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Park JH, Bae KS, Kang J, Yoon JK, Lee SH. Comprehensive Assessment of Multidrug-Resistant and Extraintestinal Pathogenic Escherichia coli in Wastewater Treatment Plant Effluents. Microorganisms 2024; 12:1119. [PMID: 38930502 PMCID: PMC11205404 DOI: 10.3390/microorganisms12061119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Multidrug-resistant (MDR) Escherichia coli poses a significant threat to public health, contributing to elevated rates of morbidity, mortality, and economic burden. This study focused on investigating the antibiotic resistance profiles, resistance and virulence gene distributions, biofilm formation capabilities, and sequence types of E. coli strains resistant to six or more antibiotic classes. Among 918 strains isolated from 33 wastewater treatment plants (WWTPs), 53.6% (492/918) demonstrated resistance, 32.5% (298/918) were MDR, and over 8% (74/918) were resistant to six or more antibiotic classes, exhibiting complete resistance to ampicillin and over 90% to sulfisoxazole, nalidixic acid, and tetracycline. Key resistance genes identified included sul2, blaTEM, tetA, strA, strB, and fimH as the predominant virulence genes linked to cell adhesion but limited biofilm formation; 69% showed no biofilm formation, and approximately 3% were strong producers. Antibiotic residue analysis detected ciprofloxacin, sulfamethoxazole, and trimethoprim in all 33 WWTPs. Multilocus sequence typing analysis identified 29 genotypes, predominantly ST131, ST1193, ST38, and ST69, as high-risk clones of extraintestinal pathogenic E. coli. This study provided a comprehensive analysis of antibiotic resistance in MDR E. coli isolated from WWTPs, emphasizing the need for ongoing surveillance and research to effectively manage antibiotic resistance.
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Affiliation(s)
- Ji-Hyun Park
- Han River Environment Research Center, National Institute of Environment Research, Yangpyeong-gun, Incheon 12585, Gyeonggi-do, Republic of Korea
| | - Kyung-Seon Bae
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Jihyun Kang
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Jeong-Ki Yoon
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Soo-Hyung Lee
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
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Hrovat K, Molan K, Seme K, Ambrožič Avguštin J. Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from lower respiratory tract samples between 2002 and 2019 in the Central Slovenia region. Ann Clin Microbiol Antimicrob 2024; 23:6. [PMID: 38218869 PMCID: PMC10790261 DOI: 10.1186/s12941-023-00664-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/21/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Antibiotic resistance is one of the most serious global health problems and threatens the effective treatment of bacterial infections. Of greatest concern are infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC). The aim of our study was to evaluate the prevalence and molecular characteristics of ESBL-EC isolated over an 18-year pre-COVID period from lower respiratory tract (LRT) samples collected from selected Slovenian hospitals. OBJECTIVES AND METHODS All isolates were identified by MALDI-TOF and phenotypically confirmed as ESBLs by a disk diffusion assay. Using a PCR approach, 487 non-repetitive isolates were assigned to phylogroups, sequence type groups, and clonal groups. Isolates were also screened for virulence-associated genes (VAGs) and antimicrobial resistance genes. RESULTS The prevalence of ESBL-EC isolates from LRT in a large university hospital was low (1.4%) in 2005 and increased to 10.8% by 2019. The resistance profile of 487 non-repetitive isolates included in the study showed a high frequency of group 1 blaCTX-M (77.4%; n = 377), blaTEM (54.4%; n = 265) and aac(6')-Ib-cr (52%; n = 253) genes and a low proportion of blaSHV and qnr genes. Isolates were predominantly assigned to phylogroup B2 (73.1%; n = 356), which was significantly associated with clonal group ST131. The ST131 group accounted for 67.6% (n = 329) of all isolates and had a higher number of virulence factor genes than the non-ST131 group. The virulence gene profile of ST131 was consistent with that of other extraintestinal pathogenic E. coli (ExPEC) strains and was significantly associated with ten of sixteen virulence factor genes tested. Using ERIC-PCR fingerprinting, isolates with the same ERIC-profile in samples from different patients, and at different locations and sampling dates were confirmed, indicating the presence of "hospital-adapted" strains. CONCLUSION Our results suggest that the ESBL-EC isolates from LRT do not represent a specific pathotype, but rather resemble other ExPEC isolates, and may be adapted to the hospital environment. To our knowledge, this is the first study of ESBL-EC isolated from LRT samples collected over a long period of time.
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Affiliation(s)
- Katja Hrovat
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Molan
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Koreň J, Andrezál M, Ozaee E, Drahovská H, Wawruch M, Liptáková A, Maliar T. High Emergence of Multidrug-Resistant Sequence Type 131 Subclade C2 among Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated from the University Hospital Bratislava, Slovakia. Antibiotics (Basel) 2023; 12:1209. [PMID: 37508305 PMCID: PMC10376107 DOI: 10.3390/antibiotics12071209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The expansion of sequence type 131 (ST131) extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) represents major worldwide challenges. E. coli strains originating from healthcare facilities (labeled No. 1 and No. 2) of the University Hospital Bratislava (UHB) were analyzed for ST131 emergence, including its (sub)lineages and clonal relatedness. Antimicrobial resistance was determined in most strains. Of a total of 354 E. coli strains, 263 (74.3%) belonged to ST131; of these, 177 (67.3%) were from No. 1. Generally, among 260 ST131 E. coli, clades A/B were confirmed in 20 (7.7%), while clade C was noted in 240 (92.3%) strains; within them, subclades were detected as follows: C0 (17; 7.1%), C1 (3; 1.2%), and C2 (220; 91.7%). Among fifteen randomly selected E. coli strains that were investigated for ST and clonal relatedness, seven STs were identified: eight (53.3%) ST131, two (13.3%) ST73, and one each (6.7%) of ST10, ST12, ST14, ST1193, and ST1196. From No. 1, two ST131 in the first internal clinic and one ST131 from No. 2 in the aftercare department were highly clonally related, suggesting possible epidemiological association. Antimicrobial resistance was as follows: ciprofloxacin 93.8%, ceftazidime 78.4%, meropenem 0%, fosfomycin 2.9% and nitrofurantoin 1.4%. Prevention of ESBL-producing E. coli dissemination, especially for ST131 clade C2, is inevitably necessary for reducing drug resistance and decreasing healthcare-associated infections.
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Affiliation(s)
- Ján Koreň
- Institute of Microbiology, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81108 Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Elham Ozaee
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Martin Wawruch
- Institute of Pharmacology and Clinical Pharmacology, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Adriána Liptáková
- Institute of Microbiology, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81108 Bratislava, Slovakia
| | - Tibor Maliar
- Department of Chemistry, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, 91701 Trnava, Slovakia
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Prevalence of Plasmid-Mediated Quinolone Resistance (PMQRs) Determinants and Whole Genome Sequence Screening of PMQR-Producing E. coli Isolated from Men Undergoing a Transrectal Prostate Biopsy. Int J Mol Sci 2022; 23:ijms23168907. [PMID: 36012180 PMCID: PMC9408980 DOI: 10.3390/ijms23168907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Fluoroquinolones (FQs) are recommended as prophylaxis for men undergoing transrectal prostate biopsy (TRUS-Bx). Recent studies suggest a significant share of FQ-resistant rectal flora in post-TRUST-Bx infections. Methods: 435 Enterobacterales isolates from 621 patients attending 12 urological departments in Poland were screened by PCR for PMQR genes. PMQR-positive isolates were tested for quinolone susceptibility and investigated by whole genome sequencing (WGS) methods. Results: In total, 32 (7.35%) E. coli strains with ciprofloxacin MIC in the range 0.125–32 mg/L harbored at least one PMQR gene. qnrS and qnrB were the most frequent genes detected in 16 and 12 isolates, respectively. WGS was performed for 28 of 32 PMQR-producing strains. A variety of serotypes and sequence types (STs) of E. coli was noticed. All strains carried at least one virulence gene. AMR genes that encoded resistance against different classes of antibiotics were identified. Additionally, five of 13 ciprofloxacin-susceptible E. coli had alterations in codon 83 of the GyrA subunits. Conclusion: This study provides information on the common presence of PMQRs among E. coli, which may explain the cause for development of post-TRUS-Bx infections. High numbers of virulence and antimicrobial resistance genes detected show a potential for analysed strains to develop infections.
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Johnston BD, Gordon DM, Burn S, Johnson TJ, Weber BP, Miller EA, Johnson JR. Novel Multiplex PCR Method and Genome Sequence-Based Analog for High-Resolution Subclonal Assignment and Characterization of Escherichia coli Sequence Type 131 Isolates. Microbiol Spectr 2022; 10:e0106422. [PMID: 35604132 PMCID: PMC9241916 DOI: 10.1128/spectrum.01064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/30/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a pandemic, multidrug-resistant extraintestinal pathogen. The multiple distinctive ST131 subclones differ for rfb and fliC alleles (O and H antigens), fimH allele (type-1 fimbriae adhesin), resistance phenotype and genotype, clinical correlates, and host predilection. Current PCR assays for detecting ST131 and its main subclones offer limited sub-ST characterization. Here we combined 22 novel and 14 published primers for a multiplex PCR assay to detect and extensively characterize ST131 isolates. The primers target mdh36, gyrB47, trpA72, sbmA, plsB, nupC, rmuC, kefC, ybbW, the O16 and O25b rfb variants, five fimH alleles (fimH22, fimH27, fimH30, fimH35, and fimH41), two fliC alleles (H4 and H5), a (subclone-specific) fluoroquinolone resistance-associated parC allele, and a (subclone-specific) prophage marker. The resulting amplicons resolve 15 molecular subsets within ST131, including 3 within clade A (H41 subclone), 5 within clade B (H22 subclone), and 7 within clade C (H30 subclone), which includes subclones C0 (H30S: 2 subsets), C1 and C1-M27 (H30R1: 2 subsets), and C2 (H30Rx: 3 subsets). Validation in three laboratories showed that this assay provides a rapid, accurate, and portable method for rapidly detecting and characterizing E. coli ST131 and its key subsets. Additionally, for users with whole genome sequencing (WGS) capability, we developed a command-line executable called ST131Typer, an in silico version of the extended multiplex PCR assay. Its accuracy was 87.8%, with most issues due to incomplete or fragmented input genome assemblies. These two novel assays should facilitate detailed ST131 subtyping using either endpoint PCR or WGS. IMPORTANCE These novel assays provide greater subclonal resolution and characterization of E. coli ST131 isolates than do the available comparable PCR assays, plus offer a novel sequence-based alternative to PCR. They may prove useful for molecular epidemiological studies, surveillance, and, potentially, clinical management.
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Affiliation(s)
- Brian D. Johnston
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
| | - David M. Gordon
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Samantha Burn
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Bonnie P. Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Elizabeth A. Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - James R. Johnson
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
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Abstract
Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.
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Dankittipong N, Fischer EAJ, Swanenburg M, Wagenaar JA, Stegeman AJ, de Vos CJ. Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms. Antibiotics (Basel) 2022; 11:antibiotics11020281. [PMID: 35203883 PMCID: PMC8868399 DOI: 10.3390/antibiotics11020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022] Open
Abstract
Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.
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Affiliation(s)
- Natcha Dankittipong
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
- Correspondence:
| | - Egil A. J. Fischer
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Manon Swanenburg
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
| | - Jaap A. Wagenaar
- Department Biomolecular Health Science, Infectious Diseases & Immunology, Utrecht University, Androclusgebouw, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Arjan J. Stegeman
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Clazien J. de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
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Ludden C, Coll F, Gouliouris T, Restif O, Blane B, Blackwell GA, Kumar N, Naydenova P, Crawley C, Brown NM, Parkhill J, Peacock SJ. Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. LANCET MICROBE 2021; 2:e472-e480. [PMID: 34485958 PMCID: PMC8410606 DOI: 10.1016/s2666-5247(21)00117-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Background Escherichia coli is a leading cause of bloodstream infections. Developing interventions to reduce E coli infections requires an understanding of the frequency of nosocomial transmission, but the available evidence is scarce. We aimed to detect and characterise transmission of E coli and associated plasmids in a hospital setting. Methods In this prospective observational cohort study, patients were admitted to two adult haematology wards at the Cambridge University Hospitals NHS Foundation Trust in England. Patients aged 16 years and older who were treated for haematological malignancies were included. Stool samples were collected from study participants on admission, once per week, and at discharge. We sequenced multiple E coli isolates (both extended spectrum β-lactamase [ESBL]-producing and non-ESBL-producing) from each stool sample. A genetic threshold to infer E coli transmission was defined by maximum within-host single nucleotide polymorphism (SNP) diversity and the probability of drawing observed pairs of between-patient isolates at different SNP thresholds. Putative transmission clusters were identified when sequences were less than the genetic threshold. Epidemiological links for each transmission event were investigated. We sequenced all E coli positive blood samples from the two adult haematology wards. Findings We recruited 174 (51%) of 338 adult patients admitted to the wards between May 13 and Nov 13, 2015. We obtained and cultured 376 stool samples from 149 patients, of which 152 samples from 97 (65%) patients grew E coli. Whole-genome sequencing was done on 970 isolates. We identified extensive diversity in the bacterial population (90 sequence types) and mixed E coli sequence type carriage. 24 (26%) patients carried two sequence types, 12 (13%) carried three, and six (6%) patients carried four or more sequence types. Using a 17 SNP cutoff we identified ten clusters in 20 patients. The largest cluster contained seven patients, whereas four patients were included in multiple clusters. Strong epidemiological links were found between patients in seven clusters. 17 (11%) of 149 patients had stool samples positive for ESBL-producing E coli, the most common of which was associated with blaCTX-M-15 (12 [71%] of 17). Long-read sequencing revealed that blaCTX-M-15 was often integrated into the chromosome, with little evidence for plasmid transmission. Seven patients developed E coli bloodstream infection, four with identical strains to those in their stool; two of these had documented nosocomial acquisition. Interpretation We provide evidence of bacterial transmission and endogenous infection during routine care by integrating genomic and epidemiological data and by determining a genetic cutoff informed by within-host diversity in the studied population. Our findings challenge single colony-based investigations, and the widely accepted notion of plasmid spread. Funding UK Department of Health, Wellcome Trust, UK National Institute for Health Research.
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Affiliation(s)
- Catherine Ludden
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Narender Kumar
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Charles Crawley
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Public Health England, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Zhong Y, Guo S, Seow KLG, Ming GOH, Schlundt J. Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Jurong Lake, Singapore with Whole-Genome-Sequencing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18030937. [PMID: 33499011 PMCID: PMC7908357 DOI: 10.3390/ijerph18030937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/06/2021] [Accepted: 01/17/2021] [Indexed: 02/07/2023]
Abstract
Background: The fast-spreading of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli (ESBL-producing E. coli) and ESBL genes has become a big challenge to public health. The risk of spreading ESBL genes and pathogens in the environment and community has raised public health concern. The characterizing and whole-genome sequencing studies of ESBL-producing bacteria from reservoir water in Singapore is still limited. Materials and methods: The reservoir water sample was taken from two randomly selected sampling points of the Chinese Garden (Jurong river reservoir), which is a popular reservoir park in Singapore. The bacteria of the water sample were collected with 0.45 µm filter membranes and enriched before processing with ESBL-producing E. coli screening. The collected ESBL positive isolates were further characterized by both phenotypic tests including disc diffusion and microdilution Minimum Inhibitory Concentration (MIC) test, and also genotypic test as whole-genome sequencing analysis. Besides, to investigate the transferability of the resistance gene, a conjugation test was performed with the J53 E. coli strain as the gene receptor. Result: Nine ESBL-producing E. coli isolates were collected and confirmed as ESBL-producing with both phenotypic and genotypic tests. A potential pathogen as ST131 clade A isolate was identified, and all isolates were determined to harbor a blaCTX-M gene. Among them, strain J1E4 was resistant to polymyxin E and confirmed to harboring a conjugatable mcr-1 gene. Further genetic environment analysis has reflected a conversed gene cluster formed by insert sequence (IS), blaCTX-M-15, and WbuC family cupin-fold metalloprotein, which may potentially jump from the plasmids to the chromosome. Conclusion: The first time we reported the whole genome sequencing (WGS) data of ESBL-producing E. coli including potential pathogen (ST131) present in reservoir water in Singapore. The ESBL-producing E. coli from reservoir water also carrying conjugatable colistin resistance genes which may become a risk to human health.
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Affiliation(s)
- Yang Zhong
- Nanyang Technological University Food Technology Centre (NAFTEC), 62 Nanyang Drive, Singapore 637459, Singapore; (S.G.); (K.L.G.S.); (G.O.H.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
- Correspondence: (Y.Z.); (J.S.)
| | - Siyao Guo
- Nanyang Technological University Food Technology Centre (NAFTEC), 62 Nanyang Drive, Singapore 637459, Singapore; (S.G.); (K.L.G.S.); (G.O.H.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Kelyn Lee Ghee Seow
- Nanyang Technological University Food Technology Centre (NAFTEC), 62 Nanyang Drive, Singapore 637459, Singapore; (S.G.); (K.L.G.S.); (G.O.H.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Glendon Ong Hong Ming
- Nanyang Technological University Food Technology Centre (NAFTEC), 62 Nanyang Drive, Singapore 637459, Singapore; (S.G.); (K.L.G.S.); (G.O.H.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
| | - Joergen Schlundt
- Nanyang Technological University Food Technology Centre (NAFTEC), 62 Nanyang Drive, Singapore 637459, Singapore; (S.G.); (K.L.G.S.); (G.O.H.M.)
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
- Correspondence: (Y.Z.); (J.S.)
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Nachimuthu R, Kannan VR, Bozdogan B, Krishnakumar V, S KP, Manohar P. CTX-M-type ESBL-mediated resistance to third-generation cephalosporins and conjugative transfer of resistance in Gram-negative bacteria isolated from hospitals in Tamil Nadu, India. Access Microbiol 2020; 3:000142. [PMID: 34151148 PMCID: PMC8209704 DOI: 10.1099/acmi.0.000142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/12/2020] [Indexed: 01/28/2023] Open
Abstract
Clinical pathogens, especially Gram-negative bacteria developing resistance to third-generation cephalosporins, are making clinical outcomes more complicated and serious. This study was undertaken to evaluate the distribution of CTX-M-type extended-spectrum β-lactamases (ESBLs) in Tamil Nadu, India. For this study, clinical samples were collected from five different hospitals located in Tamil Nadu and the ESBL-producing Gram-negative isolates were characterized. MIC was performed using cefotaxime and ceftazidime. The blaESBL-producing genes were screened using multiplex PCR for the genes, CTX-M group-1, -2, -8, -9, -26. The conjugation studies were performed using Escherichia coli AB1157 as a recipient for the isolates harbouring plasmid-borne resistance following broth-mating experiment. In total, 1500 samples were collected and 599 Gram-negative bacteria were isolated that included E. coli (n=233), Klebsiella pneumoniae (n=182), Pseudomonas aeruginosa (n=79), Citrobacter spp. (n=30), Proteus mirabilis (n=28), Salmonella spp. (n=21), Acinetobacter baumannii (n=12), Serratia spp. (n=6), Shigella spp. (n=4), Morganella morganii (n=3) and Providencia spp. (n=1). MIC results showed that 358 isolates were resistant to cefotaxime and ceftazidime. Further, ESBL gene-amplification results showed that 19 isolates had CTX-M group-1 gene including E. coli (n=16), K. pneumoniae (n=2) and P. aeruginosa (n=1) whereas one M. morganii isolate had CTX-M group-9, which was plasmid-borne. Through conjugation studies, 12/20 isolates were found to be involved in the transformation of its plasmid-borne resistance gene. Our study highlighted the importance of horizontal gene transfer in the dissemination of plasmid-borne blaCTX-M-type resistance genes among the clinical isolates.
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Affiliation(s)
- Ramesh Nachimuthu
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore-632014, India
| | - Velu Rajesh Kannan
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Bulent Bozdogan
- Medical Faculty, Medical Microbiology Department, Adnan Menderes University, Aydin, Turkey
| | | | - Karutha Pandian S
- Department of Biotechnology, Alagappa university, Karaikudi, Tamil Nadu, India
| | - Prasanth Manohar
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, International Campus, PR China, Haining, Zhejiang.,School of Medicine, The Second Affiliated Hospital Zhejiang University (SAHZU),, Hangzhou, Zhejiang, PR China
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11
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Johnston BD, Thuras PD, Johnson JR. Activity of ceftazidime-avibactam against Escherichia coli isolates from U.S. veterans (2011) in relation to co-resistance and sequence type 131 (ST131) H30 and H30Rx status. Diagn Microbiol Infect Dis 2020; 97:115034. [PMID: 32331800 DOI: 10.1016/j.diagmicrobio.2020.115034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/05/2020] [Indexed: 12/29/2022]
Abstract
Escherichia coli ST131, with its multidrug-resistance-associated H30R1 and H30Rx clonal subsets within the H30R subclone, causes most antimicrobial-resistant E. coli infections. The activity of ceftazidime-avibactam (CZA) against ST131 strains is undefined. We determined CZA MICs for 595 E. coli clinical isolates from 24 Veterans Affairs Medical Centers (2010-2011). Resistance status and MICs were compared with study resistance category (fluoroquinolone-susceptible, fluoroquinolone-resistant, and extended-spectrum beta-lactamase (ESBL)-producing); ST131, H30R1, and H30Rx status; blaCTX-M-15-like genotype; and MICs for piperacillin-tazobactam, levofloxacin, gentamicin, ceftazidime, and meropenem. Proportion resistant ranged from zero (CZA, meropenem) to 61% (levofloxacin). MICs generally increased by resistance category (from fluoroquinolone-susceptible through fluoroquinolone-resistant to ESBL), clonal subgroup (from non-ST131-H30 through H30R1 to H30Rx), and blaCTX-M-15-like status. CZA MICs were slightly but significantly greater in association with resistance (or elevated MICs) to each comparator yet remained in the susceptible range. CZA was reliably active and outperformed noncarbapenem comparators, so it should prove useful as a carbapenem-sparing alternative.
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Affiliation(s)
- Brian D Johnston
- VA Medical Center, Minneapolis, MN; University of Minnesota, Minneapolis, MN.
| | - Paul D Thuras
- VA Medical Center, Minneapolis, MN; University of Minnesota, Minneapolis, MN
| | - James R Johnson
- VA Medical Center, Minneapolis, MN; University of Minnesota, Minneapolis, MN
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12
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Dantas Palmeira J, Ferreira HMN. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world. Heliyon 2020; 6:e03206. [PMID: 32042963 PMCID: PMC7002838 DOI: 10.1016/j.heliyon.2020.e03206] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023] Open
Abstract
Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.
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Affiliation(s)
- Josman Dantas Palmeira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
| | - Helena Maria Neto Ferreira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
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13
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Chen SL, Ding Y, Apisarnthanarak A, Kalimuddin S, Archuleta S, Omar SFS, De PP, Koh TH, Chew KL, Atiya N, Suwantarat N, Velayuthan RD, Wong JGX, Lye DC. The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone. Sci Rep 2019; 9:13245. [PMID: 31519972 PMCID: PMC6744567 DOI: 10.1038/s41598-019-49467-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/24/2019] [Indexed: 01/29/2023] Open
Abstract
The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.
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Affiliation(s)
- Swaine L Chen
- Genome Institute of Singapore, Agency for Science, Technology, and Research, 60 Biopolis Street, Genome #02-01, Singapore, 138672, Singapore. .,Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Singapore.
| | - Ying Ding
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
| | - Anucha Apisarnthanarak
- Division of Infectious Diseases, Faculty of Medicine, Thammasat University Hospital, 95 Phahonyothin Rd, Khlong Nueng, Khlong Luang District, Pathum Thani, 12120, Thailand
| | - Shirin Kalimuddin
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Department of Infectious Diseases, Singapore General Hospital, Academia Level 3, 20 College Road, Singapore, 169856, Singapore
| | - Sophia Archuleta
- Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Singapore.,University Medicine Cluster, Division of Infectious Diseases, National University Hospital, , 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Sharifah Faridah Syed Omar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Partha Pratim De
- Communicable Diseases Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Tse Hsien Koh
- Department of Microbiology, Division of Pathology, Singapore General Hospital, Academia, Diagnostics Tower, Level 7, 20 College Road, Singapore, 169856, Singapore.,Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Kean Lee Chew
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Nadia Atiya
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nuntra Suwantarat
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, 12120, Thailand
| | - Rukumani Devi Velayuthan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Joshua Guo Xian Wong
- Communicable Diseases Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David C Lye
- Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore, 119228, Singapore. .,National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore. .,Communicable Diseases Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, 308433, Singapore. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore.
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14
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Thingholm KR, Hertz FB, Løbner-Olesen A, Frimodt-Møller N, Nielsen KL. Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli. Infect Drug Resist 2019; 12:2429-2435. [PMID: 31496755 PMCID: PMC6689528 DOI: 10.2147/idr.s208536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023] Open
Abstract
Background Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) causing urinary tract infections often belong to sequence type 131 (ST131), serotype O25, carrying bla CTX-M-15. Aim The main aim of this study was to examine the conjugational frequencies of E. coli with plasmids carrying bla CTX-M-15 to E. coli isolates from the fecal flora of healthy humans to determine whether ST131 is more likely to uptake or donate ESBL resistance compared to other E. coli clones. Methods Donors and recipients were all clinical isolates and did not harbor plasmids with identical incompatibility groups (Inc-groups) based on in silico analyses of Inc-groups and restriction/modification systems (R/M-systems). The in vitro conjugation experiments were performed as filter conjugation with verification of transconjugants by random amplified polymorphic DNA (RAPD) PCR and bla CTX-M-15 PCR. Results The frequencies of conjugation with bla CTX-M-15-carrying plasmids were found to be very rare with detectable conjugation frequencies in the range of 4x10-9-7x10-7 transconjugants/recipient. Recipients of O25/ST131 type yielded significantly lower conjugation frequencies compared to recipients of other O-types (P=0.004). The applied ST131/O25 donors did not yield detectable levels of transconjugants regardless of the applied recipient. Presence of sub-MIC levels of ampicillin increased plasmid transfer frequencies x100 fold (P=0.07). Conclusion The results indicate that bla CTX-M-15 is rarely transferred by conjugation to E. coli isolates of the intestinal flora, even when the gene is plasmid-borne.
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Affiliation(s)
| | - Frederik Boëtius Hertz
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark.,Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev 2730, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Section for Functional Genomics and Center for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | | | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark
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15
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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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16
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Lamut A, Peterlin Mašič L, Kikelj D, Tomašič T. Efflux pump inhibitors of clinically relevant multidrug resistant bacteria. Med Res Rev 2019; 39:2460-2504. [PMID: 31004360 DOI: 10.1002/med.21591] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/31/2019] [Accepted: 04/02/2019] [Indexed: 12/29/2022]
Abstract
Bacterial infections are an increasingly serious issue worldwide. The inability of existing therapies to treat multidrug-resistant pathogens has been recognized as an important challenge of the 21st century. Efflux pumps are important in both intrinsic and acquired bacterial resistance and identification of small molecule efflux pump inhibitors (EPIs), capable of restoring the effectiveness of available antibiotics, is an active research field. In the last two decades, much effort has been made to identify novel EPIs. However, none of them has so far been approved for therapeutic use. In this article, we explore different structural families of currently known EPIs for multidrug resistance efflux systems in the most extensively studied pathogens (NorA in Staphylococcus aureus, AcrAB-TolC in Escherichia coli, and MexAB-OprM in Pseudomonas aeruginosa). Both synthetic and natural compounds are described, with structure-activity relationship studies and optimization processes presented systematically for each family individually. In vitro activities against selected test strains are presented in a unifying manner for all the EPIs described, together with the most important toxicity, pharmacokinetic and in vivo efficacy data. A critical evaluation of lead-likeness characteristics and the potential for clinical development of the most promising inhibitors of the three efflux systems is described. This overview of EPIs is a good starting point for the identification of novel effective antibacterial drugs.
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Affiliation(s)
- Andraž Lamut
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Danijel Kikelj
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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17
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis. To date, molecular epidemiological studies have yielded numerous important insights into putative virulence factors, host-pathogen relationships, phylogenetic background, reservoirs, antimicrobial-resistant strains, clinical diagnostics, and transmission pathways of ExPEC, and have delineated areas in which further study is needed. The rapid pace of discovery of new putative virulence factors and the increasing awareness of the importance of virulence factor regulation, expression, and molecular variation should stimulate many future molecular epidemiological investigations. The growing sophistication and availability of molecular typing methodologies, and of the new computational and statistical approaches that are being developed to address the huge amounts of data that whole genome sequencing generates, provide improved tools for such studies and allow new questions to be addressed.
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18
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Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk M, Bugla-Ploskonska G, Choroszy-Krol I. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathog 2019; 11:10. [PMID: 30828388 PMCID: PMC6383261 DOI: 10.1186/s13099-019-0290-0] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/11/2019] [Indexed: 02/07/2023] Open
Abstract
Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and avian pathogenic E. coli (APEC). Virulence factors (VF) related to the pathogenicity of ExPEC are numerous and have a wide range of activities, from those related to bacteria colonization to those related to virulence, including adhesins, toxins, iron acquisition factors, lipopolysaccharides, polysaccharide capsules, and invasins, which are usually encoded on pathogenicity islands (PAIs), plasmids and other mobile genetic elements. Mechanisms underlying the dynamics of ExPEC transmission and the selection of virulent clones are still poorly understood and require further research. The time shift between colonization of ExPEC and the development of infection remains problematic in the context of establishing the relation between consumption of contaminated food and the appearance of first disease symptoms. What appears to be most difficult is to prove that ExPEC strains cause disease symptoms and to examine the mechanism of transition from the asymptomatic colonization of the intestines to the spreading of the bacteria outside the digestive system. A significant problem for researchers who are trying to ascribe ExPEC transmission to food, people or the environment is to draw the distinction between colonization of ExPEC and infection. Food safety is an important challenge for public health both at the production stage and in the course of its processing and distribution. Examination of the genetic similarity of ExPEC strains will allow to determine their origin from different sources. Many levels of genotyping have been proposed in which the typing of strains, plasmids and genes is compared in order to obtain a more complete picture of this complex problem. The aim of our study was to characterize E. coli strains isolated from humans, animals and food for the presence of bacterial genes encoding virulence factors such as toxins, and iron acquisition systems (siderophores) in the context of an increasing spread of ExPEC infections.
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Affiliation(s)
- Jolanta Sarowska
- 1Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland
| | - Bozena Futoma-Koloch
- 2Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agnieszka Jama-Kmiecik
- 1Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland
| | - Magdalena Frej-Madrzak
- 1Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland
| | - Marta Ksiazczyk
- 2Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Gabriela Bugla-Ploskonska
- 2Department of Microbiology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Irena Choroszy-Krol
- 1Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland
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Youssef MM, Rizk HA, Hassuna NA. Phenotypic and Genotypic Characterization of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Asymptomatic Bacteriuria in Pregnancy. Microb Drug Resist 2019; 25:731-738. [PMID: 30676863 DOI: 10.1089/mdr.2018.0088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Asymptomatic bacteriuria (ASB) has been consistently observed in pregnancy. However, there is a paucity of data on the prevalence and characteristics of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in ASB in pregnant women. Therefore, we sought to investigate ESBL-producing and multidrug-resistant Enterobacteriaceae in antenatal women with ASB. Urine samples were collected from 310 asymptomatic pregnant women attending primary antenatal clinics and screened for significant bacteriuria. Isolates of Enterobacteriaceae were phenotypically tested for their ESBL production. ESBL genes (CTX-M, TEM, and SHV genes) were then amplified by polymerase chain reaction (PCR). Multiplex PCRs were used to perform phylogenetic typing of ESBL-producing Escherichia coli isolates and to examine the commonality of sequence type 131 (ST131)-O25b and ST131-O16. A total of 103 (33.2%) pregnant women were positive for significant bacteriuria (80 Enterobacteriaceae). Of these isolates, 32.5% (n = 26) were ESBL producers and had a higher rate of multidrug resistance than non-ESBL producers. Genotypic characterization of ESBL-producing isolates showed that 84.6% had the blaCTX-M gene (blaCTX-M-15 = 77.3%; blaCTX-M-9 = 18.2%). None of the isolates were of the TEM or SHV type. Half of the ESBL-producing E. coli isolates were of the phylogroup B2, and 4 (20%) isolates were of the ST131-O16 clonal subgroup. This study is the first in Egypt to provide evidence for the high prevalence of ESBL-producing Enterobacteriaceae in pregnant women with ASB. It also represents an important step toward genotypic characterization of this resistant form of bacteria, which may be useful for future antimicrobial studies.
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Affiliation(s)
- Mariam M Youssef
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Hazim A Rizk
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
| | - Noha A Hassuna
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
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Barrios-Villa E, Cortés-Cortés G, Lozano-Zaraín P, Arenas-Hernández MMDLP, Martínez de la Peña CF, Martínez-Laguna Y, Torres C, Rocha-Gracia RDC. Adherent/invasive Escherichia coli (AIEC) isolates from asymptomatic people: new E. coli ST131 O25:H4/H30-Rx virotypes. Ann Clin Microbiol Antimicrob 2018; 17:42. [PMID: 30526606 PMCID: PMC6287351 DOI: 10.1186/s12941-018-0295-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/01/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The widespread Escherichia coli clone ST131 implicated in multidrug-resistant infections has been recently reported, the majority belonging to O25:H4 serotype and classified into five main virotypes in accordance with the virulence genes carried. METHODS Pathogenicity Islands I and II (PAI-I and PAI-II) were determined using conventional PCR protocols from a set of four E. coli CTXR ST131 O25:H4/H30-Rx strains collected from healthy donors' stool. The virulence genes patterns were also analyzed and compared them with the virotypes reported previously; then adherence, invasion, macrophage survival and biofilm formation assays were evaluated and AIEC pathotype genetic determinants were investigated. FINDINGS Non-reported virulence patterns were found in our isolates, two of them carried satA, papA, papGII genes and the two-remaining isolates carried cnfI, iroN, satA, papA, papGII genes, and none of them belonged to classical ST131 virotypes, suggesting an endemic distribution of virulence genes and two new virotypes. The presence of PAI-I and PAI-II of Uropathogenic E. coli was determined in three of the four strains, furthermore adherence and invasion assays demonstrated higher degrees of attachment/invasion compared with the control strains. We also amplified intI1, insA and insB genes in all four samples. INTERPRETATION The results indicate that these strains own non-reported virotypes suggesting endemic distribution of virulence genes, our four strains also belong to an AIEC pathotype, being this the first report of AIEC in México and the association of AIEC with healthy donors.
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Affiliation(s)
- Edwin Barrios-Villa
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Gerardo Cortés-Cortés
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Patricia Lozano-Zaraín
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Margarita María de la Paz Arenas-Hernández
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Claudia Fabiola Martínez de la Peña
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Rosa del Carmen Rocha-Gracia
- Benemérita Universidad Autónoma de Puebla, Posgrado en Ciencias Microbiológicas, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Puebla, Mexico
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Occurrence of risk factors and antimicrobial resistance due to genes encoding extended–spectrum β-lactamase (ESBL) – and/or AmpC β-lactamase–producing Escherichia coli isolated from the hospitalised patients. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-00167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Johnston BD, Thuras P, Johnson JR. Activity of ceftolozane-tazobactam against Escherichia coli isolates from U.S. veterans (2011) in relation to co-resistance and sequence type 131 (ST131) H30 and H30Rx status. PLoS One 2018; 13:e0200442. [PMID: 29990385 PMCID: PMC6039045 DOI: 10.1371/journal.pone.0200442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022] Open
Abstract
Background Escherichia coli sequence type 131 (ST131), with its multidrug-resistance-associated H30R1 and H30Rx clonal subsets, causes most antimicrobial-resistant E. coli infections in the U.S., especially among veterans. The activity of ceftolozane-tazobactam (C/T), a new beta-lactamase inhibitor agent, against ST131 strains, and E. coli isolates from veterans, is undefined. Methods We determined broth microdilution MICs for C/T and five comparators–piperacillin-tazobactam (TZP) levofloxacin (LVX), gentamicin (GEN), ceftazidime (CAZ), and meropenem (MEM)–for 595 clinical E. coli isolates, collected in 2011 from 24 Veterans Affairs Medical Centers across the U.S. Categorical resistance and MICs were compared statistically with resistance category (fluoroquinolone-susceptible, fluoroquinolone-resistant, and extended-spectrum beta-lactamase [ESBL]-producing) and with PCR-defined ST131, H30R1, and H30Rx status. Results Resistance prevalence was ≤ 6% for C/T (6%) and MEM (0%), vs. from 8.0% (TZP) to 59% (LVX) for the other comparators. MICs generally increased by resistance category, from fluoroquinolone-susceptible through fluoroquinolone-resistant to ESBL, and by clonal subgroup, from non-ST131-H30 through H30R1 to H30Rx. For each comparator agent except MEM, although a significantly greater fraction of resistant than susceptible isolates were C/T-resistant, only a minority of comparator-resistant isolates were C/T-resistant (i.e., 9% if LEV-resistant, 12% if GEN-resistant, 21% if CAZ-resistant, 38% if TZP-resistant). Conclusions C/T was broadly active against E. coli clinical isolates from veterans, notwithstanding significant variation by resistance category and ST131-H30R1/H30Rx status, outperforming all non-carbapenem comparators. C/T should prove useful as a carbapenem-sparing therapy for multidrug-resistant E. coli ST131 infections, including in veterans.
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Affiliation(s)
- Brian D. Johnston
- VA Medical Center, Minneapolis, MN, United States of America
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Paul Thuras
- VA Medical Center, Minneapolis, MN, United States of America
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, United States of America
| | - James R. Johnson
- VA Medical Center, Minneapolis, MN, United States of America
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail:
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Friedman ND, Levit D, Taleb E, Marcus G, Michaeli L, Broide M, Mengesha B, Zaidenstein R, Lazarovitch T, Dadon M, Kaye KS, Marchaim D. Towards a Definition for Health Care-Associated Infection. Open Forum Infect Dis 2018; 5:ofy116. [PMID: 29942821 PMCID: PMC6007215 DOI: 10.1093/ofid/ofy116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/22/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Health care-associated infection (HcAI) is a term frequently used to describe community-onset infections likely to be caused by multidrug-resistant organisms (MDROs). The most frequently used definition was developed at Duke University Medical Center in 2002 (Duke-2002). Although some professional societies have based management recommendations on Duke-2002 (or modifications thereof), neither Duke-2002 nor other variations have had their performance measured. METHODS A case-control study was conducted at Assaf Harofeh Medical Center (AHMC) of consecutive adult bloodstream infections (BSIs). A multivariable model was used to develop a prediction score for HcAI, measured by the presence of MDRO infection on admission. The performances of this new score and previously developed definitions at predicting MDRO infection on admission were measured. RESULTS Of the 504 BSI patients enrolled, 315 had a BSI on admission and 189 had a nosocomial BSI. Patients with MDRO-BSI on admission (n = 100) resembled patients with nosocomial infections (n = 189) in terms of epidemiological characteristics, illness acuity, and outcomes more than patients with non-MDRO-BSI on admission (n = 215). The performances of both the newly developed score and the Duke-2002 definition to predict MDRO infection on admission were suboptimal (area under the receiver operating characteric curve, 0.76 and 0.68, respectively). CONCLUSIONS Although the term HcAI is frequently used, its definition does not perform well at predicting MDRO infection present on admission to the hospital. A validated score that calculates the risk of MDRO infection on admission is still needed to guide daily practice and improve patient outcomes.
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Affiliation(s)
- N Deborah Friedman
- Departments of Medicine and Infectious Diseases, Barwon Health, Geelong, VIC, Australia
| | - Dana Levit
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Eyal Taleb
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Gil Marcus
- Department of Internal Medicine A, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Leah Michaeli
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Mor Broide
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Bethlehem Mengesha
- Department of Internal Medicine A, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Ronit Zaidenstein
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
- Department of Internal Medicine A, Assaf Harofeh Medical Center, Zerifin, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Tsilia Lazarovitch
- Department of Clinical Microbiology Laboratory, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Mor Dadon
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
| | - Keith S Kaye
- Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - Dror Marchaim
- Unit of Infectious Diseases, Assaf Harofeh Medical Center, Zerifin, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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24
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Moghanni M, Ghazvini K, Farsiani H, Namaei MH, Derakhshan M, Yousefi M, Maragheh A, Jamehdar SA. High prevalence of sequence type 131 isolates producing CTX-M-15 among extended-spectrum β-lactamase-producing Escherichia coli strains in northeast Iran. J Glob Antimicrob Resist 2018; 15:74-78. [PMID: 29807202 DOI: 10.1016/j.jgar.2018.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 05/08/2018] [Accepted: 05/19/2018] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES The recent expansion of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a worldwide problem. The purpose of this study was to investigate the molecular characteristics of ESBL-producing E. coli strains in Mashhad, located in the northeast of Iran. METHODS A total of 455 clinical E. coli isolates were collected at three hospitals in Mashhad between April-September 2015. Antimicrobial susceptibility was determined by the Kirby-Bauer disk diffusion test. The combination disk test was performed for phenotypic detection of ESBLs. PCR was used to screen isolates for ESBL typing. Phylogenetic groups and sequence type 131 (ST131) were determined by multiplex PCR. RESULTS The prevalence of ESBL-producing E. coli among the collected strains was 51.6% (235/455). Among the 235 ESBL-producing strains, 222 (94.5%) tested positive for CTX-M type, whilst 115 (48.9%), 92 (39.1%) and 21 (8.9%) were positive for TEM, OXA and SHV, respectively. Moreover, CTX-M-15 (94.1%; 209/222) was the most common ESBL among E. coli. Based on multiplex PCR, phylogenetic group B2 was predominant (169/235; 71.9%), followed by D (32/235; 13.6%), A (21/235; 8.9%) and B1 (13/235; 5.5%). ST131 was the predominant clonal group among the phylogenetic group B2 isolates (151/169; 89.3%). CONCLUSION The results revealed that an urgent investigation of the source and transmission pathways of the CTX-M-15-B2-ST131 E. coli clone is needed to mitigate this emergent public-health problem.
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Affiliation(s)
- Marzie Moghanni
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran
| | - Hadi Farsiani
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran
| | - Mohammad Hasan Namaei
- Infectious Diseases Research Centre, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Derakhshan
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran
| | - Masoud Yousefi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran
| | - Alimohammad Maragheh
- Medical Laboratory Basic Sciences, 17 Shahrivar Hospital, Iranian Social Security Organization, Mashhad, Iran
| | - Saeid Amel Jamehdar
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Azadi Square, Medical Campus, Mashhad 9177948564, Iran.
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Multi-faceted immunomodulatory and tissue-tropic clinical bacterial isolate potentiates prostate cancer immunotherapy. Nat Commun 2018; 9:1591. [PMID: 29686284 PMCID: PMC5913311 DOI: 10.1038/s41467-018-03900-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/20/2018] [Indexed: 02/06/2023] Open
Abstract
Immune checkpoint inhibitors have not been effective for immunologically "cold" tumors, such as prostate cancer, which contain scarce tumor infiltrating lymphocytes. We hypothesized that select tissue-specific and immunostimulatory bacteria can potentiate these immunotherapies. Here we show that a patient-derived prostate-specific microbe, CP1, in combination with anti-PD-1 immunotherapy, increases survival and decreases tumor burden in orthotopic MYC- and PTEN-mutant prostate cancer models. CP1 administered intra-urethrally specifically homes to and colonizes tumors without causing any systemic toxicities. CP1 increases immunogenic cell death of cancer cells, T cell cytotoxicity, and tumor infiltration by activated CD8 T cells, Th17 T cells, mature dendritic cells, M1 macrophages, and NK cells. CP1 also decreases intra-tumoral regulatory T cells and VEGF. Mechanistically, blocking CP1-recruited T cells from infiltrating the tumor inhibits its therapeutic efficacy. CP1 is an immunotherapeutic tool demonstrating how a tissue-specific microbe can increase tumor immunogenicity and sensitize an otherwise resistant cancer type to immunotherapy.
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Affiliation(s)
- Bente Olesen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
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27
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Chen CM, Ke SC, Li CR, Wu YC, Chen TH, Lai CH, Wu XX, Wu LT. High Diversity of Antimicrobial Resistance Genes, Class 1 Integrons, and Genotypes of Multidrug-ResistantEscherichia coliin Beef Carcasses. Microb Drug Resist 2017; 23:915-924. [DOI: 10.1089/mdr.2016.0223] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Chih-Ming Chen
- Department of Health Food, Chung Chou University of Science and Technology, Changhua, Taiwan
- Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Se-Chin Ke
- Infection Control Office, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Chia-Ru Li
- Department of Medical Research, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Ying-Chen Wu
- Graduate Institute of Veterinary Pathology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Ter-Hsin Chen
- Graduate Institute of Veterinary Pathology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Ho Lai
- Institute of Basic Medical Science, School of Medicine, China Medical University and Hospital, Taichung, Taiwan
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Department of Nursing, Asia University, Taichung, Taiwan
| | - Xin-Xia Wu
- Department of Microbiology, The Institute of Medical Science, China Medical University Hospital, Taichung, Taiwan
| | - Lii-Tzu Wu
- Department of Microbiology, The Institute of Medical Science, China Medical University Hospital, Taichung, Taiwan
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Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ, Chantratita N. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Med 2017; 9:81. [PMID: 28877757 PMCID: PMC5588602 DOI: 10.1186/s13073-017-0471-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. METHODS We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. RESULTS The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. CONCLUSIONS Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.
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Affiliation(s)
- Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Sandra Reuter
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Teemu Kallonen
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Suporn Paksanont
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sharon J Peacock
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.,Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.
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29
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El-Badawy MF, Tawakol WM, Maghrabi IA, Mansy MS, Shohayeb MM, Ashour MS. Iodometric and Molecular Detection of ESBL Production Among Clinical Isolates ofE. coliFingerprinted by ERIC-PCR: The First Egyptian Report Declares the Emergence ofE. coliO25b-ST131clone HarboringblaGES. Microb Drug Resist 2017; 23:703-717. [DOI: 10.1089/mdr.2016.0181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mohamed F. El-Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, Cairo, Egypt
- Department of Pharmaceutical Microbiology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Wael M. Tawakol
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, Cairo, Egypt
| | - Ibrahim A. Maghrabi
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Moselhy S. Mansy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Mohamed M. Shohayeb
- Department of Pharmaceutical Microbiology, College of Pharmacy, Taif University, Taif, Saudi Arabia
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Mohammed S. Ashour
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
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Epidemic Emergence in the United States of Escherichia coli Sequence Type 131- H30 (ST131- H30), 2000 to 2009. Antimicrob Agents Chemother 2017; 61:AAC.00732-17. [PMID: 28533233 DOI: 10.1128/aac.00732-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
The H30 subclone of Escherichia coli sequence type 131 (ST131-H30) has become the leading antimicrobial resistance E. coli lineage in the United States and often exhibits resistance to one or both of the two key antimicrobial classes for treating Gram-negative infections, extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs). However, the timing of and reasons for its recent emergence are inadequately defined. Accordingly, from E. coli clinical isolates collected systematically across the United States by the SENTRY Antimicrobial Surveillance Program in 2000, 2003, 2006, and 2009, 234 isolates were selected randomly, stratified by year, within three resistance categories: (i) ESC-reduced susceptibility, regardless of FQ phenotype (ESC-RS); (ii) FQ resistance, ESC susceptible (FQ-R); and (iii) FQ susceptible, ESC susceptible (FQ-S). Susceptibility profiles, phylogroup, ST, ST131 subclone, and virulence genotypes were determined, and temporal trends and between-variable associations were assessed statistically. From 2000 to 2006, concurrently with the emergence of ESC-RS and FQ-R strains, the prevalence of (virulence-associated) phylogroup B2 among such strains also rose dramatically, due entirely to rapid emergence of ST131, especially H30. By 2009, H30 was the dominant E. coli lineage overall (22%), accounting for a median of 43% of all single-agent and multidrug resistance (68% for ciprofloxacin). H30's emergence increased the net virulence gene content of resistant (especially FQ-R) isolates, giving stable overall virulence gene scores despite an approximately 4-fold expansion of the historically less virulent resistant population. These findings define more precisely the timing and tempo of H30's emergence in the United States, identify possible reasons for it, and suggest potential consequences, including more frequent and/or aggressive antimicrobial-resistant infections.
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Boll EJ, Marti R, Hasman H, Overballe-Petersen S, Stegger M, Ng K, Knøchel S, Krogfelt KA, Hummerjohann J, Struve C. Turn Up the Heat-Food and Clinical Escherichia coli Isolates Feature Two Transferrable Loci of Heat Resistance. Front Microbiol 2017; 8:579. [PMID: 28439262 PMCID: PMC5383660 DOI: 10.3389/fmicb.2017.00579] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Heat treatment is a widely used process to reduce bacterial loads in the food industry or to decontaminate surfaces, e.g., in hospital settings. However, there are situations where lower temperatures must be employed, for instance in case of food production such as raw milk cheese or for decontamination of medical devices such as thermo-labile flexible endoscopes. A recently identified locus of heat resistance (LHR) has been shown to be present in and confer heat resistance to a variety of Enterobacteriaceae, including Escherichia coli isolates from food production settings and clinical ESBL-producing E. coli isolates. Here, we describe the presence of two distinct LHR variants within a particularly heat resistant E. coli raw milk cheese isolate. We demonstrate for the first time in this species the presence of one of these LHRs on a plasmid, designated pFAM21805, also encoding type 3 fimbriae and three bacteriocins and corresponding self-immunity proteins. The plasmid was highly transferable to other E. coli strains, including Shiga-toxin-producing strains, and conferred LHR-dependent heat resistance as well as type 3 fimbriae-dependent biofilm formation capabilities. Selection for and acquisition of this “survival” plasmid by pathogenic organisms, e.g., in food production environments, may pose great concern and emphasizes the need to screen for the presence of LHR genes in isolates.
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Affiliation(s)
- Erik J Boll
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Roger Marti
- Agroscope, Division of Food Microbial Systems, Microbiological Safety of Foods of Animal Origin GroupBern, Switzerland
| | - Henrik Hasman
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | | | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Kim Ng
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Susanne Knøchel
- Department of Food Science, University of CopenhagenCopenhagen, Denmark
| | - Karen A Krogfelt
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Joerg Hummerjohann
- Agroscope, Division of Food Microbial Systems, Microbiological Safety of Foods of Animal Origin GroupBern, Switzerland
| | - Carsten Struve
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
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Namaei MH, Yousefi M, Ziaee M, Salehabadi A, Ghannadkafi M, Amini E, Askari P. First Report of Prevalence of CTX-M-15-Producing Escherichia coli O25b/ST131 from Iran. Microb Drug Resist 2017; 23:879-884. [PMID: 28437226 DOI: 10.1089/mdr.2016.0272] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence of Escherichia coli sequence type 131 (ST131) as a multidrug-resistant and virulent pathogen represents a major challenge to public health globally. Recently, the O25b/ST131 E. coli producing CTX-M-15 with high virulence potential has been reported worldwide, but has received little attention in Iran. This study is the first in Iran to specifically determine the spread of the O25b/ST131 clone producing CTX-M-15 among E. coli isolates belonging to the B2 phylogenetic group. ST131 clone in phylogenetic group B2 was detected based on PCR detection of ST131-specific single-nucleotide polymorphisms in mdh and gyrB. O25b/ST131 E. coli clone was confirmed utilizing O25b/ST131 clone allele-specific PCR for the pabB gene. All group B2 E. coli isolates were characterized based on antibiotic susceptibility, extended-spectrum β-lactamase (ESBL) enzymes, and virulence traits. Our results demonstrated that 38 out of the 154 B2 group isolates (24.7%) were identified as belonging to the ST131 clone. Furthermore, of these, 28 isolates (73.6%) were detected as O25b/ST131 clone. Antibiotic resistance of ST131 E. coli isolates to ciprofloxacin, gentamicin, cefotaxime, and aztreonam was significantly higher than non-ST131 isolates. Almost all of the O25b/ST131 isolates with the ability for ESBL production were reported as CTX-M-15 producing (95.5%). Our results showed that the most prevalent virulence trait in ST131 clone was ompT (94.7%). This study is the first to report the prevalence of the CTX-M-15-producing O25b/ST131 E. coli in Iran. Our findings reinforce the surveillance of dissemination of ST131 E. coli clone as a major drug-resistant pathogen and an important new public health threat.
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Affiliation(s)
- Mohammad Hasan Namaei
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran
| | - Masoud Yousefi
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran .,2 Department of Microbiology, School of Medicine, Birjand University of Medical Sciences , Birjand, Iran
| | - Masoud Ziaee
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran
| | - Alireza Salehabadi
- 2 Department of Microbiology, School of Medicine, Birjand University of Medical Sciences , Birjand, Iran
| | - Malaknaz Ghannadkafi
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran
| | - Elham Amini
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran
| | - Parvin Askari
- 1 Infectious Diseases Research Center, Birjand University of Medical Sciences , Birjand, Iran
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Ulstad CR, Solheim M, Berg S, Lindbæk M, Dahle UR, Wester AL. Carriage of ESBL/AmpC-producing or ciprofloxacin non-susceptible Escherichia coli and Klebsiella spp. in healthy people in Norway. Antimicrob Resist Infect Control 2016; 5:57. [PMID: 28018582 PMCID: PMC5159956 DOI: 10.1186/s13756-016-0156-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/26/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Asymptomatic carriage has been recognised as an important risk factor for infection caused by antibiotic resistant bacteria. A 14% global prevalence of Extended-Spectrum Beta-lactamase (ESBL) carriage was recently reported, but large intra-and interregional variations were observed. We investigated the faecal carriage rates of ESBL-, AmpC-producing and ciprofloxacin non-susceptible Escherichia coli and Klebsiella spp. in healthy Norwegians. METHODS Rectal samples were obtained from 284 volunteers, together with demographic data and information on recent travel history. The rectal samples were screened by selective plating and E. coli and Klebsiella spp. identified using MALDI-TOF. Phenotypic and molecular characterization of resistant isolates was also performed. RESULTS ESBL- or AmpC-producing E. coli and Klebsiella spp. were isolated from 4.9% and 3.2% of the study population, respectively. Carriage of ciprofloxacin non-susceptible isolates was detected in 9.9% of the volunteers. Molecular typing of ESBL/plasmid-mediated AmpC (pAmpC)-producing isolates suggested an allodemic situation rather than the dissemination of a specific clone in the Norwegian community. In concurrence with previous findings, travel to South-East Asia was associated with increased risk of carrying resistant E. coli or Klebsiella spp., highlighting the contribution of factors such as increased global mobility in erasing the boundaries between healthcare and community settings when it comes to spread of resistant bacteria. CONCLUSIONS Overall, our study recognised Norway as a low-incidence country for faecal carriage of resistant bacteria among healthy individuals. Furthermore, our work denoted the importance of healthy humans as a reservoir for transmission of antibiotic resistant E. coli and Klebsiella spp.
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Affiliation(s)
- Charlotte R. Ulstad
- Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Margrete Solheim
- Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Sophie Berg
- Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Morten Lindbæk
- Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Ulf R. Dahle
- Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astrid L. Wester
- Domain for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
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van den Dobbelsteen GPJM, Faé KC, Serroyen J, van den Nieuwenhof IM, Braun M, Haeuptle MA, Sirena D, Schneider J, Alaimo C, Lipowsky G, Gambillara-Fonck V, Wacker M, Poolman JT. Immunogenicity and safety of a tetravalent E. coli O-antigen bioconjugate vaccine in animal models. Vaccine 2016; 34:4152-4160. [PMID: 27395567 DOI: 10.1016/j.vaccine.2016.06.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/10/2016] [Accepted: 06/22/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Extra-intestinal pathogenic Escherichia coli (ExPEC) are major human pathogens; however, no protective vaccine is currently available. We assessed in animal models the immunogenicity and safety of a 4-valent E. coli conjugate vaccine (ExPEC-4V, serotypes O1, O2, O6 and O25 conjugated to Exotoxin A from Pseudomonas aeruginosa (EPA)) produced using a novel in vivo bioconjugation method. METHODS Three doses of ExPEC-4V (with or without aluminum hydroxide) were administered to rabbits (2μg or 20μg per O-antigen, subcutaneously), mice (0.2μg or 2μg per O-antigen, subcutaneously) and rats (0.4μg or 4μg per O-antigen, intramuscularly). Antibody persistence and boostability were evaluated in rats using O6-EPA monovalent conjugate (0.4μg O-antigen/dose, intramuscularly). Toxicity was assessed in rats (16μg total polysaccharide, intramuscularly). Serum IgG and IgM antibodies were measured by ELISA. RESULTS Robust antigen-specific IgG responses were observed in all animal models, with increased responses in rabbits when administered with adjuvant. O antigen-specific antibody responses persisted up to 168days post-priming. Booster immunization induced a rapid recall response. Toxicity of ExPEC-4V when administered to rats was considered to be at the no observed adverse effect level. CONCLUSIONS ExPEC-4V conjugate vaccine showed good immunogenicity and tolerability in animal models supporting progression to clinical evaluation.
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Affiliation(s)
- Germie P J M van den Dobbelsteen
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines and Prevention B.V. (former Crucell Holland B.V.), Part of the Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 4-6, 2333CN Leiden, The Netherlands.
| | - Kellen C Faé
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines and Prevention B.V. (former Crucell Holland B.V.), Part of the Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 4-6, 2333CN Leiden, The Netherlands.
| | - Jan Serroyen
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines and Prevention B.V. (former Crucell Holland B.V.), Part of the Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 4-6, 2333CN Leiden, The Netherlands.
| | - Ingrid M van den Nieuwenhof
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines and Prevention B.V. (former Crucell Holland B.V.), Part of the Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 4-6, 2333CN Leiden, The Netherlands.
| | - Martin Braun
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland.
| | - Micha A Haeuptle
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland; Current address: Molecular Partners AG, Wagistrasse 14, 8952 Zürich-Schlieren, Switzerland.
| | - Dominique Sirena
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland.
| | - Joerg Schneider
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland.
| | - Cristina Alaimo
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland.
| | - Gerd Lipowsky
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland.
| | | | - Michael Wacker
- LimmaTech Biologics (former GlycoVaxyn AG), Grabenstrasse 3, 8952 Schlieren, Switzerland; Current address: Wacker Biotech Consulting, Obere Hönggerstrasse 9a, 8103 Unterengstringen, Switzerland.
| | - Jan T Poolman
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines and Prevention B.V. (former Crucell Holland B.V.), Part of the Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 4-6, 2333CN Leiden, The Netherlands.
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Hefzy EM, Hassuna NA. Fluoroquinolone-Resistant Sequence Type 131 Subgroups O25b and O16 Among Extraintestinal Escherichia coli Isolates from Community-Acquired Urinary Tract Infections. Microb Drug Resist 2016; 23:224-229. [PMID: 27214282 DOI: 10.1089/mdr.2016.0040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The multidrug-resistant sequence type 131 (ST131) Escherichia coli is a spreading epidemiological burden particularly among isolates resistant to fluoroquinolones. We aimed to evaluate the commonality of ST131-O25b and ST131-O16 among fluoroquinolone-resistant E. coli isolates causing community-acquired urinary tract infections (UTIs) at Fayoum University Hospital, in Egypt. Ninety-two fluoroquinolone-resistant E. coli isolates were subjected to multiplex PCR for detection of ST131 of either O25b or O16 subgroups. Positive isolates were then assessed for antimicrobial susceptibility and virulence genotyping. Out of 92 fluoroquinolone-resistant E. coli isolates, 56 (60.9%) isolates were O25b/O16 subgroups of ST131, including 44 (78.6%) ST131-O25b and 12 (21.4%) ST131-O16 subgroups. All the O25b/O16 ST131 isolates were sensitive to meropenem, where ST131-O25b isolates were significantly more resistant to extended spectrum cephalosporins compared to S131-O16 strains. All the O25b/O16 ST131 isolates harbored three or more of the virulence factors associated with extraintestinal pathogenic E. coli status. ST131-O16 showed a significantly higher virulence score than ST131-O25b isolates. Our results bring to highlight the emergence of O25b/O16 ST131 isolates between community acquired UTIs among Egyptian patients. This is the first report for the presence of O16 isolates in Egypt, showing a lower predominance than the O25b subgroup. The high prevalence of O25b/O16 ST131 isolates requires strict stewardship on antimicrobial use, notably fluoroquinolones, to control the endemicity of such emerging multidrug-resistant clone in the community.
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Affiliation(s)
- Enas Mamdouh Hefzy
- 1 Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University , Fayoum, Egypt
| | - Noha Anwar Hassuna
- 2 Department of Microbiology and Immunology, Faculty of Medicine, Minia University , Minia, Egypt
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Nakama R, Shingaki A, Miyazato H, Higa R, Nagamoto C, Hamamoto K, Ueda S, Hachiman T, Touma Y, Miyagi K, Kawahara R, Toyosato T, Hirai I. Current status of extended spectrum β-lactamase-producing Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis in Okinawa prefecture, Japan. J Infect Chemother 2016; 22:281-6. [DOI: 10.1016/j.jiac.2016.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 11/25/2022]
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Hertz FB, Nielsen JB, Schønning K, Littauer P, Knudsen JD, Løbner-Olesen A, Frimodt-Møller N. "Population structure of drug-susceptible,-resistant and ESBL-producing Escherichia coli from community-acquired urinary tract". BMC Microbiol 2016; 16:63. [PMID: 27067536 PMCID: PMC4827192 DOI: 10.1186/s12866-016-0681-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/29/2016] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli is the most common cause of urinary tract infection (UTI). The pathogenic isolates are becoming increasingly resistant to antibiotics; with a worldwide dissemination of resistant sequence types (ST). We characterized three different uropathogenic E. coli populations, from non-hospitalized patients to describe the genetic kinship between resistant and susceptible isolates. We studied the populations by use of multi-locus sequence typing (MLST) and abbreviated-multi locus variable number of tandem repeat analysis (a-MLVA). Urine samples submitted for testing, by general practitioners, were identified at Dept. of Clinical Microbiology at Hvidovre Hospital, Denmark, from Oct. 2011 to July 2012. We included 94 fully susceptible, 94 resistant (non-ESBL) and 98 Extended Spectrum Beta-lactamases- (ESBL)-producing E. coli isolates. Results The ESBL population was dominated vastly by ST131 (51 %), ST38 (9 %) and ST69 (6 %). In the resistant group ST69 (18 %), ST73 (11 %) and ST131 (15 %) were the largest clusters. In the susceptible population more STs and a-MLVA codes were identified compared to the other groups and ST73 and ST95 were found as the only clusters with 16 % and 6 %, respectively. Ninety-eight per cent of the ESBL-producing E. coli isolates were CTX-M-producers. Conclusion ST131 dominated the population of community-associated uropathogenic ESBL-producing E. coli, but was less frequent among non-ESBL-producing E. coli. The fully susceptible E. coli population was a much more diverse group than the resistant and ESBL-producing E. coli populations. Overall, these findings suggest that dominant ESBL-producing lineages are derived from UPEC lineages already established in the general UPEC population. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0681-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederik Boëtius Hertz
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark. .,Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper Boye Nielsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Pia Littauer
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Jenny Dahl Knudsen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
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Johnson JR, Thuras P, Johnston BD, Weissman SJ, Limaye AP, Riddell K, Scholes D, Tchesnokova V, Sokurenko E. The Pandemic H30 Subclone of Escherichia coli Sequence Type 131 Is Associated With Persistent Infections and Adverse Outcomes Independent From Its Multidrug Resistance and Associations With Compromised Hosts. Clin Infect Dis 2016; 62:1529-1536. [PMID: 27025834 DOI: 10.1093/cid/ciw193] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/11/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The H30 subclone within Escherichia coli sequence type 131 (ST131-H30) has emerged rapidly to become the leading antibiotic-resistant E. coli strain. Hypervirulence, multidrug resistance, and opportunism have been proposed as explanations for its epidemic success. METHODS We assessed 1133 consecutive unique E. coli clinical isolates from 5 medical centers (2010-2011) for H30 genotype, which we compared with epidemiological and clinical data extracted from medical records by blinded reviewers. Using univariable and multivariable logistic regression analysis, we explored associations of H30 with underlying host characteristics, clinical presentations, management, and outcomes, adjusting for host characteristics. RESULTS The H30 (n = 107) isolates were associated with hosts who were older, male, locally and systemically compromised, and healthcare and antibiotic exposed. With multivariable adjustment for host factors, H30 lost its numerous significant univariable associations with initial clinical presentation, but remained strongly associated with clinical persistence (odds ratio [OR], 3.47; 95% confidence interval [CI], 1.89-6.37), microbiological persistence (OR, 4.46; 95% CI, 2.38-8.38), subsequent hospital admission (OR, 2.68; 95% CI, 1.35-5.33), and subsequent new infection (OR, 1.73; 95% CI, 1.01-3.00). These host-adjusted associations remained strong even with added adjustment for resistance to the initially prescribed antibiotics, and the adverse outcome associations (subsequent hospital admission, new infection) were independent of clinical and microbiological persistence. CONCLUSIONS In addition to targeting compromised hosts and resisting multiple antibiotics, H30 isolates may have an intrinsic ability to cause highly persistent infections and later adverse outcomes. The basis for these host- and resistance-independent associations is unclear, but they should be considered when managing patients with H30 infections.
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Affiliation(s)
- James R Johnson
- Veterans Affairs Medical Center
- University of Minnesota, Minneapolis
| | - Paul Thuras
- Veterans Affairs Medical Center
- University of Minnesota, Minneapolis
| | - Brian D Johnston
- Veterans Affairs Medical Center
- University of Minnesota, Minneapolis
| | | | | | - Kim Riddell
- Group Health Cooperative, Seattle, Washington
| | - Delia Scholes
- University of Washington
- Group Health Cooperative, Seattle, Washington
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Dautzenberg MJD, Haverkate MR, Bonten MJM, Bootsma MCJ. Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis. BMJ Open 2016; 6:e009971. [PMID: 26988349 PMCID: PMC4800154 DOI: 10.1136/bmjopen-2015-009971] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones. PRIMARY OUTCOME MEASURES A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics. RESULTS The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence. CONCLUSIONS With the currently available data, it cannot be confirmed nor rejected, that E. coli ST131 or K. pneumoniae ST258 are hyperendemic clones.
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Affiliation(s)
- M J D Dautzenberg
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M R Haverkate
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands Faculty of Sciences, Department of Mathematics, Utrecht University, Utrecht, The Netherlands
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Boll EJ, Frimodt-Møller J, Olesen B, Krogfelt KA, Struve C. Heat resistance in extended-spectrum beta-lactamase-producing Escherichia coli may favor environmental survival in a hospital setting. Res Microbiol 2016; 167:345-9. [PMID: 26946311 DOI: 10.1016/j.resmic.2016.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/30/2015] [Accepted: 02/03/2016] [Indexed: 11/16/2022]
Abstract
Nosocomial infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are a major concern worldwide. There is an urgent need to identify bacterial factors promoting survival and persistence of these organisms in the nosocomial environment. Here, we describe the presence of a gene cluster, containing the Clp ATPase ClpK, within a collection of Danish ESBL-producing E. coli isolates. The cluster conferred thermoprotection upon the isolates, and thus might facilitate survival on medical devices exposed to semi-high temperatures in a hospital setting.
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Affiliation(s)
- Erik J Boll
- Department of Microbiology & Infection Control, Statens Serum Institut, Denmark
| | | | - Bente Olesen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Karen A Krogfelt
- Department of Microbiology & Infection Control, Statens Serum Institut, Denmark
| | - Carsten Struve
- Department of Microbiology & Infection Control, Statens Serum Institut, Denmark.
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Sarkar S, Vagenas D, Schembri MA, Totsika M. Biofilm formation by multidrug resistant Escherichia coli ST131 is dependent on type 1 fimbriae and assay conditions. Pathog Dis 2016; 74:ftw013. [PMID: 26940589 DOI: 10.1093/femspd/ftw013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2016] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) has emerged as a pandemic lineage of important multidrug resistant pathogens worldwide. Despite many studies examining the epidemiology of ST131, only a few studies to date have investigated the capacity of ST131 strains to form biofilms. Some of these studies have reported contrasting findings, with no specific ST131 biofilm-promoting factors identified. Here, we examined a diverse collection of ST131 isolates for in vitro biofilm formation in different media and assay conditions, including urine from healthy adult women. We found significant differences among strains and assay conditions, which offers an explanation for the contrasting findings reported by previous studies using a single condition. Importantly, we showed that expression of type 1 fimbriae is a critical determinant for biofilm formation by ST131 strains and that inhibition of the FimH adhesin significantly reduces biofilm formation. We also offer direct genetic evidence for the contribution of type 1 fimbriae in biofilm formation by the reference ST131 strain EC958, a representative of the clinically dominant H30-Rx ST131 subgroup. This is the first study of ST131 biofilm formation in biologically relevant conditions and paves the way for the application of FimH inhibitors in treating drug resistant ST131 biofilm infections.
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Affiliation(s)
- Sohinee Sarkar
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia Australian Infectious Disease Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
| | - Dimitrios Vagenas
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia Australian Infectious Disease Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
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Can F, Kurt-Azap O, Nurtop E, Ispir P, Seref C, Ergonul O. Molecular epidemiology of bloodstream-associated Escherichia coli ST131 H30-Rx subclone infection in a region with high quinolone resistance. J Med Microbiol 2016; 65:306-310. [PMID: 26795934 DOI: 10.1099/jmm.0.000224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bloodstream infections caused by Escherichia coli ST131 and ST131 H30-Rx subclones have emerged worldwide. This study was carried out to evaluate the prevalence of the ST131-Rx subclone and characterize the virulence properties of the Rx isolates among the bloodstream E. coli isolates. A total of 297 non-duplicated E. coli bloodstream isolates were studied. Antibiotic susceptibilities were tested using the disc diffusion method. PCR amplification and sequencing was used to identify ST131 and H30-Rx, the virulence gene, the β-lactamase and virotype. Quinolone resistance among bacteraemic E. coli strains was 51 %, and it was 98 % among E. coli ST131 isolates. The ST131 isolates accounted for 16 % (49) of all isolates and all ST131 isolates belonged to the extraintestinal pathogenic E. coli. The proportion of H30 subclone among the ST131 isolates was 98 %, and 75 % of H30 isolates belonged to the H30-Rx subclone. The prevalence of ST131 increased from 13 to 23 % in 4 years; however, there was a decrease in the ratio of H30-Rx infections. CTX-M-15 was detected in 85 % of ST131 and all of the H30-Rx isolates. The virulence genes associated with adhesion, cell protection, iron uptake and toxins (papA, iha, kpsMTII, iut and sat) were more common in ST131 than in non-ST131 isolates. Most of the ST131 and H30-Rx isolates were of the C virotype. All papA-positive isolates were in virotype C. The E. coli ST131 clone has increased rapidly among bloodstream isolates. However, a decrease in the proportion of the H30-Rx subclone in the quinolone-resistant population suggests the possibility of dissemination of other virulent and quinolone-resistant subclones in hospital settings.
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Affiliation(s)
- Fusun Can
- Koc University, School of Medicine, Clinical Microbiology Department, Istanbul, Turkey
| | - Ozlem Kurt-Azap
- Baskent University, School of Medicine, Department of Infectious Diseases, Ankara, Turkey
| | - Elif Nurtop
- Koc University, School of Medicine, Clinical Microbiology Department, Istanbul, Turkey
| | - Pelin Ispir
- Koc University, School of Medicine, Clinical Microbiology Department, Istanbul, Turkey
| | - Ceren Seref
- Koc University, School of Medicine, Clinical Microbiology Department, Istanbul, Turkey
| | - Onder Ergonul
- Koc University, School of Medicine, Infectious Diseases Department, Istanbul, Turkey
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Activity of Eravacycline against Escherichia coli Clinical Isolates Collected from U.S. Veterans in 2011 in Relation to Coresistance Phenotype and Sequence Type 131 Genotype. Antimicrob Agents Chemother 2015; 60:1888-91. [PMID: 26666925 DOI: 10.1128/aac.02403-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/05/2015] [Indexed: 11/20/2022] Open
Abstract
Eravacycline is a novel broad-spectrum fluorocycline with potent Gram-negative activity, including for multidrug-resistant strains. Among 472 Escherichia coli clinical isolates from 24 Veterans Affairs medical centers (in 2011), divided equally as susceptible versus resistant to fluoroquinolones, broth microdilution eravacycline MICs were distributed unimodally, ranging from 0.03 to 1.0 μg/ml (MIC50 of 0.125 μg/ml, MIC90 of 0.25 μg/ml). Eravacycline MICs were ∼ 2-fold higher among fluoroquinolone-resistant, gentamicin-resistant, multidrug-resistant, and sequence type 131 (ST131) isolates (P < 0.01 for each comparison).
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Relationship between phylogenetic groups, antibiotic resistance and patient characteristics in terms of adhesin genes in cystitis and pyelonephritis isolates of Escherichia coli. Microb Pathog 2015; 89:188-94. [DOI: 10.1016/j.micpath.2015.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 11/23/2022]
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Kakkanat A, Totsika M, Schaale K, Duell BL, Lo AW, Phan MD, Moriel DG, Beatson SA, Sweet MJ, Ulett GC, Schembri MA. The role of H4 flagella in Escherichia coli ST131 virulence. Sci Rep 2015; 5:16149. [PMID: 26548325 PMCID: PMC4637896 DOI: 10.1038/srep16149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/02/2015] [Indexed: 01/04/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug resistant clone associated with urinary tract and bloodstream infections. Most ST131 strains exhibit resistance to multiple antibiotics and cause infections associated with limited treatment options. The largest sub-clonal ST131 lineage is resistant to fluoroquinolones, contains the type 1 fimbriae fimH30 allele and expresses an H4 flagella antigen. Flagella are motility organelles that contribute to UPEC colonisation of the upper urinary tract. In this study, we examined the specific role of H4 flagella in ST131 motility and interaction with host epithelial and immune cells. We show that the majority of H4-positive ST131 strains are motile and are enriched for flagella expression during static pellicle growth. We also tested the role of H4 flagella in ST131 through the construction of specific mutants, over-expression strains and isogenic mutants that expressed alternative H1 and H7 flagellar subtypes. Overall, our results revealed that H4, H1 and H7 flagella possess conserved phenotypes with regards to motility, epithelial cell adhesion, invasion and uptake by macrophages. In contrast, H4 flagella trigger enhanced induction of the anti-inflammatory cytokine IL-10 compared to H1 and H7 flagella, a property that may contribute to ST131 fitness in the urinary tract.
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Affiliation(s)
- Asha Kakkanat
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kolja Schaale
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Duell
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Alvin W Lo
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Danilo G Moriel
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Matthew J Sweet
- Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Glen C Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
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Nyholm O, Halkilahti J, Wiklund G, Okeke U, Paulin L, Auvinen P, Haukka K, Siitonen A. Comparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains. PLoS One 2015; 10:e0135936. [PMID: 26313149 PMCID: PMC4551483 DOI: 10.1371/journal.pone.0135936] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 07/29/2015] [Indexed: 12/15/2022] Open
Abstract
Background Shigatoxigenic Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC) cause serious foodborne infections in humans. These two pathogroups are defined based on the pathogroup-associated virulence genes: stx encoding Shiga toxin (Stx) for STEC and elt encoding heat-labile and/or est encoding heat-stable enterotoxin (ST) for ETEC. The study investigated the genomics of STEC/ETEC hybrid strains to determine their phylogenetic position among E. coli and to define the virulence genes they harbor. Methods The whole genomes of three STEC/ETEC strains possessing both stx and est genes were sequenced using PacBio RS sequencer. Two of the strains were isolated from the patients, one with hemolytic uremic syndrome, and one with diarrhea. The third strain was of bovine origin. Core genome analysis of the shared chromosomal genes and comparison with E. coli and Shigella spp. reference genomes was performed to determine the phylogenetic position of the STEC/ETEC strains. In addition, a set of virulence genes and ETEC colonization factors were extracted from the genomes. The production of Stx and ST were studied. Results The human STEC/ETEC strains clustered with strains representing ETEC, STEC, enteroaggregative E. coli, and commensal and laboratory-adapted E. coli. However, the bovine STEC/ETEC strain formed a remote cluster with two STECs of bovine origin. All three STEC/ETEC strains harbored several other virulence genes, apart from stx and est, and lacked ETEC colonization factors. Two STEC/ETEC strains produced both toxins and one strain Stx only. Conclusions This study shows that pathogroup-associated virulence genes of different E. coli can co-exist in strains originating from different phylogenetic lineages. The possibility of virulence genes to be associated with several E. coli pathogroups should be taken into account in strain typing and in epidemiological surveillance. Development of novel hybrid E. coli strains may cause a new public health risk, which challenges the traditional diagnostics of E. coli infections.
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Affiliation(s)
- Outi Nyholm
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare (THL), Helsinki, Finland
- * E-mail:
| | - Jani Halkilahti
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Gudrun Wiklund
- Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - Uche Okeke
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kaisa Haukka
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare (THL), Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anja Siitonen
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare (THL), Helsinki, Finland
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47
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Variation in resistance traits, phylogenetic backgrounds, and virulence genotypes among Escherichia coli clinical isolates from adjacent hospital campuses serving distinct patient populations. Antimicrob Agents Chemother 2015; 59:5331-9. [PMID: 26100703 DOI: 10.1128/aac.00048-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/10/2015] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the H30 and H30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive E. coli clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The H30 and H30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131 per se, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131, bla CTX-M-15 was confined to H30Rx isolates and other bla CTX-M variants to non-Rx H30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the H30 and H30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive virulence gene associations that may confer fitness advantages over other resistant E. coli.
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48
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Anes J, McCusker MP, Fanning S, Martins M. The ins and outs of RND efflux pumps in Escherichia coli. Front Microbiol 2015; 6:587. [PMID: 26113845 PMCID: PMC4462101 DOI: 10.3389/fmicb.2015.00587] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 05/28/2015] [Indexed: 11/13/2022] Open
Abstract
Infectious diseases remain one of the principal causes of morbidity and mortality in the world. Relevant authorities including the WHO and CDC have expressed serious concern regarding the continued increase in the development of multidrug resistance among bacteria. They have also reaffirmed the urgent need for investment in the discovery and development of new antibiotics and therapeutic approaches to treat multidrug resistant (MDR) bacteria. The extensive use of antimicrobial compounds in diverse environments, including farming and healthcare, has been identified as one of the main causes for the emergence of MDR bacteria. Induced selective pressure has led bacteria to develop new strategies of defense against these chemicals. Bacteria can accomplish this by several mechanisms, including enzymatic inactivation of the target compound; decreased cell permeability; target protection and/or overproduction; altered target site/enzyme and increased efflux due to over-expression of efflux pumps. Efflux pumps can be specific for a single substrate or can confer resistance to multiple antimicrobials by facilitating the extrusion of a broad range of compounds including antibiotics, heavy metals, biocides and others, from the bacterial cell. To overcome antimicrobial resistance caused by active efflux, efforts are required to better understand the fundamentals of drug efflux mechanisms. There is also a need to elucidate how these mechanisms are regulated and how they respond upon exposure to antimicrobials. Understanding these will allow the development of combined therapies using efflux inhibitors together with antibiotics to act on Gram-negative bacteria, such as the emerging globally disseminated MDR pathogen Escherichia coli ST131 (O25:H4). This review will summarize the current knowledge on resistance-nodulation-cell division efflux mechanisms in E. coli, a bacteria responsible for community and hospital-acquired infections, as well as foodborne outbreaks worldwide.
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Affiliation(s)
- João Anes
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Matthew P McCusker
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
| | - Marta Martins
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, UCD Centre for Molecular Innovation and Drug Discovery, University College Dublin Dublin, Ireland
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Pathogenesis of human diffusely adhering Escherichia coli expressing Afa/Dr adhesins (Afa/Dr DAEC): current insights and future challenges. Clin Microbiol Rev 2015; 27:823-69. [PMID: 25278576 DOI: 10.1128/cmr.00036-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pathogenicity and clinical pertinence of diffusely adhering Escherichia coli expressing the Afa/Dr adhesins (Afa/Dr DAEC) in urinary tract infections (UTIs) and pregnancy complications are well established. In contrast, the implication of intestinal Afa/Dr DAEC in diarrhea is still under debate. These strains are age dependently involved in diarrhea in children, are apparently not involved in diarrhea in adults, and can also be asymptomatic intestinal microbiota strains in children and adult. This comprehensive review analyzes the epidemiology and diagnosis and highlights recent progress which has improved the understanding of Afa/Dr DAEC pathogenesis. Here, I summarize the roles of Afa/Dr DAEC virulence factors, including Afa/Dr adhesins, flagella, Sat toxin, and pks island products, in the development of specific mechanisms of pathogenicity. In intestinal epithelial polarized cells, the Afa/Dr adhesins trigger cell membrane receptor clustering and activation of the linked cell signaling pathways, promote structural and functional cell lesions and injuries in intestinal barrier, induce proinflammatory responses, create angiogenesis, instigate epithelial-mesenchymal transition-like events, and lead to pks-dependent DNA damage. UTI-associated Afa/Dr DAEC strains, following adhesin-membrane receptor cell interactions and activation of associated lipid raft-dependent cell signaling pathways, internalize in a microtubule-dependent manner within urinary tract epithelial cells, develop a particular intracellular lifestyle, and trigger a toxin-dependent cell detachment. In response to Afa/Dr DAEC infection, the host epithelial cells generate antibacterial defense responses. Finally, I discuss a hypothetical role of intestinal Afa/Dr DAEC strains that can act as "silent pathogens" with the capacity to emerge as "pathobionts" for the development of inflammatory bowel disease and intestinal carcinogenesis.
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50
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Downing T. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics. Microorganisms 2015; 3:236-67. [PMID: 27682088 PMCID: PMC5023239 DOI: 10.3390/microorganisms3020236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 11/16/2022] Open
Abstract
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)-a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Faculty of Science and Health, Dublin City University, Dublin 9, Ireland.
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