greater increase in serotype-specific IgG antibodies (except O25B at the lowest dose, 103 [72%] of 144). At day 360, 66% (95% CI 56·47-74·33) of participants in group 2 and 71% (62·13-78·95) of participants in group 4 selected for long-term follow-up maintained a two times or greater increase in serotype-specific antibody compared with baseline. INTERPRETATION EXPEC4V seemed well tolerated and elicited robust and functional antibody responses across all serotypes, doses, and age groups. For the two dosages evaluated (4:4:4:8 μg and 8:8:8:16 μg), the immune response persisted for 1 year. FUNDING Janssen Pharmaceuticals.
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Affiliation(s)
- Robert W Frenck
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - John Ervin
- Centre for Pharmaceutical Research, Kansas City, MO, USA
| | | | | | | | - Oscar Go
- Janssen Research & Development, Raritan, NJ, USA
| | | | | | - Jan Poolman
- Janssen Vaccines & Prevention, Leiden, Netherlands
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Secreted proteases: A new insight in the pathogenesis of extraintestinal pathogenic Escherichia coli. Int J Med Microbiol 2019; 309:159-168. [DOI: 10.1016/j.ijmm.2019.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 11/20/2022] Open
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Anjum M, Madsen JS, Nesme J, Jana B, Wiese M, Jasinskytė D, Nielsen DS, Sørensen SJ, Dalsgaard A, Moodley A, Bortolaia V, Guardabassi L. Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli. Antimicrob Agents Chemother 2019; 63:e02528-18. [PMID: 30885897 PMCID: PMC6496067 DOI: 10.1128/aac.02528-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical blaCMY-2-harboring plasmids introduced into the human fecal microbiota by two Escherichia coli strains isolated from a human and from poultry meat. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and green fluorescent protein [GFP]), allowing fluorescence-activated cell sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established in vitro gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6, and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 102 CFU/ml. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that the plasmids were predominantly acquired by Enterobacteriaceae species, such as E. coli and Hafnia alvei Our experimental data demonstrate that exogenous E. coli of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Small amounts of the exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Džiuginta Jasinskytė
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
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Sary K, Fairbrother JM, Arsenault J, de Lagarde M, Boulianne M. Antimicrobial Resistance and Virulence Gene Profiles Among Escherichia coli Isolates from Retail Chicken Carcasses in Vietnam. Foodborne Pathog Dis 2019; 16:298-306. [PMID: 30767657 DOI: 10.1089/fpd.2018.2555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This study evaluated virulence and resistance profiles of Escherichia coli in chicken carcasses from three retail systems in Vietnam. Fresh chicken carcasses from traditional markets and fresh and frozen chicken carcasses from supermarkets were sampled in Vietnam. E. coli isolates from carcass rinses were characterized for extraintestinal pathogenic E. coli (ExPEC) virulence factors (iucD, cnf, papC, tsh, KpsMT II, afa, and sfa) and for phenotypical antimicrobial resistance by Sensititre ARIS® as well as genotypically by polymerase chain reaction. An elevated proportion (30% to 70%) of samples resistant to antimicrobials critically important for human medicine was observed in routine isolates, with no significant differences between the three retail systems. Multidrug-resistant (MDR) ExPEC isolates of phylogroup B1 and, of greater concern, of phylogroup F were detected. Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase-producing E. coli possessing blaCTX-M or blaCMY-2 resistance genes, respectively, were found. The presence of ExPEC with a high level of antimicrobial resistance (more than 50% of isolates) and MDR (91% of isolates) and detection of ESBL-producing E. coli underline the potential health threat for humans associated with mishandled chicken carcasses or consumption of undercooked chicken meat in Vietnam.
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Affiliation(s)
- Kathleen Sary
- 1 Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Canada
| | - John Morris Fairbrother
- 2 OIE Reference Laboratory for Escherichia coli (EcL), Université de Montréal, Saint-Hyacinthe, Canada
| | - Julie Arsenault
- 3 Swine and Poultry Infectious Diseases Research Center (CRIPA), Université de Montréal, Saint-Hyacinthe, Canada
| | - Maud de Lagarde
- 2 OIE Reference Laboratory for Escherichia coli (EcL), Université de Montréal, Saint-Hyacinthe, Canada
| | - Martine Boulianne
- 1 Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Canada
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65
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Chen X, Zou Q, Zhang W, Wang R, Yu F, Chen Y. Clinical features and microbiological characteristics of hospital- and community-onset Escherichia coli bloodstream infection. J Med Microbiol 2019; 68:178-187. [PMID: 30624177 DOI: 10.1099/jmm.0.000904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
PURPOSE Escherichia coli is a leading cause of bloodstream infection (BSI) in hospitals and communities. METHODOLOGY We conducted a retrospective study in 2015 to evaluate the clinical features and microbiological characteristics of E. coli BSI acquired in the hospital and community. RESULTS A total of 100 patients with E. coli BSI were enrolled, among whom 60 % had hospital-onset (HO) BSI while 40 % had community-onset (CO) BSI. Patients with HO BSI had higher percentages of haematological disorders, immunosuppression conditions, underwent surgery within 2 weeks and had a higher 30-day mortality. The prevalences of multidrug-resistant and extended-spectrum β-lactamase-producing strains were 81 and 60 %, respectively. Resistance percentages to ampicillin, ampicillin-sulbactam, cefazolin, ceftriaxone, ciprofloxacin and levofloxacin were greater than 50 %. Of the 43 different sequence types (STs) identified, ST131 (15.3 %) was the most common. The serum agglutination rate was 52 % in which 13 O and 11 H serogroups were observed. Among the 36 detected virulence factor (VF) genes, IutA (66 %) and traT (61 %) were the most predominant. papA, papC and papEF were different between the CO and HO BSI groups. VF scores were high (mean >7) in the frequently detected ST95, ST1193 and ST131. CONCLUSION This study revealed that the clinical features of HO and CO E. coli BSI were different. STs and serotypes showed a great diversity in this region while VF genes of the isolates varied between clones.
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Affiliation(s)
- Xiao Chen
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,2State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Qianda Zou
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Weili Zhang
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,2State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Ruonan Wang
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Fei Yu
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Yu Chen
- 1Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,2State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
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Nagarjuna D, Mittal G, Dhanda RS, Gaind R, Yadav M. Alarming levels of antimicrobial resistance among sepsis patients admitted to ICU in a tertiary care hospital in India - a case control retrospective study. Antimicrob Resist Infect Control 2018; 7:150. [PMID: 30555689 PMCID: PMC6286518 DOI: 10.1186/s13756-018-0444-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/22/2018] [Indexed: 01/22/2023] Open
Abstract
Background Hospital acquired infections (HAI) are principal threats to the patients of intensive care units. An increase in the antimicrobial resistance (AMR) observed in gram negative bacteria is a great challenge to deal with. HAI and AMR lead to prolonged hospitalization and additional doses of anti-microbial treatment affecting patient's fitness and finances. Present study was undertaken to determine the pathotypes, genetic diversity and the antimicrobial resistance of E.coli in isolates from the patients admitted to intensive care unit at a tertiary care hospital in Delhi, India. Methods E.coli isolates (N = 77) obtained from the blood culture of patients diagnosed with sepsis and the isolates (N = 71) from the stool culture of patients admitted in intensive care unit (ICU) but not diagnosed with sepsis were investigated for their pathotypes, adherence patterns and genetic diversity by Enterobacterial Repeated Intergenic Consensus-polymerase chain reaction (ERIC-PCR). A Kirby-Bauer Disc diffusion test and antimicrobial susceptibility assays were performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Extended-spectrum β-lactamase (ESBL) genes and sequence type 131 (ST131) clone were characterised genotypically by gene-specific PCRs. Results Pathotypes analysis revealed 46 and 16% of the blood E.coli isolates were ETEC and EAEC respectively, in contrast to the fecal isolates wherein 22% of the isolates were ETEC and 28.5% were EAEC. EPEC, STEC and EIEC pathotypes were not detected in blood or fecal isolates. Of all the isolates studied, more than 90% of the blood and 70% of the fecal isolates were found to be resistant to cephalosporins. On the other hand, 68% of blood and 44% of the fecal isolates were found to be ESBL producers. Interestingly 83% of the blood isolates contained CTX-M15, whereas only 21% of them contained CTX-M9 genes. On the other hand CTX-M15 genes were found in 90% and CTX-M9 genes were found in 63% of the fecal isolates. Conclusion The antimicrobial resistant profile found in this study is alarming and poses a great threat to public health. Apparently an increased antimicrobial resistance to the extensively used cephalosporins is affecting an optimal drug therapy for patients. In addition, the presence of catheters, prolonged duration of stay in the hospital and poor hygienic conditions due to infrequent urination of the patient can lead to an additional vulnerability. Therefore continuous surveillance and rational use of antibiotics along with effective hygienic measures are urgently recommended in such settings.
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Affiliation(s)
- D Nagarjuna
- 1Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007 India.,4Current address: Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667 India
| | - Gajanand Mittal
- Department of Microbiology, Vardhman Mahavir Medical College (VMMC) and Safdarjung Hospital, Delhi, 110029 India
| | - Rakesh Singh Dhanda
- Stem Cell Laboratory, Longboat Explorers AB, SMiLE Incubator, Scheelevägen 2, 22381 Lund, Sweden
| | - Rajni Gaind
- Department of Microbiology, Vardhman Mahavir Medical College (VMMC) and Safdarjung Hospital, Delhi, 110029 India
| | - Manisha Yadav
- 1Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007 India.,5Current address: Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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Carattoli A, Villa L, Fortini D, García-Fernández A. Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae. Plasmid 2018; 118:102392. [PMID: 30529488 DOI: 10.1016/j.plasmid.2018.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 11/22/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
IncI1 has become one of the most common plasmid families in contemporary Enterobacteriaceae from both human and animal sources. In clinical epidemiology, this plasmid type ranks first as the confirmed vehicle of transmission of extended spectrum beta-lactamase and plasmid AmpC genes in isolates from food-producing animals. In this review, we describe the epidemiology and evolution of IncI1 plasmids and closely related IncIγ plasmids. We highlight the emergence of epidemic plasmids circulating among different bacterial hosts in geographically distant countries, and we address the phylogeny of the IncI1 and IncIγ family based on plasmid Multilocus Sequence Typing.
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Affiliation(s)
- Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Prevalence of ST131 Clone Producing Both ESBL CTX-M-15 and AAC(6′)Ib-cr Among Ciprofloxacin-Resistant Escherichia coli Isolates from Yemen. Microb Drug Resist 2018; 24:1537-1542. [DOI: 10.1089/mdr.2018.0024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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69
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An ounce of prevention. Clin Microbiol Infect 2018; 24:1037-1038. [DOI: 10.1016/j.cmi.2018.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/19/2018] [Accepted: 08/19/2018] [Indexed: 11/22/2022]
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70
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Mendes RE, Castanheira M, Woosley LN, Stone GG, Bradford PA, Flamm RK. Molecular β-lactamase characterization of Gram-negative pathogens recovered from patients enrolled in the ceftazidime-avibactam phase 3 trials (RECAPTURE 1 and 2) for complicated urinary tract infections: Efficacies analysed against susceptible and resistant subsets. Int J Antimicrob Agents 2018; 52:287-292. [DOI: 10.1016/j.ijantimicag.2018.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 03/12/2018] [Accepted: 04/04/2018] [Indexed: 01/27/2023]
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71
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Anjum M, Madsen JS, Espinosa-Gongora C, Jana B, Wiese M, Nielsen DS, Sørensen SJ, Moodley A, Bortolaia V, Guardabassi L. A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities. J Microbiol Methods 2018; 152:18-26. [PMID: 30030013 DOI: 10.1016/j.mimet.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022]
Abstract
IncI1 plasmids play a central role in the transfer of antimicrobial resistance genes among Enterobacteriaceae in animals and humans. Knowledge on the dynamics of IncI1 plasmid transfer is limited, mainly due to lack of culture-independent methods that can quantify donor strain survival and plasmid transfer in complex microbial communities. The aim of this study was to develop a culture-independent method to study the dynamics of IncI1 plasmids transfer by fluorescence-activated cell sorting. We genetically modified three wild-type Escherichia coli of animal (n = 2) and human (n = 1) origin carrying blaCMY-2 or blaCTX-M-1 on two epidemic IncI1 plasmids (pST12 and pST7). Non-coding regions on the chromosome and on the IncI1 plasmid of each strain were tagged with mCherry (red) and GFPmut3 (green) fluorescent proteins, respectively, using lambda recombineering. A gene cassette expressing mCherry and lacIq was inserted into the chromosome, whereas the plasmid was marked with a GFPmut3 cassette with LacIq repressible promoter. Therefore, gfpmut3 was repressed in donor strains but expressed in recipient strains acquiring the plasmids. We demonstrated that genetic engineering of the strains did not affect the growth rate and plasmid transfer-ability in filter and broth matings. A proof-of-concept experiment using the CoMiniGut, an in vitro model of the colon, proved the validity of our method for studying the survival of wild-type E. coli and horizontal transfer of IncI1 plasmids under different pH and oxygen conditions. The dual-labeling method by fluorescent proteins is useful to determine persistence of exogenous E. coli and transfer dynamics of IncI1 plasmids in microbial communities.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Jonas Stenløkke Madsen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Dennis Sandris Nielsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs. Lyngby, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark.
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Phan MD, Nhu NTK, Achard MES, Forde BM, Hong KW, Chong TM, Yin WF, Chan KG, West NP, Walker MJ, Paterson DL, Beatson SA, Schembri MA. Modifications in the pmrB gene are the primary mechanism for the development of chromosomally encoded resistance to polymyxins in uropathogenic Escherichia coli. J Antimicrob Chemother 2018; 72:2729-2736. [PMID: 29091192 DOI: 10.1093/jac/dkx204] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
Objectives Polymyxins remain one of the last-resort drugs to treat infections caused by MDR Gram-negative pathogens. Here, we determined the mechanisms by which chromosomally encoded resistance to colistin and polymyxin B can arise in the MDR uropathogenic Escherichia coli ST131 reference strain EC958. Methods Two complementary approaches, saturated transposon mutagenesis and spontaneous mutation induction with high concentrations of colistin and polymyxin B, were employed to select for mutations associated with resistance to polymyxins. Mutants were identified using transposon-directed insertion-site sequencing or Illumina WGS. A resistance phenotype was confirmed by MIC and further investigated using RT-PCR. Competitive growth assays were used to measure fitness cost. Results A transposon insertion at nucleotide 41 of the pmrB gene (EC958pmrB41-Tn5) enhanced its transcript level, resulting in a 64- and 32-fold increased MIC of colistin and polymyxin B, respectively. Three spontaneous mutations, also located within the pmrB gene, conferred resistance to both colistin and polymyxin B with a corresponding increase in transcription of the pmrCAB genes. All three mutations incurred a fitness cost in the absence of colistin and polymyxin B. Conclusions This study identified the pmrB gene as the main chromosomal target for induction of colistin and polymyxin B resistance in E. coli.
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Affiliation(s)
- Minh-Duy Phan
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Maud E S Achard
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Kar Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala, Lumpur, Malaysia
| | - Nicholas P West
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark J Walker
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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Shelburne SA, Kim J, Munita JM, Sahasrabhojane P, Shields RK, Press EG, Li X, Arias CA, Cantarel B, Jiang Y, Kim MS, Aitken SL, Greenberg DE. Whole-Genome Sequencing Accurately Identifies Resistance to Extended-Spectrum β-Lactams for Major Gram-Negative Bacterial Pathogens. Clin Infect Dis 2018; 65:738-745. [PMID: 28472260 DOI: 10.1093/cid/cix417] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022] Open
Abstract
Background There is marked interest in using DNA-based methods to detect antimicrobial resistance (AMR), with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole-genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR. Methods Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the 4 most common gram-negative bacteria causing bloodstream infections in neutropenic patients. The WGS data, including both gene presence/absence and detection of mutations in an array of AMR-relevant genes, were used to predict resistance to 4 β-lactams commonly used in the empiric treatment of neutropenic fever. The genotypic predictions were then compared to phenotypic resistance as determined by BMD and by commercial methods during routine patient care. Results Of 133 putative instances of resistance to the β-lactams of interest identified by WGS, only 87 (65%) would have been detected by a typical PCR-based approach. The sensitivity, specificity, and positive and negative predictive values for WGS in predicting AMR were 0.87, 0.98, 0.97, and 0.91, respectively. Using BMD as the gold standard, our genotypic resistance prediction approach had a significantly higher positive predictive value compared to minimum inhibitory concentrations generated by commercial methods (0.97 vs 0.92; P = .025). Conclusions These data demonstrate the potential feasibility of using WGS to guide antibiotic treatment decisions for patients with life-threatening infections for an array of medically important pathogens.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.,Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston
| | - Jiwoong Kim
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas
| | - Jose M Munita
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School at Houston.,Genomics and Resistant Microbes Group, Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Pranoti Sahasrabhojane
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan K Shields
- Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Ellen G Press
- Department of Medicine, University of Pittsburgh, Pennsylvania
| | - Xiqi Li
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center
| | - Cesar A Arias
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School at Houston.,Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston.,Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Brandi Cantarel
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas
| | - Ying Jiang
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Min S Kim
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas
| | - Samuel L Aitken
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Division of Pharmacy, MD Anderson Cancer Center, Houston
| | - David E Greenberg
- Center for Antimicrobial Resistance and Microbial Genomics, Division of Infectious Diseases, University of Texas McGovern Medical School at Houston.,Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Microbiology, University of Texas Southwestern, Dallas
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74
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Ortega-Paredes D, Barba P, Mena-López S, Espinel N, Zurita J. Escherichia coli hyperepidemic clone ST410-A harboring bla CTX-M-15 isolated from fresh vegetables in a municipal market in Quito-Ecuador. Int J Food Microbiol 2018; 280:41-45. [PMID: 29777948 DOI: 10.1016/j.ijfoodmicro.2018.04.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/02/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
Dissemination of Extended spectrum β-lactamases (ESBL) Enterobacteriaceae is a major medical threat. Vegetables and fruits, which are usually consumed raw, are a very suitable pathway for the spread of these bacteria from farm-to-fork. However, limited information exists regarding resistant bacteria and epidemic clones that are disseminated in vegetables and tap water in South America. We processed a total of 90 samples in triplicate of nine typically consumed raw vegetables from a central municipal market, and tap water samples were processed from twenty-one locations in Quito, Ecuador. The samples were analyzed for total coliforms and ESBL Enterobacteriaceae contamination using the dilution filtration method. ESBL Escherichia coli isolates were phenotypically and genotypically characterized. The water was free of Enterobacteriaceae, but all the vegetables and fruits (except for blackberries) presented total coliform counts. Watercress had the highest load of total coliforms (3.3 × 10E4). ESBL E. coli was detected in alfalfa, leaf lettuce and parsley/cilantro samples. Alfalfa had the highest load of ESBL E. coli/total coliforms (1/3.3 × 10E2). We identified E. coli ST44-A and ST410-A harboring blaCTX-M-15 downstream of ISEcp1. Alfalfa and parsley/cilantro were contaminated with hyperepidemic E. coli ST410-A, which was resistant to quinolones and harbored blaCTX-M-15. For the first time, we report ESBL E. coli ST410-A from vegetables and express an alert regarding the health risk this could represent.
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Affiliation(s)
- David Ortega-Paredes
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Quito, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Pedro Barba
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Santiago Mena-López
- Pontificia Universidad Católica del Ecuador, Escuela de Ciencias Geográficas, Quito, Ecuador
| | - Nathaly Espinel
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Quito, Ecuador
| | - Jeannete Zurita
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Quito, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador.
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75
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Abstract
Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.
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76
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Campos ACC, Andrade NL, Ferdous M, Chlebowicz MA, Santos CC, Correal JCD, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Rossen JWA. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front Microbiol 2018; 9:243. [PMID: 29503639 PMCID: PMC5821075 DOI: 10.3389/fmicb.2018.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/31/2018] [Indexed: 01/09/2023] Open
Abstract
Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.
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Affiliation(s)
- Ana Carolina C Campos
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nathália L Andrade
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mithila Ferdous
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Monika A Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Carla C Santos
- Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Julio C D Correal
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Controle de Infecções, Hospital Rio Laranjeiras, Rio de Janeiro, Brazil
| | - Jerome R Lo Ten Foe
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ana Cláudia P Rosa
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo V Damasco
- Departamento de Doenças Infecciosas e Parasitárias, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Doenças Infecciosas e Parasitárias, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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77
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Ma L, Green SI, Trautner BW, Ramig RF, Maresso AW. Metals Enhance the Killing of Bacteria by Bacteriophage in Human Blood. Sci Rep 2018; 8:2326. [PMID: 29396496 PMCID: PMC5797145 DOI: 10.1038/s41598-018-20698-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Multidrug-resistant bacterial pathogens are a major medical concern. E. coli, particularly the pathotype extraintestinal pathogenic E. coli (ExPEC), is a leading cause of bloodstream infections. As natural parasites of bacteria, bacteriophages are considered a possible solution to treat patients infected with antibiotic resistant strains of bacteria. However, the development of phage as an anti-infective therapeutic is hampered by limited knowledge of the physiologic factors that influence their properties in complex mammalian environments such as blood. To address this barrier, we tested the ability of phage to kill ExPEC in human blood. Phages are effective at killing ExPEC in conventional media but are substantially restricted in this ability in blood. This phage killing effect is dependent on the levels of free metals and is inhibited by the anticoagulant EDTA. The EDTA-dependent inhibition of ExPEC killing is overcome by exogenous iron, magnesium, and calcium. Metal-enhanced killing of ExPEC by phage was observed for several strains of ExPEC, suggesting a common mechanism. The addition of metals to a murine host infected with ExPEC stimulated a phage-dependent reduction in ExPEC levels. This work defines a role for circulating metals as a major factor that is essential for the phage-based killing of bacteria in blood.
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Affiliation(s)
- Li Ma
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Sabrina I Green
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Barbara W Trautner
- Michael E. Debakey Veterans Affairs Medical Center, Houston, TX, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert F Ramig
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- Molecular Virology and Microbiology Department, Baylor College of Medicine, Houston, TX, USA.
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78
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Hughes D, Andersson DI. Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol Rev 2018; 41:374-391. [PMID: 28333270 PMCID: PMC5435765 DOI: 10.1093/femsre/fux004] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.
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Affiliation(s)
- Diarmaid Hughes
- Corresponding author: Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582), Uppsala University, S-751 23 Uppsala, Sweden. Tel: +46 18 4714507; E-mail:
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79
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Vila J, Sáez-López E, Johnson JR, Römling U, Dobrindt U, Cantón R, Giske CG, Naas T, Carattoli A, Martínez-Medina M, Bosch J, Retamar P, Rodríguez-Baño J, Baquero F, Soto SM. Escherichia coli: an old friend with new tidings. FEMS Microbiol Rev 2018; 40:437-463. [PMID: 28201713 DOI: 10.1093/femsre/fuw005] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/23/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
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Affiliation(s)
- J Vila
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - E Sáez-López
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J R Johnson
- VA Medical Center, Minneapolis, MN, USA, and University of Minnesota, Minneapolis, MN, USA
| | - U Römling
- Karolinska Institute, Stockholm, Sweden
| | - U Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - C G Giske
- Karolinska Institute, Stockholm, Sweden
| | - T Naas
- Hôpital de Bicêtre, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - A Carattoli
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Martínez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona, Spain
| | - J Bosch
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | - P Retamar
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - J Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - F Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - S M Soto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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80
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Paitan Y. Current Trends in Antimicrobial Resistance of Escherichia coli. Curr Top Microbiol Immunol 2018; 416:181-211. [PMID: 30088148 DOI: 10.1007/82_2018_110] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Escherichia coli is the most common Gram-negative bacterial pathogen, presenting both a clinical and an epidemiological challenge. In the last decade, several successful multidrug-resistant high-risk strains, such as strain E. coli ST131 have evolved, mainly due to the growing selective pressure of antimicrobial use. These strains present enhanced fitness and pathogenicity, effective transmission and colonization abilities, global distribution due to efficient dissemination, and resistance to various antimicrobial resistances. Here, we describe the emerging trends and epidemiology of resistant E. coli, including carbapenemase-producing E. coli, E. coli ST131 and colistin resistant E. coli.
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Affiliation(s)
- Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44282, Kfar Saba, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 39978, Tel Aviv, Israel.
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81
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Abstract
Escherichia coli has a complex and versatile nature and continuously evolves from non-virulent isolates to highly pathogenic strains causing severe diseases and outbreaks. Broadly protective vaccines against pathogenic E. coli are not available and the rising in both, multi-drug resistant and hypervirulent isolates, raise concern for healthcare and require continuous efforts in epidemiologic surveillance and disease monitoring. The evolving knowledge on E. coli pathogenesis mechanisms and on the mediated immune response following infection or vaccination, together with advances in the "omics" technologies, is opening new perspectives toward the design and development of effective and innovative E. coli vaccines.
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82
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Frequency and Mechanisms of Spontaneous Fosfomycin Nonsusceptibility Observed upon Disk Diffusion Testing of Escherichia coli. J Clin Microbiol 2017; 56:JCM.01368-17. [PMID: 29093108 DOI: 10.1128/jcm.01368-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022] Open
Abstract
Fosfomycin maintains activity against most Escherichia coli clinical isolates, but the growth of E. coli colonies within the zone of inhibition around the fosfomycin disk is occasionally observed upon susceptibility testing. We aimed to estimate the frequency of such nonsusceptible inner colony mutants and identify the underlying resistance mechanisms. Disk diffusion testing of fosfomycin was performed on 649 multidrug-resistant E. coli clinical isolates collected between 2011 and 2015. For those producing inner colonies inside the susceptible range, the parental strains and their representative inner colony mutants were subjected to MIC testing, whole-genome sequencing, reverse transcription-quantitative PCR (qRT-PCR), and carbohydrate utilization studies. Of the 649 E. coli clinical isolates, 5 (0.8%) consistently produced nonsusceptible inner colonies. Whole-genome sequencing revealed the deletion of uhpT encoding hexose-6-phosphate antiporter in 4 of the E. coli inner colony mutants, while the remaining mutant contained a nonsense mutation in uhpA The expression of uhpT was absent in the mutant strains with uhpT deletion and was not inducible in the strain with the uhpA mutation, unlike in its parental strain. All 5 inner colony mutants had reduced growth on minimal medium supplemented with glucose-6-phosphate. In conclusion, fosfomycin-nonsusceptible inner colony mutants can occur due to the loss of function or induction of UhpT but are rare among multidrug-resistant E. coli clinical strains. Considering that these mutants carry high biological costs, we suggest that fosfomycin susceptibility of strains that generate inner colony mutants can be interpreted on the basis of the zone of inhibition without accounting for the inner colonies.
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83
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Abbanat D, Davies TA, Amsler K, He W, Fae K, Janssen S, Poolman JT, van den Dobbelsteen GPJM. Development and Qualification of an Opsonophagocytic Killing Assay To Assess Immunogenicity of a Bioconjugated Escherichia coli Vaccine. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:e00123-17. [PMID: 28971965 PMCID: PMC5717180 DOI: 10.1128/cvi.00123-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/20/2017] [Indexed: 12/16/2022]
Abstract
The global burden of disease caused by extraintestinal pathogenic Escherichia coli (ExPEC) is increasing as the prevalence of multidrug-resistant strains rises. A multivalent ExPEC O-antigen bioconjugate vaccine could have a substantial impact in preventing bacteremia and urinary tract infections. Development of an ExPEC vaccine requires a readout to assess the functionality of antibodies. We developed an opsonophagocytic killing assay (OPA) for four ExPEC serotypes (serotypes O1A, O2, O6A, and O25B) based on methods established for pneumococcal conjugate vaccines. The performance of the assay was assessed with human serum by computing the precision, linearity, trueness, total error, working range, and specificity. Serotypes O1A and O6A met the acceptance criteria for precision (coefficient of variation for repeatability and intermediate precision, ≤50%), linearity (90% confidence interval of the slope of each strain, 0.80, 1.25), trueness (relative bias range, -30% to 30%), and total error (total error range, -65% to 183%) at five serum concentrations and serotypes O2 and O25B met the acceptance criteria at four concentrations (the lowest concentration for serotypes O2 and O25B did not meet the system suitability test of maximum killing of ≥85% of E. coli cells). All serotypes met the acceptance criteria for specificity (opsonization index value reductions of ≤20% for heterologous serum preadsorption and ≥70% for homologous serum preadsorption). The assay working range was defined on the basis of the lowest and highest concentrations at which the assay jointly fulfilled the target acceptance criteria for linearity, precision, and accuracy. An OPA suitable for multiple E. coli serotypes has been developed, qualified, and used to assess the immunogenicity of a 4-valent E. coli bioconjugate vaccine (ExPEC4V) administered to humans.
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Affiliation(s)
- Darren Abbanat
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Todd A Davies
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Karen Amsler
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Wenping He
- Janssen Research & Development, Raritan, New Jersey, USA
| | - Kellen Fae
- Janssen Vaccines & Prevention B.V., Bacterial Vaccines Discovery & Early Development, Leiden, The Netherlands
| | - Sarah Janssen
- Janssen Vaccines & Prevention B.V., Statistics & Decision Sciences, Leiden, The Netherlands
| | - Jan T Poolman
- Janssen Vaccines & Prevention B.V., Bacterial Vaccines Discovery & Early Development, Leiden, The Netherlands
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84
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Aktaş E, Otlu B, Erdemir D, Ekici H, Bulut E. A First Insight into Escherichia coli ST131 High-Risk Clone Among Extended-Spectrum Beta-Lactamase-Producing Urine Isolates in Istanbul with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry and Real-Time PCR. Microb Drug Resist 2017; 23:1032-1036. [DOI: 10.1089/mdr.2017.0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Elif Aktaş
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Barış Otlu
- Department of Medical Microbiology, Inonu University Faculty of Medicine, Malatya, Turkey
| | - Duygu Erdemir
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Hatice Ekici
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Emin Bulut
- Clinical Microbiology Laboratory, Sisli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
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85
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Affiliation(s)
- Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
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86
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Enioutina EY, Teng L, Fateeva TV, Brown JCS, Job KM, Bortnikova VV, Krepkova LV, Gubarev MI, Sherwin CMT. Phytotherapy as an alternative to conventional antimicrobials: combating microbial resistance. Expert Rev Clin Pharmacol 2017; 10:1203-1214. [PMID: 28836870 DOI: 10.1080/17512433.2017.1371591] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION In the modern antimicrobial era, the rapid spread of resistance to antibiotics and introduction of new and mutating viruses is a global concern. Combating antimicrobial resistant microbes (AMR) requires coordinated international efforts that incorporate new conventional antibiotic development as well as development of alternative drugs with antimicrobial activity, management of existing antimicrobials, and rapid detection of AMR pathogens. Areas covered: This manuscript discusses some conventional strategies to control microbial resistance. The main purpose of the manuscript is to present information on specific herbal medicines that may serve as good treatment alternatives to conventional antimicrobials for infections sensitive to conventional as well as resistant strains of microorganisms. Expert commentary: Identification of potential new antimicrobials is challenging; however, one source for potential structurally diverse and complex antimicrobials are natural products. Natural products may have advantages over other post-germ theory antimicrobials. Many antimicrobial herbal medicines possess simultaneous antibacterial, antifungal, antiprotozoal and/or antiviral properties. Herbal products have the potential to boost host resistance to infections, particularly in immunocompromised patients. Antimicrobial broad-spectrum activity in conjunction with immunostimulatory properties may help to prevent microbial resistance to herbal medicine. As part of the efforts to broaden use of herbal medicines to treat microbial infections, pre-clinical and clinical testing guidelines of these compounds as a whole should be implemented to ensure consistency in formulation, efficacy and safety.
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Affiliation(s)
- Elena Yu Enioutina
- a Division of Clinical Pharmacology, the Department of Pediatrics, School of Medicine , University of Utah , Salt Lake City , UT , USA.,b Department of Pathology, School of Medicine , University of Utah , Salt Lake City , UT , USA
| | - Lida Teng
- c Department of Drug Policy & Management (DPM), Graduate School of Pharmaceutical Sciences , The University of Tokyo , Tokyo , Japan
| | - Tatyana V Fateeva
- d Center of Medicine , All-Russian Research Institute of Medicinal and Aromatic Plants (VILAR) , Moscow , Russia
| | - Jessica C S Brown
- b Department of Pathology, School of Medicine , University of Utah , Salt Lake City , UT , USA
| | - Kathleen M Job
- a Division of Clinical Pharmacology, the Department of Pediatrics, School of Medicine , University of Utah , Salt Lake City , UT , USA
| | - Valentina V Bortnikova
- d Center of Medicine , All-Russian Research Institute of Medicinal and Aromatic Plants (VILAR) , Moscow , Russia
| | - Lubov V Krepkova
- d Center of Medicine , All-Russian Research Institute of Medicinal and Aromatic Plants (VILAR) , Moscow , Russia
| | | | - Catherine M T Sherwin
- a Division of Clinical Pharmacology, the Department of Pediatrics, School of Medicine , University of Utah , Salt Lake City , UT , USA.,f Department of Pharmacology and Toxicology , University of Utah , Salt Lake City , UT , USA
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87
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Alonso CA, González-Barrio D, Ruiz-Fons F, Ruiz-Ripa L, Torres C. High frequency of B2 phylogroup among non-clonally related fecal Escherichia coli isolates from wild boars, including the lineage ST131. FEMS Microbiol Ecol 2017; 93:3003317. [PMID: 28365752 DOI: 10.1093/femsec/fix016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/11/2017] [Indexed: 11/14/2022] Open
Abstract
Wild boars are worldwide distributed mammals which population is increasing in many regions, like the Iberian Peninsula, leading to an increased exposition to humans. They are considered reservoirs of different zoonotic pathogens and have been postulated as potential vectors of antimicrobial-resistant (AMR) bacteria. This study aimed to determine the prevalence of antimicrobial resistance and phylogenetic distribution of Escherichia coli from wild boar feces. Antimicrobial resistance and integron content was genetically characterized and E. coli of B2 phylogroup was further analyzed by molecular typing and virulence genotyping. The prevalence of AMR E. coli was low, with only 7.5% of isolates being resistant against at least one antimicrobial, mainly ampicillin, tetracycline and/or sulfonamide. An unexpected elevated rate of B2 phylogroup (47.5%) was identified, most of them showing unrelated pulsed-field-gel-electrophoresis patterns. ST131/B2 (fimH 22 sublineage), ST28/B2, ST1170/B2, ST681/B2 and ST625/B2 clones, previously described in extraintestinal infections in humans, were detected in B2 isolates, and carried one or more genes associated with extraintestinal pathogenic E. coli (ExPEC). This study demonstrated a low prevalence of antimicrobial resistance in E. coli from wild boars, although they are not exempt of AMR bacteria, and a predominance of genetically diverse B2 phylogroup, including isolates carrying ExPEC which may contribute to the spread of virulence determinants among different ecosystems.
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Affiliation(s)
- Carla Andrea Alonso
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - David González-Barrio
- Health and Biotechnology (SaBio) Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), 13071 Ciudad Real, Spain
| | - Francisco Ruiz-Fons
- Health and Biotechnology (SaBio) Group, Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), 13071 Ciudad Real, Spain
| | - Laura Ruiz-Ripa
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
| | - Carmen Torres
- Área Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain
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88
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Direct and convenient measurement of plasmid stability in lab and clinical isolates of E. coli. Sci Rep 2017; 7:4788. [PMID: 28684862 PMCID: PMC5500522 DOI: 10.1038/s41598-017-05219-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/25/2017] [Indexed: 01/01/2023] Open
Abstract
Plasmids are important mobile elements in bacteria, contributing to evolution, virulence, and antibiotic resistance. Natural plasmids are generally large and maintained at low copy number and thus prone to be lost. Therefore, dedicated plasmid maintenance systems have evolved, leading to plasmid loss rates as low as 1 per 107 divisions. These low rates complicate studies of plasmid loss, as traditional techniques for measuring plasmid loss are laborious and not quantitative. To overcome these limitations, we leveraged a stringent negative selection system to develop a method for performing direct, quantitative measurements of plasmid loss in E. coli. We applied our method to gain mechanistic insights into a heterologously reconstituted segregation system in lab strains and clinical isolates of E. coli. We also performed direct stability studies of a currently circulating resistance plasmid in a clinical isolate, strain EC958, which is a member of the rapidly expanding global ST131 E. coli clone. Our results establish the foundational assays required to screen for small molecules targeting plasmid stability, which could complement current strategies for reducing the spread of antibiotic resistance, complementing other strategies for treating antibiotic resistant bacteria.
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89
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High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli. Antimicrob Agents Chemother 2017; 61:AAC.00265-17. [PMID: 28416542 PMCID: PMC5444143 DOI: 10.1128/aac.00265-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/07/2017] [Indexed: 02/05/2023] Open
Abstract
Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification.
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90
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Van Tyne D, Ciolino JB, Wang J, Durand ML, Gilmore MS. Novel Phagocytosis-Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli From Keratitis. JAMA Ophthalmol 2017; 134:1306-1309. [PMID: 27631542 DOI: 10.1001/jamaophthalmol.2016.3283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are highly antibiotic resistant, and primary ocular infection by ESBL E coli has rarely been reported. A novel mutation conferring phagocytosis resistance would position a strain well to infect the cornea. Observations A woman with recurrent keratitis presented with a corneal ulcer, which was culture positive for ESBL E coli. Resistant to nearly all other antimicrobials, the infection was treated with amikacin and polymyxin B-trimethoprim, and the ulcer resolved over 3 weeks. Analysis of the E coli genome showed it to belong to multilocus sequence type 131 (ST131). This isolate was found to possess a novel deletion in yrfF, an essential regulator of bacterial capsule synthesis. Disruption of yrfF, which confers mucoidy and increased virulence, has not been previously observed in ESBL E coli from any infection site. This novel variant was experimentally proven to cause the mucoid phenotype, and corresponding resistance to phagocytic killing. Conclusions and Relevance Increased resistance to immune clearance in an ESBL E coli lineage already known for its virulence is an unsettling development. This phenotype, which likely positioned it as an unusual cause of corneal ulcer, can be easily recognized in the laboratory, which should help limit its spread.
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Affiliation(s)
- Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts2Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Joseph B Ciolino
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Jay Wang
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Marlene L Durand
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts3Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts4Infectious Disease Service, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts2Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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91
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Prevalence and genetic diversity of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in nursing homes in Bavaria, Germany. Vet Microbiol 2017; 200:138-141. [DOI: 10.1016/j.vetmic.2015.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022]
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92
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Stapleton PJ, Lundon DJ, McWade R, Scanlon N, Hannan MM, O'Kelly F, Lynch M. Antibiotic resistance patterns of Escherichia coli urinary isolates and comparison with antibiotic consumption data over 10 years, 2005-2014. Ir J Med Sci 2017; 186:733-741. [PMID: 28054236 DOI: 10.1007/s11845-016-1538-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/25/2016] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Escherichia coli is a common cause of urinary tract infections (UTI). Reviews of antibiotic resistance of this organism can inform choice of empiric treatment of UTI and other infections and strategies for combating antimicrobial resistance. We reviewed laboratory and hospital pharmacy records to assess trends in non-susceptibility rates and the effect of antimicrobial stewardship interventions. METHODS A retrospective observational study of isolates of E. coli from MSU samples at a Dublin teaching hospital from inpatients and community, obtained from January 2005 to December 2014. Susceptibility to a panel of antibiotics was determined using the disc diffusion method, as well as extended-spectrum beta-lactamase (ESBL) production status. Trends in resistance were plotted graphically and analysed in a descriptive manner. RESULTS Except for nitrofurantoin and gentamicin, non-susceptibility increased for all antimicrobials tested. Co-amoxiclav non-susceptibility reached 48% in hospital and 32.6% in the community by 2014. Piperacillin-tazobactam non-susceptibility increased from 6.8 to 23.8% in hospital and from <1 to 12.5% in community, with similar increases for ESBL producing isolates. Ciprofloxacin non-susceptibility peaked at 25.5% in hospital in 2012 and 11.44% in the community in 2014. CONCLUSION Escherichia coli isolates from community MSU samples have high rates of non-susceptibility to trimethoprim and co-amoxiclav. Nitrofurantoin remains the best empiric therapy for cystitis. Increasing non-susceptibility to co-amoxiclav and piperacillin-tazobactam in hospital isolates is concerning. Ciprofloxacin non-susceptibility is increasing faster in the community than in hospital. A sharp reduction in hospital fluoroquinolone consumption did not result in a significant reduction in ciprofloxacin non-susceptibility of hospital E. coli isolates.
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Affiliation(s)
- P J Stapleton
- Department of Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland.
| | - D J Lundon
- Department of Urology and Reconstructive Surgery, Mater Misericordiae University Hospital, Dublin, Ireland
| | - R McWade
- Department of Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - N Scanlon
- Department of Pharmacy, Mater Misericordiae University Hospital, Dublin, Ireland
| | - M M Hannan
- Department of Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - F O'Kelly
- Department of Urology and Reconstructive Surgery, Mater Misericordiae University Hospital, Dublin, Ireland
| | - M Lynch
- Department of Clinical Microbiology, Mater Misericordiae University Hospital, Dublin, Ireland
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93
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Kittinger C, Lipp M, Folli B, Kirschner A, Baumert R, Galler H, Grisold AJ, Luxner J, Weissenbacher M, Farnleitner AH, Zarfel G. Enterobacteriaceae Isolated from the River Danube: Antibiotic Resistances, with a Focus on the Presence of ESBL and Carbapenemases. PLoS One 2016; 11:e0165820. [PMID: 27812159 PMCID: PMC5094594 DOI: 10.1371/journal.pone.0165820] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/18/2016] [Indexed: 01/24/2023] Open
Abstract
In a clinical setting it seems to be normal these days that a relevant proportion or even the majority of different bacterial species has already one or more acquired antibiotic resistances. Unfortunately, the overuse of antibiotics for livestock breeding and medicine has also altered the wild-type resistance profiles of many bacterial species in different environmental settings. As a matter of fact, getting in contact with resistant bacteria is no longer restricted to hospitals. Beside food and food production, the aquatic environment might also play an important role as reservoir and carrier. The aim of this study was the assessment of the resistance patterns of Escherichia coli and Klebsiella spp. out of surface water without prior enrichment and under non-selective culture conditions (for antibiotic resistance). In addition, the presence of clinically important extended spectrum beta lactamase (ESBL) and carbapenmase harboring Enterobacteriaceae should be investigated. During Joint Danube Survey 3 (2013), water samples were taken over the total course of the River Danube. Resistance testing was performed for 21 different antibiotics. Samples were additionally screened for ESBL or carbapenmase harboring Enterobacteriaceae. 39% of all isolated Escherichia coli and 15% of all Klebsiella spp. from the river Danube had at least one acquired resistance. Resistance was found against all tested antibiotics except tigecycline. Taking a look on the whole stretch of the River Danube the proportion of multiresistances did not differ significantly. In total, 35 ESBL harboring Enterobacteriaceae, 17 Escherichia coli, 13 Klebsiella pneumoniae and five Enterobacter spp. were isolated. One Klebsiella pneumoniae harboring NMD-1 carbapenmases and two Enterobacteriaceae with KPC-2 could be identified. Human generated antibiotic resistance is very common in E. coli and Klebsiella spp. in the River Danube. Even isolates with resistance patterns normally associated with intensive care units are present.
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Affiliation(s)
- Clemens Kittinger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Michaela Lipp
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Bettina Folli
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Alexander Kirschner
- Institute for Hygiene and Applied Immunology, Water Hygiene, Medical University of Vienna, Vienna, Austria
- Interuniversity Cooperation Centre for Water and Health
| | - Rita Baumert
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Herbert Galler
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Andrea J. Grisold
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Josefa Luxner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Melanie Weissenbacher
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Andreas H. Farnleitner
- Interuniversity Cooperation Centre for Water and Health
- Institute of Chemical Engineering, Research Group Environmental Microbiology and Molecular Ecology, Vienna University of Technology, Vienna, Austria
| | - Gernot Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
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94
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GERHOLD G, SCHULZE MH, GROSS U, BOHNE W. Multilocus sequence typing and CTX-M characterization of ESBL-producing E. coli: a prospective single-centre study in Lower Saxony, Germany. Epidemiol Infect 2016; 144:3300-3304. [PMID: 27357252 PMCID: PMC9150193 DOI: 10.1017/s0950268816001412] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/02/2016] [Accepted: 06/12/2016] [Indexed: 01/09/2023] Open
Abstract
The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria is a serious threat for current healthcare settings. In this study we investigated the molecular epidemiology of ESBL-producing E. coli at the University Medical Center Göttingen in Lower Saxony, Germany. All E. coli isolates with an ESBL phenotype were collected during a 6-month period in 2014. Multilocus sequence typing and CTX-M characterization were performed on 160 isolates. Of the ESBL-producing isolates 95·6% were CTX-M positive. Compared to recent Germany-wide studies, we found CTX-M-1 to occur in higher frequency than CTX-M-15 (44·4% vs. 34·4%). CTX-M-14 and CTX-M-27 were detected at 9·4% and 5·0%, respectively. The globally dominant sequence type (ST) 131, which is often associated with CTX-M-15, occurred at a relatively low rate of 24%. Major non-ST131 sequence types were ST101 (5%), ST58 (5%), ST10 (4·4%), ST38 (4·4%), ST410 (3·8%) and ST453 (3·1%). Several of these major sequence types were previously shown to be associated with livestock farming. Together, our study indicates that E. coli lineage distribution in individual healthcare settings can significantly differ from average numbers obtained in nationwide studies.
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Affiliation(s)
- G. GERHOLD
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - M. H. SCHULZE
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - U. GROSS
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - W. BOHNE
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
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95
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Ny S, Löfmark S, Börjesson S, Englund S, Ringman M, Bergström J, Nauclér P, Giske CG, Byfors S. Community carriage of ESBL-producing Escherichia coli is associated with strains of low pathogenicity: a Swedish nationwide study. J Antimicrob Chemother 2016; 72:582-588. [PMID: 27798205 DOI: 10.1093/jac/dkw419] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/29/2016] [Accepted: 09/05/2016] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Community carriage of ESBL-producing Escherichia coli (EPE) is common worldwide and there is a need to understand the connection between carriage and infection. We compared the molecular characteristics of EPE among Swedish community carriers with those of EPE causing invasive infections. METHODS We collected 2134 faecal samples from randomly selected Swedish inhabitants and examined them for the presence of EPE. All participating volunteers answered a questionnaire about putative risk factors for EPE carriage. Suspected EPE isolates (n = 418) from patients with bloodstream infection (BSI) were collected from Swedish laboratories. Isolates were genotypically and phenotypically characterized. RESULTS Our results show that the EPE population found in carriers generally had lower pathogenicity compared with the isolates from BSIs, since carriers had a lower proportion of E. coli belonging to phylogroup B2, ST131 and ST131 subclone H30-Rx. Isolates from carriers also had lower levels of multiresistance. The Swedish carriage rate of EPE was 4.7% (101/2134) among healthy volunteers. Risk factors associated with carriage were travel to countries in Asia (OR = 3.6, 95% CI = 1.4-9.2) and Africa (OR = 3.6, 95% CI = 1.7-7.7) and a diet without pork (OR = 0.5, 95% CI = 0.3-0.8 for pork eaters). CONCLUSIONS E. coli host factors previously associated with higher pathogenicity were all more common in BSIs compared with carriers. This indicates that the risk of invasive infection with EPE may be relatively modest in many community carriers and that EPE carriage of high-risk strains should be the focus of attention for prevention.
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Affiliation(s)
- Sofia Ny
- Public Health Agency of Sweden, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Stockholm, Sweden
| | | | | | | | - Maj Ringman
- Public Health Agency of Sweden, Stockholm, Sweden
| | | | - Pontus Nauclér
- Infectious Disease Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Stockholm, Sweden .,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Byfors
- Public Health Agency of Sweden, Stockholm, Sweden
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96
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Giedraitienė A, Vitkauskienė A, Pavilonis A, Patamsytė V, Genel N, Decre D, Arlet G. Prevalence of O25b-ST131 clone among Escherichia coli strains producing CTX-M-15, CTX-M-14 and CTX-M-92 β-lactamases. Infect Dis (Lond) 2016; 49:106-112. [PMID: 27563748 DOI: 10.1080/23744235.2016.1221531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Dissemination of multidrug-resistant Escherichia coli is closely associated with the worldwide spread of a single clone ST131, which is the main cause of urinary tract and bloodstream infections in patients from nursing homes and immunocompromised patients. The aim of our study was to determine the prevalence of ST131 clone and the replicons involved in the spread of blaCTX-M genes among O25b-ST131 CTX-M-producing E. coli isolates in Lithuania. METHODS The strains included in this study were screened for CTX-M β-lactamase-encoding genes, phylogenetic groups and ST131 clone by PCR. Bacterial conjugation was performed to identify plasmid replicon types responsible for blaCTX-M genes dissemination. RESULTS A total of 158 E. coli clinical non-duplicate ESBL isolates were analyzed. Nearly half (n = 67, 42.4%) of the investigated E. coli isolates belonged to phylogenetic group B2. The isolates producing CTX-M-92 β-lactamases were identified to be the ST131 clone more frequently than the non-ST131 clone (11.5% vs. 3.1%, p = .035). The CTX-M-15 isolates were identified as ST131 isolates less frequently than non-ST131 isolates (50.8% vs. 71.1%; p = .015). The ST131 clone isolates contained type L/M and A/C replicons; a fused FII/FIB replicon was found in four isolates (23.5%). Type HI1 replicon was identified in ST131 E. coli isolates producing CTX-M-15 β-lactamases. CONCLUSIONS This study demonstrates the predominance of the ST131 clone among CTX-M β-lactamase-producing E. coli isolates. Dissemination of blaCTX-M genes in ST131 strains can be linked not only to highly adapted IncF plasmids such as FII/FIB and FII, but also to plasmid replicon types A/C, L/M and HI1.
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Affiliation(s)
- Agnė Giedraitienė
- a Institute of Microbiology and Virology, Veterinary Academy , Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Astra Vitkauskienė
- b Department of Laboratory Medicine, Medical Academy , Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Alvydas Pavilonis
- a Institute of Microbiology and Virology, Veterinary Academy , Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Vaiva Patamsytė
- c Institute of Cardiology, Medical Academy , Lithuanian University of Health Sciences , Kaunas , Lithuania
| | - Nathalie Genel
- d Laboratoire de Bacteriologie, Faculte de Médecine , Universite Pierre et Marie Curie Paris 6 , Paris , France
| | - Dominique Decre
- d Laboratoire de Bacteriologie, Faculte de Médecine , Universite Pierre et Marie Curie Paris 6 , Paris , France.,e Service de Microbiologie , Hopital Saint Antoine, APHP , Paris , France
| | - Guillaume Arlet
- d Laboratoire de Bacteriologie, Faculte de Médecine , Universite Pierre et Marie Curie Paris 6 , Paris , France.,f Service de Bacteriologie , Hopital Tenon, APHP , Paris , France
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97
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Fuzi M. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria. Front Microbiol 2016; 7:1017. [PMID: 27458434 PMCID: PMC4935693 DOI: 10.3389/fmicb.2016.01017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 01/24/2023] Open
Abstract
Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis UniversityBudapest, Hungary
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98
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Abstract
UNLABELLED Escherichia colisequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n= 215) of sequenced ST131E. coliisolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of ablaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration ofblaCTX-Mwithin subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, theblaCTX-M-14/14-likegroup. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages ofE. coli These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. IMPORTANCE Escherichia coli, perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specificE. colilineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.
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99
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Escherichia coli Pyruvate Dehydrogenase Complex Is an Important Component of CXCL10-Mediated Antimicrobial Activity. Infect Immun 2015; 84:320-8. [PMID: 26553462 PMCID: PMC4694015 DOI: 10.1128/iai.00552-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/02/2015] [Indexed: 02/03/2023] Open
Abstract
Chemokines are best recognized for their role within the innate immune system as chemotactic cytokines, signaling and recruiting host immune cells to sites of infection. Certain chemokines, such as CXCL10, have been found to play an additional role in innate immunity, mediating CXCR3-independent killing of a diverse array of pathogenic microorganisms. While this is still not clearly understood, elucidating the mechanisms underlying chemokine-mediated antimicrobial activity may facilitate the development of novel therapeutic strategies effective against antibiotic-resistant Gram-negative pathogens. Here, we show that CXCL10 exerts antibacterial effects on clinical and laboratory strains of Escherichia coli and report that disruption of pyruvate dehydrogenase complex (PDHc), which converts pyruvate to acetyl coenzyme A, enables E. coli to resist these antimicrobial effects. Through generation and screening of a transposon mutant library, we identified two mutants with increased resistance to CXCL10, both with unique disruptions of the gene encoding the E1 subunit of PDHc, aceE. Resistance to CXCL10 also occurred following deletion of either aceF or lpdA, genes that encode the remaining two subunits of PDHc. Although PDHc resides within the bacterial cytosol, electron microscopy revealed localization of immunogold-labeled CXCL10 to the bacterial cell surface in both the E. coli parent and aceE deletion mutant strains. Taken together, our findings suggest that while CXCL10 interacts with an as-yet-unidentified component on the cell surface, PDHc is an important mediator of killing by CXCL10. To our knowledge, this is the first description of PDHc as a key bacterial component involved in the antibacterial effect of a chemokine.
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100
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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: 111] [Impact Index Per Article: 12.3] [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.
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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
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