1
|
Aydın E, Kocaaga M, Temel A. Association of antibiotic resistance and biofilm formation in Escherichia coli ST131/O25b. Acta Microbiol Immunol Hung 2024. [PMID: 39037809 DOI: 10.1556/030.2024.02275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Urinary tract infections are becoming difficult to treat every year due to antibiotic resistance. Uropathogenic Escherichia coli (UPEC) isolates pose a threat with a combined expression of multidrug-resistance and biofilm formation. ST131 clone is a high-risk pandemic clone due to its strong association with antimicrobial resistance, which has been reported frequently in recent years. This study aims to define risk factors, clinical outcomes, and bacterial genetics associated with ST131/O25b UPEC. In this study, antibiotic susceptibility and species-level identification of 61 clinical E. coli strains were determined by automated systems. Detection of extended-spectrum beta-lactamases was assessed by double-disk synergy test. Biofilm formation was quantified by spectrophotometric method. Virulence genes (iutA, sfa cnf-1, iroN, afa, papA, fimA), antibiotic resistance genes (blaCTX-M, blaTEM, blaSHV, blaOXA, qnrA, qnrB, qnrS, ant(2')-Ia, ant(3)-Ia, aac(3)-IIa, mcr-1, mcr-2, mcr-3, mcr-4) were investigated by PCR. The following beta-lactamase genes were identified, blaTEM (n = 53, 86.8%), blaCTX-M (n = 59, 96.7%), blaSHV (n = 47, 77.0%), and blaOXA-1 (n = 27, 44.2%). Our data revealed that 93.4% of (57/61) E. coli isolates were biofilm-producers. O25pabBspe and trpA2 were investigated for the presence of ST131/O25b clone. Among multidrug resistant isolates, co-existence of O25pabBspe and trpA2 was detected in 29 isolates (47.5%). The fimH30 and H30Rx subclones were detected in four isolates that are strong biofilm-producers. These results suggest that clinical E. coli strains may become reservoirs of virulence and antibiotic resistance genes. This study demonstrates a significant difference in biofilm formation between E. coli ST131 and non-ST131 isolates. Moreover, 86.21% (n = 25) of ST131 isolates produced strong to moderate biofilms, while only 43.75% (n = 14) of non-ST131 isolates showed the ability to form strong biofilms. Presence of iutA and fimA genes in the majority of ST131 strains showed an important role in biofilm formation. These findings suggest application of iutA and fimA gene suppressors in treatment of infections caused by biofilm-producing drug-resistant ST131 strains.
Collapse
Affiliation(s)
- Elif Aydın
- 1Vocational School of Health Services, Kütahya Health Sciences University, 43100, Kütahya, Turkey
- 2Laboratory of Medical Microbiology, Yunus Emre State Hospital, 26663, Eskişehir, Turkey
| | - Mustafa Kocaaga
- 2Laboratory of Medical Microbiology, Yunus Emre State Hospital, 26663, Eskişehir, Turkey
| | - Aybala Temel
- 3Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Çelebi University, 35620, Izmir, Turkey
| |
Collapse
|
2
|
Hemati S, Halimi S, Jabalameli F, Emaneini M, Beigverdi R. Phylogenetic group, antibiotic resistance, virulence gene, and genetic diversity of Escherichia coli causing bloodstream infections in Iran. Front Microbiol 2024; 15:1426510. [PMID: 39101041 PMCID: PMC11294173 DOI: 10.3389/fmicb.2024.1426510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/09/2024] [Indexed: 08/06/2024] Open
Abstract
Escherichia coli is one of the most important pathogens causing bloodstream infections (BSIs) throughout the world. We sought to characterize the phylogroup classification, major human sequence types (STs), antimicrobial resistance, presence of selected antimicrobial resistance and virulence genes, and genetic diversity of E. coli isolated from patients with BSIs at the University Hospital in Iran. A total of 100 E. coli bloodstream isolates were collected between December 2020 and June 2022. This study used PCR to investigate phylogenetic groups (A, B1, B2, C, D, E, and F), four major STs (ST69, ST73, ST95, and ST131), antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and pathogenicity islands (PAIs). Antimicrobial susceptibility testing was done by disk diffusion method. Genetic diversity was analyzed by repetitive element sequence-based PCR (REP-PCR). The phylogenetic group B2 (32%) predominated, followed by phylogenetic group E (25%). ST131 (28%) was the most prevalent ST and the majority of these isolates (89.3%) were of serotype O25b. Most of E. coli isolates (75%) were categorized as multidrug resistant (MDR) with high rates of resistance (>55%) to ampicillin, trimethoprim-sulfamethoxazole, ciprofloxacin, cefazolin, and ceftriaxone. The most frequent ARGs were bla TEM (66%), sul1 (57%), and sul2 (51%). The most prevalent VAGs and PAIs were fimH (type 1 fimbriae adhesin; 85%), aer (iucC) (aerobactin; 79%), traT (serum resistance; 77%), iutA (aerobactin siderophore receptor; 69%), and PAI IV536 (75%), respectively. The highest rate of ARGs and VAGs was observed in the ST131 isolates. REP-PCR analysis showed high diversity among the studied isolates. The high prevalence of MDR septicemic E. coli with different types of ARGs, VAGs and genotypes is an extremely worrisome sign of BSIs treatment and poses a major threat for hospitalized patients. Active surveillance, stringent prescribing policies, increasing the awareness of ARGs among clinicians and re-defining the infection control measures are essential to curb the dissemination of these strains.
Collapse
Affiliation(s)
| | | | | | | | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Markusková B, Elnwrani S, Andrezál M, Sedláčková T, Szemes T, Slobodníková L, Kajsik M, Drahovská H. Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains. Arch Virol 2024; 169:142. [PMID: 38851653 PMCID: PMC11162368 DOI: 10.1007/s00705-024-06063-x] [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: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024]
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections, and strains that are resistant to antibiotics are a major problem in treating these infections. Phage therapy is a promising alternative approach that can be used to treat infections caused by polyresistant bacterial strains. In the present study, 16 bacteriophages isolated from sewage and surface water were investigated. Phage host specificity was tested on a collection of 77 UPEC strains. The phages infected 2-44 strains, and 80% of the strains were infected by at least one phage. The susceptible E. coli strains belonged predominantly to the B2 phylogenetic group, including strains of two clones, CC131 and CC73, that have a worldwide distribution. All of the phages belonged to class Caudoviricetes and were identified as members of the families Straboviridae, Autographiviridae, and Drexlerviridae and the genera Kagunavirus, Justusliebigvirus, and Murrayvirus. A phage cocktail composed of six phages - four members of the family Straboviridae and two members of the family Autographiviridae - was prepared, and its antibacterial activity was tested in liquid medium. Complete suppression of bacterial growth was observed after 5-22 hours of cultivation, followed by partial regrowth. At 24 hours postinfection, the cocktail suppressed bacterial growth to 43-92% of control values. Similar results were obtained when testing the activity of the phage cocktail in LB and in artificial urine medium. The results indicate that our phage cocktail has potential to inhibit bacterial growth during infection, and they will therefore be preserved in the national phage bank, serving as valuable resources for therapeutic applications.
Collapse
Affiliation(s)
- Barbora Markusková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sulafa Elnwrani
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tatiana Sedláčková
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Szemes
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lívia Slobodníková
- Institute of Microbiology, Faculty of Medicine, Comenius University in Bratislava and University Hospital Bratislava, Bratislava, Slovakia
| | - Michal Kajsik
- University Science Park, Comenius University in Bratislava, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
| |
Collapse
|
4
|
Carrera Páez LC, Olivier M, Gambino AS, Poklepovich T, Aguilar AP, Quiroga MP, Centrón D. Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes. Front Cell Infect Microbiol 2024; 14:1368622. [PMID: 38741889 PMCID: PMC11089171 DOI: 10.3389/fcimb.2024.1368622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.
Collapse
Affiliation(s)
- Laura Camila Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Martin Olivier
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, QC, Canada
| | - Anahí Samanta Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, Instituto Nacional de Enfermedades Infecciosas - La Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Andrea Pamela Aguilar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| |
Collapse
|
5
|
Zhao YC, Sun ZH, Xiao MX, Li JK, Liu HY, Cai HL, Cao W, Feng Y, Zhang BK, Yan M. Analyzing the correlation between quinolone-resistant Escherichia coli resistance rates and climate factors: A comprehensive analysis across 31 Chinese provinces. ENVIRONMENTAL RESEARCH 2024; 245:117995. [PMID: 38145731 DOI: 10.1016/j.envres.2023.117995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND The increasing problem of bacterial resistance, particularly with quinolone-resistant Escherichia coli (QnR eco) poses a serious global health issue. METHODS We collected data on QnR eco resistance rates and detection frequencies from 2014 to 2021 via the China Antimicrobial Resistance Surveillance System, complemented by meteorological and socioeconomic data from the China Statistical Yearbook and the China Meteorological Data Service Centre (CMDC). Comprehensive nonparametric testing and multivariate regression models were used in the analysis. RESULT Our analysis revealed significant regional differences in QnR eco resistance and detection rates across China. Along the Hu Huanyong Line, resistance rates varied markedly: 49.35 in the northwest, 54.40 on the line, and 52.30 in the southeast (P = 0.001). Detection rates also showed significant geographical variation, with notable differences between regions (P < 0.001). Climate types influenced these rates, with significant variability observed across different climates (P < 0.001). Our predictive model for resistance rates, integrating climate and healthcare factors, explained 64.1% of the variance (adjusted R-squared = 0.641). For detection rates, the model accounted for 19.2% of the variance, highlighting the impact of environmental and healthcare influences. CONCLUSION The study found higher resistance rates in warmer, monsoon climates and areas with more public health facilities, but lower rates in cooler, mountainous, or continental climates with more rainfall. This highlights the strong impact of climate on antibiotic resistance. Meanwhile, the predictive model effectively forecasts these resistance rates using China's diverse climate data. This is crucial for public health strategies and helps policymakers and healthcare practitioners tailor their approaches to antibiotic resistance based on local environmental conditions. These insights emphasize the importance of considering regional climates in managing antibiotic resistance.
Collapse
Affiliation(s)
- Yi-Chang Zhao
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China
| | - Zhi-Hua Sun
- International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China; China Pharmaceutical University, Nanjing, Jiangsu, 210009, PR China
| | - Ming-Xuan Xiao
- International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China; China Pharmaceutical University, Nanjing, Jiangsu, 210009, PR China
| | - Jia-Kai Li
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China
| | - Huai-Yuan Liu
- International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China; China Pharmaceutical University, Nanjing, Jiangsu, 210009, PR China
| | - Hua-Lin Cai
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China
| | - Wei Cao
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Medical Laboratory, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Yu Feng
- China Pharmaceutical University, Nanjing, Jiangsu, 210009, PR China
| | - Bi-Kui Zhang
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China.
| | - Miao Yan
- The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China; International Research Center for Precision Medicine, Transformative Technology and Software Services, Hunan, PR China.
| |
Collapse
|
6
|
Peirano G, Castellanos LR, Matsumura Y, Chaffee R, Castañeda-Mogollón D, Pillai DR, Pitout JDD. Clinical validation of loop-mediated isothermal amplification for the detection of Escherichia coli sequence type complex 131. J Clin Microbiol 2024; 62:e0168723. [PMID: 38385692 PMCID: PMC10935629 DOI: 10.1128/jcm.01687-23] [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: 12/13/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
The dissemination of Escherichia coli multidrug-resistant (MDR) STc131 is related to its persistence in the human gastrointestinal tract as efficient gut colonizers. Infection and prevention measures are the cornerstones for preventing STc131 spread. Oral decolonization therapies that target ST131 are being developed. There are no rapid methods available to identify STc131 in human specimens. A loop-mediated isothermal amplification (LAMP) assay (named LAMP-ST131) was developed for the detection of STc131 on well-characterized E. coli isolates and then compared to culture and PCR for urines and stool swabs. With E. coli isolates (n = 720), LAMP-ST131 had a sensitivity (sens) of 100% [95% confidence interval (C.I.) = 98.1-100%)] and a specificity (spec) of 98.9% (95% C.I. = 97.5-99.5%). On urines (n = 550), LAMP-ST131 had a sens of 97.6% (95% C.I. = 89.68-94.33%) and a spec of 92.3% (95% C.I. = 87.68-99.88%), while on stool swabs (n = 278), LAMP-ST131 had a sens of 100% (95% C.I. = 88.7-100%) and a spec of 83.9% (95% C.I. = 78.8-87.9%). LAMP-ST131 detected 10 (urines) and 100 (stool swabs) gene copies/μL. LAMP-ST131 accurately identified STc131 within E. coli isolates and human specimens. The implementation of LAMP-ST131 will aid genomic surveys, enable the rapid implementation of effective infection prevention measures, and identify patients suitable for ST131 decolonization therapies. Such approaches will curb the spread of STc131 and decrease incidence rates of global MDR E. coli infections. IMPORTANCE We developed an accurate non-culture-based loop-mediated isothermal amplification (LAMP) methodology for the detection of (sequence type) STc131 among Escherichia coli isolates and human specimens. The use of LAMP-ST131 for global genomic surveillance studies and to identify patients that are suitable for ST131 decolonization therapies will be important for decreasing multidrug-resistant E. coli infections across the globe.
Collapse
Affiliation(s)
- Gisele Peirano
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | | | | | - Ryan Chaffee
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Dylan R. Pillai
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| |
Collapse
|
7
|
Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [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] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
Collapse
Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
| |
Collapse
|
8
|
de Lagarde M, Fairbrother JM, Archambault M, Dufour S, Francoz D, Massé J, Lardé H, Aenishaenslin C, Paradis ME, Terrat Y, Roy JP. Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada. Front Microbiol 2024; 14:1304678. [PMID: 38304859 PMCID: PMC10830774 DOI: 10.3389/fmicb.2023.1304678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024] Open
Abstract
Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX-M-15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination.
Collapse
Affiliation(s)
- Maud de Lagarde
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
| | - John Morris Fairbrother
- World Organization of Animal Health Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Swine and Poultry Infectious Diseases Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Marie Archambault
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
- Swine and Poultry Infectious Diseases Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Simon Dufour
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David Francoz
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
| | - Jonathan Massé
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Hélène Lardé
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, St. Kitts, St. Kitts and Nevis
| | - Cécile Aenishaenslin
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Centre de recherche en santé publique de l’Université de Montréal et du Centre Intégré Universitaire de Santé et de Service Sociaux (CIUSSS) du Centre-Sud-de-l’Île-de-Montréal, Montréal, QC, Canada
| | - Marie-Eve Paradis
- Association des médecins vétérinaires praticiens du Québec, Saint-Hyacinthe, QC, Canada
| | - Yves Terrat
- Consortium Santé Numérique de l’Université de Montréal, Montréal, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement Front de Recherche du Québec – Nature et Technologie (FRQNT) Op+lait, Saint-Hyacinthe, QC, Canada
| |
Collapse
|
9
|
Romdhani A, Cheriet S, Abbassi MS, Lengliz S, Hynds P, Boutiba-Ben Boubaker I, Landolsi RB. High-risk clonal lineages among extended-spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae from urban and rural stagnant water samples in Tunisia. Acta Microbiol Immunol Hung 2023; 70:304-310. [PMID: 38063903 DOI: 10.1556/030.2023.02120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/25/2023] [Indexed: 12/18/2023]
Abstract
This study sought to investigate the occurrence and subsequently to characterize extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae from urban and rural stagnant water samples during the wet season (December to February) in several regions of northern Tunisia. From 56 stagnant water samples, 14 ESBL-producing Enterobacteriaceae were recovered, including 9 Escherichia coli, 3 Klebsiella pneumoniae, and 2 K. oxytoca. Most isolates were multidrug-resistant, with ESBL production primarily encoded by blaCTX-M-15 (n = 8) and blaCTX-M-1 (n = 4) followed by blaCTX-M-55 (n = 1) and blaTEM-26 (n = 1). One K. pneumoniae isolate co-harbored blaKPC and blaCTX-M-15 genes. Class 1 integrons were detected in 4 isolates, however, sul1, sul2, and aac(6')-Ib-cr genes were detected in eleven, two, and four isolates, respectively. The nine E. coli isolates belonged to seven sequence types namely, B2/ST131 (3 isolates), A/ST164, A/ST10, A/ST224, A/ST38, A/ST155, and A/ST69 (each of them one isolate). The three K. pneumoniae isolates were assigned to three sequence types: ST101, ST405 (harboring CTX-M-15 and KPC), and ST1564. Overall, the phenotypic and genotypic traits of collected isolates mirror the molecular epidemiology of ESBL-producing enterobacteria in Tunisia and highlight the potential role of stagnant water in both urban and rural areas as a reservoir of ESBL-producing Enterobacteriaceae.
Collapse
Affiliation(s)
- Amel Romdhani
- 1University of Tunis El Manar, Institute of Veterinary Research of Tunisia, 1006, Tunis, Tunisia
- 2Manouba University, Laboratory of Biotechnology and Valorization of Bio-Geo-Resources LR11ES31, Higher Institute of Biotechnology of Sidi Thabet, Biotechnopole Sidi Thabet, Ariana, Tunisia
| | - Sarah Cheriet
- 1University of Tunis El Manar, Institute of Veterinary Research of Tunisia, 1006, Tunis, Tunisia
| | - Mohamed Salah Abbassi
- 1University of Tunis El Manar, Institute of Veterinary Research of Tunisia, 1006, Tunis, Tunisia
- 3University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory «Antimicrobial Resistance», LR99ES09, 1006, Tunis, Tunisia
| | - Sana Lengliz
- 1University of Tunis El Manar, Institute of Veterinary Research of Tunisia, 1006, Tunis, Tunisia
- 4Laboratory of Materials, Molecules and Application, Preparatory Institute for Scientific and Technical Studies LR11ES22, University of Carthage, Tunis, Tunisia
| | - Paul Hynds
- 5Environmental Sustainability and Health Institute (ESHI), Technological University Dublin, Grangegorman, Dublin 7, Dublin, Republic of Ireland
| | - Ilhem Boutiba-Ben Boubaker
- 3University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory «Antimicrobial Resistance», LR99ES09, 1006, Tunis, Tunisia
| | - Ramzi Boubaker Landolsi
- 2Manouba University, Laboratory of Biotechnology and Valorization of Bio-Geo-Resources LR11ES31, Higher Institute of Biotechnology of Sidi Thabet, Biotechnopole Sidi Thabet, Ariana, Tunisia
| |
Collapse
|
10
|
Kedišaletše M, Phumuzile D, Angela D, Andrew W, Mae NF. Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review. J Glob Antimicrob Resist 2023; 35:297-306. [PMID: 37879456 DOI: 10.1016/j.jgar.2023.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVES Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends. METHODS A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa. RESULTS One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%. CONCLUSION Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.
Collapse
Affiliation(s)
- Moloto Kedišaletše
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Dube Phumuzile
- Synthetic Biology Center, NextGeneration Health, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Dramowski Angela
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Whitelaw Andrew
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Newton-Foot Mae
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| |
Collapse
|
11
|
Literacka E, Konior M, Izdebski R, Żabicka D, Herda M, Gniadkowski M, Korzeniewski K. High risk of intestinal colonization with ESBL-producing Escherichia coli among soldiers of military contingents in specific geographic regions. Eur J Clin Microbiol Infect Dis 2023; 42:1523-1530. [PMID: 37857920 PMCID: PMC10651695 DOI: 10.1007/s10096-023-04684-9] [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: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
One-hundred Polish soldiers of a contingent in Afghanistan in 2019 were screened for Enterobacterales resistant to newer-generation β-lactams at their departure and return. Seventeen percent were colonized in the gut at the departure, whereas 70% acquired carriage in Afghanistan. The commonest organisms were extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec; 96.6%). All isolates were sequenced and were clonally diverse overall, even within the same sequence type, indicating that independent acquisitions mainly. ESBL-Ec were often multi-drug-resistant. Soldiers stationing in certain regions are at high risk of acquiring resistant bacteria that may cause endogenous infection, be transmitted to vulnerable individuals, and spread resistance genes.
Collapse
Affiliation(s)
- E Literacka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland.
| | - M Konior
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Herda
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - K Korzeniewski
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
| |
Collapse
|
12
|
Salamzade R, McElheny CL, Manson AL, Earl AM, Shaikh N, Doi Y. Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere 2023; 8:e0018423. [PMID: 37581436 PMCID: PMC10597468 DOI: 10.1128/msphere.00184-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/15/2023] [Indexed: 08/16/2023] Open
Abstract
Escherichia coli is the most common cause of urinary tract infections (UTIs) in children, and yet the underlying mechanisms of virulence and antibiotic resistance and the overall population structure of the species is poorly understood within this age group. To investigate whether uropathogenic E. coli (UPEC) from children who developed pyelonephritis carried specific genetic markers, we generated whole-genome sequence data for 96 isolates from children with UTIs. This included 57 isolates from children with either radiologically confirmed pyelonephritis or cystitis and 27 isolates belonging to the well-known multidrug-resistant sequence type ST131, selected to investigate their population structure and antibiotic resistance characteristics. We observed a UPEC population structure that is similar to those reported in adults. In comparison with prior investigations, we found that the full pap operon was more common among UPEC from pediatric cases of pyelonephritis. Further, in contrast with recent reports that the P-fimbriae adhesin-encoding papGII allele is substantially more prevalent in invasive UPEC from adults, we found papGII was common to both invasive and non-invasive UPEC from children. Among the set of ST131 isolates from children with UTIs, we found antibiotic resistance was correlated with known genetic markers of resistance, as in adults. Unexpectedly, we observed that fimH30, an allele of the fimbrial gene fimH often used as a proxy to type ST131 isolates into the most drug-resistant subclade C, was carried by some of the subclade A and subclade B isolates, suggesting that the fimH30 allele could confer a selective advantage for UPEC. IMPORTANCE Urinary tract infections (UTIs), which are most often caused by Escherichia coli, are not well studied in children. Here, we examine genetic characteristics that differentiate UTI-causing bacteria in children that either remain localized to the bladder or are involved in more serious kidney infections. We also examine patterns of antibiotic resistance among strains from children that are part of E. coli sequence type 131, a group of bacteria that commonly cause UTIs and are known to have high levels of drug resistance. This work provides new insight into the virulence and antibiotic resistance characteristics of the bacteria that cause UTIs in children.
Collapse
Affiliation(s)
- Rauf Salamzade
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abigail L. Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Nader Shaikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Fujita Health University School of Medicine, Aichi, Japan
| |
Collapse
|
13
|
Amato HK, Loayza F, Salinas L, Paredes D, García D, Sarzosa S, Saraiva-Garcia C, Johnson TJ, Pickering AJ, Riley LW, Trueba G, Graham JP. Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador. Sci Rep 2023; 13:14854. [PMID: 37684276 PMCID: PMC10491794 DOI: 10.1038/s41598-023-39532-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/26/2023] [Indexed: 09/10/2023] Open
Abstract
The coronavirus 2019 (COVID-19) pandemic has had significant impacts on health systems, population dynamics, public health awareness, and antibiotic stewardship, which could affect antibiotic resistant bacteria (ARB) emergence and transmission. In this study, we aimed to compare knowledge, attitudes, and practices (KAP) of antibiotic use and ARB carriage in Ecuadorian communities before versus after the COVID-19 pandemic began. We leveraged data collected for a repeated measures observational study of third-generation cephalosporin-resistant E. coli (3GCR-EC) carriage among children in semi-rural communities in Quito, Ecuador between July 2018 and September 2021. We included 241 households that participated in surveys and child stool sample collection in 2019, before the pandemic, and in 2021, after the pandemic began. We estimated adjusted Prevalence Ratios (aPR) and 95% Confidence Intervals (CI) using logistic and Poisson regression models. Child antibiotic use in the last 3 months declined from 17% pre-pandemic to 5% in 2021 (aPR: 0.30; 95% CI 0.15, 0.61) and 3GCR-EC carriage among children declined from 40 to 23% (aPR: 0.48; 95% CI 0.32, 0.73). Multi-drug resistance declined from 86 to 70% (aPR: 0.32; 95% CI 0.13; 0.79), the average number of antibiotic resistance genes (ARGs) per 3GCR-EC isolate declined from 9.9 to 7.8 (aPR of 0.79; 95% CI 0.65, 0.96), and the diversity of ARGs was lower in 2021. In the context of Ecuador, where COVID-19 prevention and control measures were strictly enforced after its major cities experienced some of the world's the highest mortality rates from SARS-CoV-2 infections, antibiotic use and ARB carriage declined in semi-rural communities of Quito from 2019 to 2021.
Collapse
Affiliation(s)
- Heather K Amato
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA.
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Diana Paredes
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Daniela García
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Soledad Sarzosa
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Carlos Saraiva-Garcia
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Amy J Pickering
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Jay P Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, USA
| |
Collapse
|
14
|
Tickler IA, Kawa D, Obradovich AE, Fang FC, Tenover FC. Characterization of Carbapenemase- and ESBL-Producing Gram-Negative Bacilli Isolated from Patients with Urinary Tract and Bloodstream Infections. Antibiotics (Basel) 2023; 12:1386. [PMID: 37760683 PMCID: PMC10525328 DOI: 10.3390/antibiotics12091386] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
A total of 199 Gram-negative bacterial isolates from urinary tract infections and 162 from bloodstream infections were collected from 12 healthcare systems throughout the United States between May 2021 and August 2022. The isolates, phenotypically non-susceptible to 2nd or 3rd generation cephalosporins or carbapenems, were characterized through antimicrobial susceptibility testing and whole genome sequence analysis to obtain a broad snapshot of beta-lactamase-mediated resistance among these two sample types. Overall, 23 different carbapenemase genes were detected among 13 species (20.5% of isolates). The blaKPC-3 and blaKPC-2 subtypes were the most common carbapenemase genes identified, followed by blaNDM and the co-carriage of two different blaOXA carbapenemases by Acinetobacter baumannii isolates. All carbapenemase-producing A. baumannii isolates were mCIM negative. Extended-spectrum beta-lactamase genes were identified in 66.2% of isolates; blaCTX-M-15 was the most common. AmpC genes, both plasmid and chromosomal, were detected in 33.2% of isolates. Importantly, 2.8%, 8.3%, and 22.2% of blaKPC-positive organisms were susceptible to ertapenem, imipenem, and meropenem, respectively. The correlation between broth microdilution and disk diffusion results was high for most drugs except cefepime, where the detection of resistance was statistically lower by disk diffusion. Thus, there were gaps in the accuracy of susceptibility testing for some mechanisms of resistance.
Collapse
Affiliation(s)
| | | | - Anne E. Obradovich
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Ferric C. Fang
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Fred C. Tenover
- College of Arts & Sciences, University of Dayton, Dayton, OH 45469, USA
| | | |
Collapse
|
15
|
López-Siles M, Moure Z, Muadica AS, Sánchez S, Cruces R, Ávila A, Lara N, Köster PC, Dashti A, Oteo-Iglesias J, Carmena D, McConnell MJ. Fecal carriage of extended-spectrum beta-lactamase-producing Enterobacterales in healthy Spanish schoolchildren. Front Microbiol 2023; 14:1035291. [PMID: 37362938 PMCID: PMC10288999 DOI: 10.3389/fmicb.2023.1035291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Background Extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) are a serious threat among emerging antibiotic resistant bacteria. Particularly, the number of cases of ESBL-E infections reported in children has been increasing in recent years, and approved antibiotic treatments for this age group are limited. However, information regarding the prevalence of colonization in European children, risk factors associated with colonization, and the characteristics of the colonizing strains is scarce. The aims of this study were to determine the prevalence of ESBL-E colonization in fecal samples of apparently healthy schoolchildren, to identify lifestyle routines associated with colonization, and to characterize clonal relationships and mechanisms of resistance in ESBL-E isolates. Methods A cohort of 887 healthy children (3-13 years old) from seven primary and secondary schools in the Madrid metropolitan area was recruited between April-June 2018, and sociodemographic information and daily habits were collected. Fecal samples were screened for ESBL-E carriage in selective medium. ESBL-E isolates were further characterized by assessing molecular epidemiology (PFGE and MLST), ESBL gene carriage, and antibiotic resistance profile. This information was analyzed in conjunction with the metadata of the participants in order to identify external factors associated with ESBL-E carriage. Results Twenty four ESBL-E, all but one Escherichia coli, were detected in 23 children (prevalence: 2.6%; 95% CI: 1.6-3.6%). Of these, seven contained the blaCTX-M-14 allele, five the blaCTX-M-15, five the blaSHV-12, three the blaCTX-M-27, three the blaCTX-M-32, and one the blaCTX-M-9. Significant clonal diversity was observed among the isolates that grouped into 22 distinct clusters (at <85% similarity of PFGE profile). ESBL-producing E. coli isolates belonged to 12 different STs, with ST10 (25%) and ST131 (17%) being the most frequent. Apart from ß-lactams, resistance to trimethoprim/sulfamethoxazole (46%), ciprofloxacin (33%), levofloxacin (33%), tobramycin (21%), and gentamicin (8%) were the most frequently detected. Conclusion The prevalence of ESBL-E in the studied cohort of children was lower than the average colonization rate previously detected in Europe for both children and adults. E. coli was the main ESBL-producing species detected and CTX-M were the most frequently identified ESBLs. High ST diversity suggests polyclonal dissemination. Compared to other STs, ST131 isolates were associated with resistance to various antimicrobials.
Collapse
Affiliation(s)
- Mireia López-Siles
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Serra Húnter Fellow, Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, Girona, Spain
| | - Zaira Moure
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria, (IDIVAL), Santander, Spain
| | - Aly Salimo Muadica
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Ciências e Tecnologia, Universidade Licungo, Quelimane, Mozambique
| | - Sergio Sánchez
- Reference and Research Laboratory of Food and Waterborne Bacterial Infections, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Cruces
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Alicia Ávila
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pamela Carolina Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Michael J. McConnell
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
16
|
Celebi D, Aydın E, Rakici E, Baser S, Celebi O, Taghizadehghalehjoughi A. Evaluation of presence of clone ST131 and biofilm formation in ESBL producing and non-producing Escherichia coli strains. Mol Biol Rep 2023:10.1007/s11033-023-08532-z. [PMID: 37256442 DOI: 10.1007/s11033-023-08532-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Escherichia coli ST131 is a pandemic clone associated with multidrug resistance, starting with beta-lactamase production and fluoroquinolone resistance in the first place, leading to significant systemic infections. Clones that develop due to the frequency of antimicrobial resistance and the rate of spread in our country are important issues that need to be investigated. This study aims to investigate the incidence of ST131which is a "high-risk pandemic clone E. coli" in ESBL-producing and non-ESBL-producing strains, as well as their biofilm-forming abilities and antibiotic resistance rates. MATERIALS AND METHODS A total of 86 E. coli isolates were used in the study. Bacterial identifications were performed by conventional and automated methods. The double disc synergy method was used to demonstrate the presence of ESBL. Molecular studies in all E. coli strains were performed by real-time PCR method. FINDINGS 86 strains were studied, of which 83.72% were urine, 6.98% were wound, 4.65% were blood, and 2.33% were tracheal aspirate and sputum. 79.07% of these strains were ESBL-positive. 58.1% of the strains were female, whereas 41.9% were male patients, and the average age was 46.2. Out of 86 strains, 38.72% were ST131 positive, the H30 subclone was detected in 27.27% of them, and the H30-Rx subclone was detected in all of the H30 subclone positive strains. The presence of the ESBL resistance gene was detected at the rate of TEM 41.86%, SHV 37.21%, CTX-M 36.04%, and OXA 4.65%. Most commonly SHV gene (54.54%) was seen in ST131 clone-positive samples. Finally, while it was found that 48.83% of the strains formed biofilm by any method, biofilm formation was detected in 69.7% of the samples that were positive for the ST131 clone. RESULT Our study can reveal the dramatic prevalence of the ESBL-producing E. coli strains along with the high-risk ST131 clone, the dominance of the H30Rx subclone of this risky clone, as well as the importance of the influence of resistance mechanisms along with resistance and biofilm.
Collapse
Affiliation(s)
- Demet Celebi
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, 25240, Erzurum, Turkey.
- Ataturk University Vaccine Application, and Development Center, Ataturk University, 25240, Erzurum, Turkey.
| | - Elif Aydın
- Tavsanli Vocational School of Health Services, Kutahya Health Sciences University, 430200, Kutahya, Turkey
| | - Erva Rakici
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey
| | - Sumeyye Baser
- Department of Medical Microbiology, Faculty of Medicine, Ataturk University, 25240, Erzurum, Turkey
| | - Ozgur Celebi
- Department of Medical Microbiology, Faculty of Medicine, Ataturk University, 25240, Erzurum, Turkey
| | - Ali Taghizadehghalehjoughi
- Department of Medical Pharmacology, Faculty of Medicine, Şeyh Edebali University, 11000, Bilecik, Turkey
| |
Collapse
|
17
|
Aljohani RH, ElFeky DS, Alswaji AA, Alrashidi E, Okdah L, Alalwan B, Aljohani SM, Balkhy HH, Redhwan A, Alghoribi MF. Genomic Characterization of Uropathogenic Escherichia coli Isolates from Tertiary Hospitals in Riyadh, Saudi Arabia. Int J Mol Sci 2023; 24:7582. [PMID: 37108743 PMCID: PMC10141978 DOI: 10.3390/ijms24087582] [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: 02/25/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infections (UTIs) in hospitalised and non-hospitalised patients. Genomic analysis was used to gain further insight into the molecular characteristics of UPEC isolates from Saudi Arabia. A total of 165 isolates were collected from patients with UTIs between May 2019 and September 2020 from two tertiary hospitals in Riyadh, Saudi Arabia. Identification and antimicrobial susceptibility testing (AST) were performed using the VITEK system. Extended-spectrum β-lactamase (ESBL)-producing isolates (n = 48) were selected for whole genome sequencing (WGS) analysis. In silico analysis revealed that the most common sequence types detected were ST131 (39.6%), ST1193 (12.5%), ST73 (10.4%), and ST10 (8.3%). Our finding showed that blaCTX-M-15 gene was detected in the majority of ESBL isolates (79.2%), followed by blaCTX-M-27 (12.5%) and blaCTX-M-8 (2.1%). ST131 carried blaCTX-M-15 or blaCTX-M-27, and all ST73 and ST1193 carried blaCTX-M-15. The relatively high proportion of ST1193 in this study was notable as a newly emerged lineage in the region, which warrants further monitoring.
Collapse
Affiliation(s)
- Rawan H. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Dalia S. ElFeky
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Abdulrahman A. Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Eisa Alrashidi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Bassam Alalwan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Sameera M. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
| | | | - Alya Redhwan
- Department of Health, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
| |
Collapse
|
18
|
Mohapatra S, Ghosh D, Vivekanandan P, Chunchanur S, Venugopal S, Tak V, Panigrahy R, Chaudhuri S, Pundir S, Sharma T, Kocher D, Singh H, Gautam H, Sood S, Das BK, Kapil A, Kumar A, Kumari R, Kalaivani M, Rangaiah A, Salve HR, Malhotra S, Kant S, Hari P. Genome profiling of uropathogenic E. coli from strictly defined community-acquired UTI in paediatric patients: a multicentric study. Antimicrob Resist Infect Control 2023; 12:36. [PMID: 37072773 PMCID: PMC10114455 DOI: 10.1186/s13756-023-01233-z] [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: 12/22/2022] [Accepted: 03/22/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Urinary tract infection (UTI) in children is a common bacterial infection. The emergence of extended-spectrum beta-lactamases (ESBLs) poses a major challenge against the treatment of uropathogens. We aimed to characterize the E. coli isolates recovered from children with UTI for their resistance profile and circulating sequence types (ST). METHODS Children (> 1.5-18 years of age) from different community health centres of India with symptoms of UTI were enrolled. Isolates causing significant bacteriuria were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility by the automated system, VITEK-2 (Biomeriux, Durhum, US). Nineteen E. coli isolates (15 ESBL positive and 4 ESBL negative) were sequenced in Oxford Nanopore platform followed by core-genome phylogeny, accessory genome cluster analysis, identification of sequence types, mobile genetic elements, genetic antimicrobial resistance markers. The correlation between detection of antimicrobial resistance genes with phenotypic resistance profiles was also investigated. RESULTS Eleven percent of children had significant bacteriuria [male:female-1:1, > 50% were 11-18 years of age group]. E. coli was predominant (86%) followed by K. pneumoniae (11%). Susceptibility of E. coli was highest against fosfomycin (100%) followed by carbapenems (90.7%) and nitrofurantoin (88.8%). ST131 (15.8%) and ST167 (10.5%) found as high-risk clones with the presence of plasmid [IncFIB (63.1%), IncFIA (52.6%)], and composite transposon [Tn2680 (46.6%)] in many isolates. Few isolates coharboured multiple beta-lactamases including blaNDM-5 (33.3%), blaOXA-1 (53.3%), blaCTX-M-15 (60%) and blaTEM-4 (60%). CONCLUSIONS This study highlights horizontal transmission of resistance genes and plasmids in paediatric patients at community centers across the nation harbouring multidrug-resistant genes such as blaNDM-5 and blaCTX-M-15 associated with high-risk clones ST131 and ST167. The data is alarming and emphasizes the need for rapid identification of resistance markers to reduce the spread in community. To our knowledge, this is the first multicentric study targeting paediatric UTI patients from the community setting of India.
Collapse
Affiliation(s)
| | - Dipannita Ghosh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Sneha Chunchanur
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, India
| | - Shwetha Venugopal
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, India
| | - Vibhor Tak
- Department of Microbiology, AIIMS, Jodhpur, India
| | | | - Susmita Chaudhuri
- Translational Health Science and Technology Institute, Faridabad, India
| | - Swati Pundir
- Department of Microbiology, AIIMS, New Delhi, India
| | - Tanya Sharma
- Department of Biomedical Informatics, ICMR, New Delhi, India
| | | | - Harpreet Singh
- Department of Biomedical Informatics, ICMR, New Delhi, India
| | | | - Seema Sood
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Arti Kapil
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Rajesh Kumari
- Department of Obstetrics and Gynaecology, AIIMS, New Delhi, India
| | | | - Ambica Rangaiah
- Department of Microbiology, Bangalore Medical College and Research Institute, Bengaluru, India
| | | | | | - Shashi Kant
- Centre for Community Medicine, AIIMS, New Delhi, India
| | - Pankaj Hari
- Department of Paediatrics, AIIMS, New Delhi, India
| |
Collapse
|
19
|
Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
Collapse
Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
| | | |
Collapse
|
20
|
Pitout JDD, Chen L. The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli. Infect Dis Ther 2023; 12:1029-1041. [PMID: 36947392 PMCID: PMC10147871 DOI: 10.1007/s40121-023-00791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.
Collapse
Affiliation(s)
- Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.
- Dynacare Laboratories, Alberta, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| |
Collapse
|
21
|
ESBL Displace: A Protocol for an Observational Study to Identify Displacing Escherichia coli Strain Candidates from ESBL-Colonized Travel Returners Using Phenotypic, Genomic Sequencing and Metagenome Analysis. MICROBIOLOGY RESEARCH 2023. [DOI: 10.3390/microbiolres14010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Introduction: Invading extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-PE), non-ESBL E. coli, and other bacteria form a complex environment in the gut. The duration and dynamics of ESBL-PE colonization varies among individuals. Understanding the factors associated with colonization may lead to decolonization strategies. In this study, we aim to identify (i) single E. coli strains and (ii) microbiome networks that correlate with retention or decline of colonization, and (iii) pan-sensitive E. coli strains that potentially could be used to displace ESBL-PE during colonization. Methods and analysis: We recruit healthy travellers to Southeast Asia for a one-year prospective observational follow-up study. We collect and biobank stool, serum, and peripheral blood mononuclear cells (PBMCs) at predefined timepoints. Additional information is collected with questionnaires. We determine the colonization status with ESBL-PE and non-ESBL E. coli and quantify cell densities in stools and ratios over time. We characterize multiple single bacterial isolates per patient and timepoint using whole genome sequencing (WGS) and 16S/ITS amplicon-based and shotgun metagenomics. We determine phylogenetic relationships between isolates, antimicrobial resistance (AMR; phenotypic and genotypic), and virulence genes. We describe the bacterial and fungal stool microbiome alpha and beta diversity on 16S/ITS metagenomic data. We describe patterns in microbiome dynamics to identify features associated with protection or risk of ESBL-PE colonization. Ethics and dissemination: The study is registered (clinicaltrials.gov; NCT04764500 on 09/02/2019) and approved by the Ethics Committee (EKNZ project ID 2019-00044). We will present anonymized results at conferences and in scientific journals. Bacterial sequencing data will be shared via publicly accessible databases according to FAIR principles.
Collapse
|
22
|
Neffe L, Forde TL, Oravcova K, Köhler U, Bautsch W, Tomasch J, Häussler S. Genomic epidemiology of clinical ESBL-producing Enterobacteriaceae in a German hospital suggests infections are primarily community- and regionally-acquired. Microb Genom 2022; 8:mgen000901. [PMID: 36748515 PMCID: PMC9837565 DOI: 10.1099/mgen.0.000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Clinical Enterobacteriaceae isolates that produce extended-spectrum β-lactamases (ESBLs) have been increasingly reported at a global scale. However, comprehensive data on the molecular epidemiology of ESBL-producing strains are limited and few studies have been conducted in non-outbreak situations.We used whole-genome sequencing to describe the population structure of 294 ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates that were recovered from a German community hospital throughout a 1 year sampling period in a non-outbreak situation.We found a high proportion of E. coli isolates (61.5 %) belonged to the globally disseminated extraintestinal pathogenic ST131, whereas a wider diversity of STs was observed among K. pneumoniae isolates. The E. coli ST131 population in this study was shaped by multiple introductions of strains as demonstrated by contextual genomic analysis including ST131 strains from other geographical sources. While no recent common ancestor of the isolates of the current study and other international isolates was found, our clinical isolates clustered with those previously recovered in the region. Furthermore, we found that the isolation of ESBL-producing clinical strains in hospitalized patients could only rarely be associated with likely patient-to-patient transmission, indicating primarily a community and regional acquisition of strains.Further genomic analyses of clinical, carriage and environmental isolates is needed to uncover hidden transmissions and thus discover the most common sources of ESBL-producing pathogen infections in our hospitals.
Collapse
Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ute Köhler
- Städtisches Klinikum Braunschweig gGmbH, Germany
| | | | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany,Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany,*Correspondence: Susanne Häussler,
| |
Collapse
|
23
|
Pérez-Etayo L, González D, Vitas AI. Clonal Complexes 23, 10, 131 and 38 as Genetic Markers of the Environmental Spread of Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli. Antibiotics (Basel) 2022; 11:1465. [PMID: 36358120 PMCID: PMC9686695 DOI: 10.3390/antibiotics11111465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
In accordance with the global action plan on antimicrobial resistance adopted by the World Health Assembly in 2015, there is a need to develop surveillance programs for antimicrobial resistant bacteria. In this context, we have analyzed the clonal diversity of Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from aquatic environments and human and food samples in Spain, with the aim of determining possible clonal complexes (CCs) that act as markers of the potential risk of transmission of these resistant bacteria. The phylogenetic groups, sequence types (STs) and CCs were determined by different Polymerase Chain Reaction (PCR) and Multilocus Sequence Typing (MLST) techniques. Phylogroup A was prevalent and was mainly present in food and water strains, while human strains were mostly associated with phylogroup B2. According to the observed prevalence in the different niches, CC23 and CC10 are proposed as markers of phylogroups A and C, related with the spread of blaCTX-M1 and blaCTX-M15 genes. Similarly, CC131 and CC38 could be associated to the dissemination of pathogenic strains (phylogroups B2 and D) carrying mainly blaCTX-M14 and blaCTX-M15 genes. Some strains isolated from wastewater treatment plants (WWTPs) showed identical profiles to those isolated from other environments, highlighting the importance that water acquires in the dissemination of bacterial resistance. In conclusion, the detection of these genetic markers in different environments could be considered as an alert in the spread of ESBL.
Collapse
Affiliation(s)
- Lara Pérez-Etayo
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| |
Collapse
|
24
|
Balbuena-Alonso MG, Cortés-Cortés G, Kim JW, Lozano-Zarain P, Camps M, Del Carmen Rocha-Gracia R. Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid 2022; 123-124:102650. [PMID: 36130651 PMCID: PMC10896638 DOI: 10.1016/j.plasmid.2022.102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.
Collapse
Affiliation(s)
- María G Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico; Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico.
| |
Collapse
|
25
|
Mushtaq S, Garello P, Vickers A, Woodford N, Livermore DM. Activity of ertapenem/zidebactam (WCK 6777) against problem Enterobacterales. J Antimicrob Chemother 2022; 77:2772-2778. [PMID: 35972407 PMCID: PMC9384802 DOI: 10.1093/jac/dkac280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Background Secondary healthcare will remain pressured for some years, both because SARS-CoV-2 will circulate as a nosocomial pathogen, and owing to backlogs of patients awaiting delayed elective procedures. These stresses will drive the use of Outpatient Parenteral Antibiotic Therapy (OPAT), which will need to cover increasingly resistant Gram-negative opportunists. We evaluated the activity of ertapenem/zidebactam, proposed for 2 + 2 g q24h administration. Materials and methods MICs were determined, by BSAC agar dilution, for 1632 Enterobacterales submitted to the UK national reference laboratory for investigation of antimicrobial resistance. Results Over 90% of Escherichia coli with AmpC, ESBLs, KPC, metallo- or OXA-48 carbapenemases were inhibited by ertapenem/zidebactam 1:1 at ertapenem’s current 0.5 mg/L breakpoint. For other major Enterobacterales, the proportions inhibited by ertapenem/zidebactam 1:1 at 0.5 mg/L were mostly 65% to 90% but were lower for Klebsiella pneumoniae/oxytoca with metallo- or OXA-48 β-lactamases. However, animal studies support an 8 mg/L breakpoint for ertapenem/zidebactam, based on a shortened T>MIC being needed compared with ertapenem alone. On this basis ertapenem/zidebactam would count as active against 90%–100% of isolates in all groups except K. pneumoniae/oxytoca with MBLs (±OXA-48), where MICs and percent susceptibility vary substantially even with inocula within the BSAC acceptable range. Conclusions Ertapenem/zidebactam has a proposed once-daily regimen well suited to OPAT. Even on highly conservative breakpoint projections, it has potential against MDR E. coli, including metallo-carbapenemase producers. If trial data sustain the 8 mg/L breakpoint indicated by animal experiments, its potential will extend widely across infections due to ESBL-, AmpC- and carbapenemase-producing Enterobacterales.
Collapse
Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, United Kingdom Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Paolo Garello
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, United Kingdom Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Anna Vickers
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, United Kingdom Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, United Kingdom Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David M Livermore
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Reference Services Division, United Kingdom Health Security Agency, 61 Colindale Avenue, London NW9 5EQ, UK.,Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| |
Collapse
|
26
|
Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
Collapse
Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
| |
Collapse
|
27
|
Escherichia coli ST1193: Following in the Footsteps of E. coli ST131. Antimicrob Agents Chemother 2022; 66:e0051122. [PMID: 35658504 DOI: 10.1128/aac.00511-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli ST1193 is an emerging global multidrug (MDR) high-risk clone and an important cause of community-onset urinary and bloodstream infections. ST1193 is imitating E. coli ST131, the most successful MDR clone of all time. Both clones emerged in the early 1990s by acquiring quinolone resistance-determining region (QRDR) mutations, IncF plasmids, virulence factors, and type 1 pilus (fimH) recombination. They are the only MDR clones that are dominant among unselected E. coli populations. ST131 is the most frequent clone and ST1193 the second most frequent clone among fluoroquinolone/cephalosporin-resistant E. coli isolates. Both clones have played pivotal roles in the global spread of MDR E. coli. ST1193 originated from ST clonal complex 14 (STc14), is lactose nonfermenting, belongs to phylogenetic group B2, and contains the O type O75. Global ST1193 prevalence has been increasing since 2012, even replacing ST131 in certain regions. blaCTX-M genes are rapidly expanding among ST1193 isolates, a scenario that occurred with ST131 during the 2000s. A validated PCR will enable global surveys to determine the extent of ST1193 among One Health E. coli isolates. The rapid emergence of ST1193 is concerning and is adding to the public health burden of MDR E. coli clones. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST1193. Such information will aid with management and prevention strategies. The medical community can ill afford to ignore the spread of another global successful MDR high-risk E. coli clone, especially one that is following in the footsteps of E. coli ST131.
Collapse
|
28
|
Kvesić M, Šamanić I, Novak A, Fredotović Ž, Dželalija M, Kamenjarin J, Goić Barišić I, Tonkić M, Maravić A. Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment. Front Microbiol 2022; 13:858821. [PMID: 35602062 PMCID: PMC9121779 DOI: 10.3389/fmicb.2022.858821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.
Collapse
Affiliation(s)
- Marija Kvesić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region, University of Split, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Anita Novak
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Kamenjarin
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goić Barišić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
- *Correspondence: Ana Maravić,
| |
Collapse
|
29
|
Chang SM, Chen JW, Tsai CS, Ko WC, Scaria J, Wang JL. Antimicrobial-Resistant Escherichia coli Distribution and Whole-Genome Analysis of Sequence Type 131 Escherichia coli Isolates in Public Restrooms in Taiwan. Front Microbiol 2022; 13:864209. [PMID: 35495726 PMCID: PMC9044074 DOI: 10.3389/fmicb.2022.864209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022] Open
Abstract
The threat of antibiotic-resistant bacteria to public health may originate from public restrooms. To better understand the community burden of antimicrobial-resistant Escherichia coli and sequence type complex 131 E. coli (STc131) in the public restroom, we performed a surveillance in public restrooms in southern Taiwan. Swabs were sampled from randomly selected public restrooms in Tainan, Taiwan in 2019. Antimicrobial susceptibility, phylogenetic grouping, and multiplex PCR were performed for the major ST complex in the B2 phylogenetic group. If STc131 isolates were identified, the whole-genome sequencing was performed. A total of 613 collection sites found 132 sites (21.5%) positive for E. coli. The most common phylogenetic group was A (30.9%) followed by B2 (30.3%). Ceftriaxone-resistant E. coli and extended-spectrum β-lactamases–producing E. coli were found in 2.4 and 1.0% of total public restrooms, respectively. The isolates in rural areas had higher ceftriaxone non-susceptibility than those in the city centers (3.9 vs. 1.2%, P = 0.038). Nine STc131 isolates were found in public restrooms, and most (77.8%) belonged to the subtype fimH41, whereas 22.2% belonged to fimH30. With the inclusion of STc131 isolates from human and dog fecal colonization in Taiwan, whole-genome sequencing was performed in 35 isolates. A large cluster of fimH41 in SNP-tree and GrapeTree was found from different sources (human, dog, and environment) and geographical areas. In conclusion, our surveillance of antimicrobial-resistant E. coli showed a higher prevalence of E. coli detected in public restrooms in the rural areas compared to those in city centers. The whole-genome sequence implies that fimH41 STc131 strains are successfully circulated in the community in Taiwan.
Collapse
Affiliation(s)
- Szu-Min Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jenn-Wei Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Shiang Tsai
- Department of Internal Medicine, National Cheng Kung University Hospital, Dou-Liou Branch, College of Medicine, National Cheng Kung University, Yunlin, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States
| | - Jiun-Ling Wang
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
30
|
Bueris V, Sellera FP, Fuga B, Sano E, Carvalho MPN, Couto SCF, Moura Q, Lincopan N. Convergence of virulence and resistance in international clones of WHO critical priority enterobacterales isolated from Marine Bivalves. Sci Rep 2022; 12:5707. [PMID: 35383231 PMCID: PMC8983722 DOI: 10.1038/s41598-022-09598-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022] Open
Abstract
The global spread of critical-priority antimicrobial-resistant Enterobacterales by food is a public health problem. Wild-caught seafood are broadly consumed worldwide, but exposure to land-based pollution can favor their contamination by clinically relevant antimicrobial-resistant bacteria. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we performed genomic surveillance and cell culture-based virulence investigation of WHO critical priority Enterobacterales isolated from marine bivalves collected in the Atlantic Coast of South America. Broad-spectrum cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli isolates were recovered from eight distinct geographical locations. These strains harbored blaCTX-M-type or blaCMY-type genes. Most of the surveyed genomes confirmed the convergence of wide virulome and resistome (i.e., antimicrobials, heavy metals, biocides, and pesticides resistance). We identified strains belonging to the international high-risk clones K. pneumoniae ST307 and E. coli ST131 carrying important virulence genes, whereas in vitro experiments confirmed the high virulence potential of these strains. Thermolabile and thermostable toxins were identified in some strains, and all of them were biofilm producers. These data point to an alarming presence of resistance and virulence genes in marine environments, which may favor horizontal gene transfer and the spread of these traits to other bacterial species.
Collapse
Affiliation(s)
- Vanessa Bueris
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil. .,Laboratory of Genetics, Butantan Institute, São Paulo, Brazil.
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.,School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Elder Sano
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Marcelo P N Carvalho
- Department of Veterinary Clinic and Surgery, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
31
|
Montes-Robledo A, Baldiris-Avila R, Galindo JF. D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli. Antibiotics (Basel) 2021; 10:antibiotics10091072. [PMID: 34572654 PMCID: PMC8465801 DOI: 10.3390/antibiotics10091072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.
Collapse
Affiliation(s)
- Alfredo Montes-Robledo
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
| | - Rosa Baldiris-Avila
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
- Grupo de Investigación CIPTEC, Facultad de Ingeniería, Fundacion Universitaria Tecnologico Comfenalco—Cartagena, Cartagena de Indias 13001, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
| | - Johan Fabian Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 11321, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
| |
Collapse
|
32
|
Karlowsky JA, Walkty A, Golden AR, Baxter MR, Denisuik AJ, McCracken M, Mulvey MR, Adam HJ, Zhanel GG. ESBL-positive Escherichia coli and Klebsiella pneumoniae isolates from across Canada: CANWARD surveillance study, 2007-18. J Antimicrob Chemother 2021; 76:2815-2824. [PMID: 34378029 DOI: 10.1093/jac/dkab269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES ESBL-producing Escherichia coli and Klebsiella pneumoniae are pathogens of increasing importance in Canada and elsewhere in the world. The purpose of this study was to phenotypically and molecularly characterize ESBL-producing E. coli and K. pneumoniae clinical isolates obtained from patients attending Canadian hospitals over a 12 year period. METHODS Isolates were collected between January 2007 and December 2018 as part of an ongoing national surveillance study (CANWARD). ESBL production was confirmed using the CLSI (M100) phenotypic method. Susceptibility testing was carried out using custom broth microdilution panels, and all isolates underwent WGS. RESULTS In total, 671 E. coli and 141 K. pneumoniae were confirmed to be ESBL producers. The annual proportion of ESBL-producing isolates increased for both E. coli (from 3.3% in 2007 to 11.2% in 2018; P < 0.0001) and K. pneumoniae (from 1.3% in 2007 to 9.3% in 2018; P < 0.0001). The most frequent STs were ST131 for E. coli [62.4% (419/671) of isolates] and ST11 [7.8% (11/141)] and ST147 [7.8% (11/141)] for K. pneumoniae. Overall, 97.2% of ESBL-producing E. coli and K. pneumoniae isolates were MDR. blaCTX-M-15 predominated in both ESBL-producing E. coli (62.3% of isolates) and ESBL-producing K. pneumoniae (48.9% of isolates). CONCLUSIONS The proportion of ESBL-producing E. coli, especially ST131, and K. pneumoniae, especially ST11 and ST147, in Canada increased significantly from 2007 to 2018. Continued prospective surveillance of these evolving MDR and at times XDR pathogens is imperative.
Collapse
Affiliation(s)
- James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada.,Clinical Microbiology, Health Sciences Centre/Diagnostic Services, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Andrew Walkty
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada.,Clinical Microbiology, Health Sciences Centre/Diagnostic Services, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Alyssa R Golden
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Andrew J Denisuik
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Melissa McCracken
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada.,Clinical Microbiology, Health Sciences Centre/Diagnostic Services, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| |
Collapse
|
33
|
The Pheno- and Genotypic Characterization of Porcine Escherichia coli Isolates. Microorganisms 2021; 9:microorganisms9081676. [PMID: 34442755 PMCID: PMC8400056 DOI: 10.3390/microorganisms9081676] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Escherichia (E.) coli is the main causative pathogen of neonatal and post-weaning diarrhea and edema disease in swine production. There is a significant health concern due to an increasing number of human infections associated with food and/or environmental-borne pathogenic and multidrug-resistant E. coli worldwide. Monitoring the presence of pathogenic and antimicrobial-resistant E. coli isolates is essential for sustainable disease management in livestock and human medicine. A total of 102 E. coli isolates of diseased pigs were characterized by antimicrobial and biocide susceptibility testing. Antimicrobial resistance genes, including mobile colistin resistance genes, were analyzed by PCR and DNA sequencing. The quinolone resistance-determining regions of gyrA and parC in ciprofloxacin-resistant isolates were analyzed. Clonal relatedness was investigated by two-locus sequence typing (CH clonotyping). Phylotyping was performed by the Clermont multiplex PCR method. Virulence determinants were analyzed by customized DNA-based microarray technology developed in this study for fast and economic molecular multiplex typing. Thirty-five isolates were selected for whole-genome sequence-based analysis. Most isolates were resistant to ampicillin and tetracycline. Twenty-one isolates displayed an ESBL phenotype and one isolate an AmpC β-lactamase-producing phenotype. Three isolates had elevated colistin minimal inhibitory concentrations and carried the mcr-1 gene. Thirty-seven isolates displayed a multi-drug resistance phenotype. The most predominant β-lactamase gene classes were blaTEM-1 (56%) and blaCTX-M-1 (13.71%). Mutations in QRDR were observed in 14 ciprofloxacin-resistant isolates. CH clonotyping divided all isolates into 51 CH clonotypes. The majority of isolates belonged to phylogroup A. Sixty-four isolates could be assigned to defined pathotypes wherefrom UPEC was predominant. WGS revealed that the most predominant sequence type was ST100, followed by ST10. ST131 was detected twice in our analysis. This study highlights the importance of monitoring antimicrobial resistance and virulence properties of porcine E. coli isolates. This can be achieved by applying reliable, fast, economic and easy to perform technologies such as DNA-based microarray typing. The presence of high-risk pathogenic multi-drug resistant zoonotic clones, as well as those that are resistant to critically important antibiotics for humans, can pose a risk to public health. Improved protocols may be developed in swine farms for preventing infections, as well as the maintenance and distribution of the causative isolates.
Collapse
|
34
|
Bulut ME, Hürkal G, Dalgıç N. Investigation of High-Risk ST131 Clone in Extended Spectrum β-Lactamase–Producing Escherichia coli Isolates in Children. J PEDIAT INF DIS-GER 2021. [DOI: 10.1055/s-0041-1730995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
Objective Antimicrobial resistance poses a serious threat to children's health. In recent years, high-risk Escherichia coli ST131 has become an important target for global surveillance studies. The E.coli ST131 clone is associated with extended spectrum β-lactamase (ESBL) production, as well as multidrug resistance and treatment failure. Studies on this clone in the pediatric age group are limited. We aim to investigate the rate of high-risk E. coli ST131 clone in ESBL-positive E. coli isolates obtained from pediatric patients.
Methods A total of 292 ESBL-positive E. coli isolates from clinical samples of pediatric patients was included in the study. MALDI-TOF MS system was used for bacterial identification. Susceptibility tests were performed using BD Phoenix automated system. ST131 detection was done by MALDI-TOF-MS. Fisher's exact test was used to compare the groups (significance <0.05).
Results A total of 292 isolates was analyzed. The high-risk ST131 clone was detected in 117 (40%) of the 292 ESBL-positive isolates. ST131 rates were found to be significantly higher in children under the age of 5 years compared with children over the age of 5 years (49.3 vs. 31.1%, p = 0.0019). Ciprofloxacin resistance was higher in ST131 isolates (45.6 vs. 31.7%; p < 0.05).
Conclusion The rate of the ST131 clone was found to be high in the pediatric population. The significantly high rate of resistance to ciprofloxacin, which is not commonly used in the pediatric population, in ST131 isolates reveals the importance of the spread of high-risk clones for the development of resistance.
Collapse
Affiliation(s)
- Mehmet E. Bulut
- Department of Medical Microbiology, Health Sciences University, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Turkey
| | - Gülen Hürkal
- Department of Medical Microbiology, Health Sciences University, Sisli Hamidiye Etfal Training and Research Hospital, Istanbul, Turkey
| | - Nazan Dalgıç
- Division of Pediatric Infectious Diseases, Health Sciences University, Sariyer Etfal Training and Research Hospital, Istanbul, Turkey
| |
Collapse
|
35
|
Taati Moghadam M, Mirzaei M, Fazel Tehrani Moghaddam M, Babakhani S, Yeganeh O, Asgharzadeh S, Farahani HE, Shahbazi S. The Challenge of Global Emergence of Novel Colistin-Resistant Escherichia coli ST131. Microb Drug Resist 2021; 27:1513-1524. [PMID: 33913748 DOI: 10.1089/mdr.2020.0505] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Escherichia coli ST131 is one of the high-risk multidrug-resistant clones with a global distribution and the ability to persist and colonize in a variety of niches. Carbapenemase-producing E. coli ST131 strains with the ability to resist last-line antibiotics (i.e., colistin) have been recently considered a significant public health. Colistin is widely used in veterinary medicine and therefore, colistin-resistant bacteria can be transmitted from livestock to humans through food. There are several mechanisms of resistance to colistin, which include chromosomal mutations and plasmid-transmitted mcr genes. E. coli ST131 is a great model organism to investigate the emergence of superbugs. This microorganism has the ability to cause intestinal and extraintestinal infections, and its accurate identification as well as its antibiotic resistance patterns are vitally important for a successful treatment strategy. Therefore, further studies are required to understand the evolution of this resistant organism for drug design, controlling the evolution of other nascent emerging pathogens, and developing antibiotic stewardship programs. In this review, we will discuss the importance of E. coli ST131, the mechanisms of resistance to colistin as the last-resort antibiotic against resistant Gram-negative bacteria, reports from different regions regarding E. coli ST131 resistance to colistin, and the most recent therapeutic approaches against colistin-resistance bacteria.
Collapse
Affiliation(s)
- Majid Taati Moghadam
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrnaz Mirzaei
- Department of Microbiology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | | | - Sajad Babakhani
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Omid Yeganeh
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Asgharzadeh
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
36
|
de Lagarde M, Vanier G, Arsenault J, Fairbrother JM. High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population. Antibiotics (Basel) 2021; 10:antibiotics10030244. [PMID: 33671102 PMCID: PMC8000703 DOI: 10.3390/antibiotics10030244] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022] Open
Abstract
The definition of a high risk clone for antibiotic resistance dissemination was initially established for human medicine. We propose a revised definition of a high risk clone adapted to the One Health context. Then, we applied our criteria to a cluster of enrofloxacin non susceptible ETEC:F4 isolates which emerged in 2013 in diseased pigs in Quebec. The whole genomes of 183 ETEC:F4 strains isolated in Quebec from 1990 to 2018 were sequenced. The presence of virulence and resistance genes and replicons was examined in 173 isolates. Maximum likelihood phylogenetic trees were constructed based on SNP data and clones were identified using a set of predefined criteria. The strains belonging to the clonal lineage ST100/O149:H10 isolated in Quebec in 2013 or later were compared to ETEC:F4 whole genome sequences available in GenBank. Prior to 2000, ETEC:F4 isolates from pigs in Quebec were mostly ST90 and belonged to several serotypes. After 2000, the isolates were mostly ST100/O149:H10. In this article, we demonstrated the presence of a ETEC:F4 high risk clone. This clone (1) emerged in 2013, (2) is multidrug resistant, (3) has a widespread distribution over North America and was able to persist several months on farms, and (4) possesses specific virulence genes. It is crucial to detect and characterize high risk clones in animal populations to increase our understanding of their emergence and their dissemination.
Collapse
Affiliation(s)
- Maud de Lagarde
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada; (M.d.L.); (G.V.)
| | - Ghyslaine Vanier
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada; (M.d.L.); (G.V.)
| | - Julie Arsenault
- Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada;
- Groupe de Recherche en Epidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada
| | - John Morris Fairbrother
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada; (M.d.L.); (G.V.)
- Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S2M2, Canada;
- Correspondence:
| |
Collapse
|
37
|
Szmolka A, Wami H, Dobrindt U. Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. Front Microbiol 2021; 12:642125. [PMID: 33717039 PMCID: PMC7947892 DOI: 10.3389/fmicb.2021.642125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/03/2021] [Indexed: 01/06/2023] Open
Abstract
Introduction Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. Objectives In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. Results The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. Conclusion This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.
Collapse
Affiliation(s)
- Ama Szmolka
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Haleluya Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| |
Collapse
|
38
|
Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
Collapse
Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
| |
Collapse
|
39
|
Genetic Features of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Poultry in Mayabeque Province, Cuba. Antibiotics (Basel) 2021; 10:antibiotics10020107. [PMID: 33499392 PMCID: PMC7910960 DOI: 10.3390/antibiotics10020107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/13/2021] [Accepted: 01/17/2021] [Indexed: 02/07/2023] Open
Abstract
A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013–2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec). Sixty-two 3GC-R-Ec isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R-Ec isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes blaCTX-M-1 (n = 27), blaCTX-M-15 (n = 4), and blaCTX-M-1 together with blaLAP-2 (n = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (sul1, sul2, sul3), trimethoprim (dfrA1, dfrA7, dfrA12, dfrA14, dfrA17), tetracyclines (tet(A), tet(B)), aminoglycosides (aac(6′)-Ib-cr, strA, strB), chloramphenicol (cmlA1, floR), macrolides (mph(A), mph(D)), and quinolones (qnrS, qnrB, aac(6′)-Ib-cr) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A (n = 25), B1 (n = 5), and D (n = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing E. coli in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.
Collapse
|
40
|
Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
Collapse
Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
| |
Collapse
|
41
|
Hastak P, Fourment M, Darling AE, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex. Emerg Microbes Infect 2020; 9:1780-1792. [PMID: 32686595 PMCID: PMC7473005 DOI: 10.1080/22221751.2020.1797541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/14/2020] [Indexed: 11/25/2022]
Abstract
The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.
Collapse
Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Mathieu Fourment
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| |
Collapse
|
42
|
Mihai AD, Chircov C, Grumezescu AM, Holban AM. Magnetite Nanoparticles and Essential Oils Systems for Advanced Antibacterial Therapies. Int J Mol Sci 2020; 21:ijms21197355. [PMID: 33027980 PMCID: PMC7582471 DOI: 10.3390/ijms21197355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Essential oils (EOs) have attracted considerable interest in the past few years, with increasing evidence of their antibacterial, antiviral, antifungal, and insecticidal effects. However, as they are highly volatile, the administration of EOs to achieve the desired effects is challenging. Therefore, nanotechnology-based strategies for developing nanoscaled carriers for their efficient delivery might offer potential solutions. Owing to their biocompatibility, biodegradability, low toxicity, ability to target a tissue specifically, and primary structures that allow for the attachment of various therapeutics, magnetite nanoparticles (MNPs) are an example of such nanocarriers that could be used for the efficient delivery of EOs for antimicrobial therapies. The aim of this paper is to provide an overview of the use of EOs as antibacterial agents when coupled with magnetite nanoparticles (NPs), emphasizing the synthesis, properties and functionalization of such NPs to enhance their efficiency. In this manner, systems comprising EOs and MNPs could offer potential solutions that could overcome the challenges associated with biofilm formation on prosthetic devices and antibiotic-resistant bacteria by ensuring a controlled and sustained release of the antibacterial agents.
Collapse
Affiliation(s)
- Antonio David Mihai
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1–7 Gheorghe Polizu Street, 011061 Bucharest, Romania; (A.D.M.); (C.C.)
| | - Cristina Chircov
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1–7 Gheorghe Polizu Street, 011061 Bucharest, Romania; (A.D.M.); (C.C.)
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1–7 Gheorghe Polizu Street, 011061 Bucharest, Romania; (A.D.M.); (C.C.)
- Correspondence: or ; Tel.: +40-21-318-1000
| | - Alina Maria Holban
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 1–3 Portocalelor Lane, Sector 5, 77206 Bucharest, Romania; or
| |
Collapse
|
43
|
Zhi S, Stothard P, Banting G, Scott C, Huntley K, Ryu K, Otto S, Ashbolt N, Checkley S, Dong T, Ruecker NJ, Neumann NF. Characterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater. WATER RESEARCH 2020; 182:115827. [PMID: 32580076 DOI: 10.1016/j.watres.2020.115827] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 05/29/2023]
Abstract
A growing body of evidence has demonstrated that extraintestinal pathogenic E. coli (ExPEC), such as the urinary pathogenic E. coli (UPEC), are common constituents of treated wastewater, and therefore represent a potential public health risk. However, no single virulence gene, or set of virulence genes, can be used to conclusively identify this genetically diverse pathotype. As such we sought to identify and characterize the public health relevance of potential UPEC found in treated sewage/wastewater using a comparative genomics approach. Presumptive wastewater UPEC (W-UPEC) were initially identified by virulence gene screening against 5 virulence genes, and for which isolates containing ≥3 virulence genes were whole genome sequenced (n = 24). Single nucleotide polymorphic (SNP) spanning tree analysis demonstrated that many of these wastewater UPEC (WUPEC) were virtually identical at the core genome (0.4 Mbp) when compared to clinical UPEC (C-UPEC) sequences obtained from NCBI, varying by as little as 1 SNP. Remarkably, at the whole genome level, W-UPEC isolates displayed >96% whole genome similarity to C-UPEC counterparts in NCBI, with one strain demonstrating 99.5% genome similarity to a particular C-UPEC strain. The W-UPEC populations were represented by sequence types (ST) known to be clinically important, including ST131, ST95, ST127 and ST640. Many of the W-UPEC carried the exact same complement of virulence genes as their most closely related C-UPEC strains. For example, O25b-ST131 W-UPEC strains possessed the same 80 virulence genes as their most closely related C-UPEC counterparts. Concerningly, W-UPEC strains also carried a plethora of antibiotic resistance genes, and O25b-ST131strains were designated as extended spectrum beta-lactamase (ESBL) producing E. coli by both genome profiling and phenotypic resistance testing. W-UPEC ST131 strains were found in the effluents of a single treatment plant at different times, as well as different wastewater treatment plants, suggesting a differentially ability to survive wastewater treatment. Indeed, in sewage samples treated with chlorine doses sufficient for inducing a ∼99.99% reduction in total E. coli levels, UPEC represented a significant proportion of the chlorine-resistant population. By contrast, no Shiga toxin-producing E. coli were observed in these chlorinated sewage libraries. Our results suggest that clinically-relevant UPEC exist in treated wastewater effluents and that they appear to be specifically adapted to survive wastewater treatment processes.
Collapse
Affiliation(s)
- Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
| | - Paul Stothard
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Candis Scott
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kristin Huntley
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Simon Otto
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sylvia Checkley
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tao Dong
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Norma J Ruecker
- City of Calgary, Water Quality Services, Calgary, Alberta, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
44
|
de Lagarde M, Vanier G, Desmarais G, Kohan-Ghadr HR, Arsenault J, Fairbrother JM. A new multidrug-resistant enterotoxigenic Escherichia coli pulsed-field gel electrophoresis cluster associated with enrofloxacin non-susceptibility in diseased pigs. J Appl Microbiol 2020; 130:707-721. [PMID: 32767832 PMCID: PMC7984379 DOI: 10.1111/jam.14816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/13/2020] [Accepted: 08/03/2020] [Indexed: 12/31/2022]
Abstract
Aims To describe the temporal trends in Escherichia coli pathotypes and antimicrobial resistance detected in isolates from diseased‐pig cases submitted to the EcL from 2008 to 2016, in Quebec, Canada, and to investigate the presence of spatiotemporal and phylogenetic clusters. Methods and Results Detection of 12 genes coding for virulence factors in pathogenic E. coli in pigs by PCR and antimicrobial resistance standard disc diffusion assay were performed. Demographic and clinical data were entered in the Animal Pathogenic and Zoonotic E. coli (APZEC) database. ETEC:F4 was the most prevalent pathovirotype among the 3773 cases submitted. The LT:STb:F4 virotype was predominant until 2014, then was overtaken by the LT:STb:STa:F4 virotype. More than 90% of the ETEC:F4 isolates were multidrug resistant. A spatiotemporal cluster of LT:STb:STa:F4 isolates non‐susceptible to enrofloxacin was detected between 4/2015 and 9/2016. Pulsed‐field gel electrophoresis analysis of 137 ETEC:F4 isolates revealed the presence of a cluster composed mainly of LT:STb:STa:F4 isolates non‐susceptible to enrofloxacin. Conclusions The APZEC database was useful to highlight temporal trends in E. coli pathotypes. A high‐risk ETEC:F4 clone might disseminate in the pig population in Quebec since 2015. Significance and Impact of the Study Surveillance is crucial to identify new clones and develop control strategies.
Collapse
Affiliation(s)
- M de Lagarde
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - G Vanier
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - G Desmarais
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - H-R Kohan-Ghadr
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - J Arsenault
- Swine and Poultry Infectious Research Center (CRIPA-FQRNT), and Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - J M Fairbrother
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Swine and Poultry Infectious Research Center (CRIPA-FQRNT), and Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| |
Collapse
|
45
|
Hiyama Y, Sato T, Takahashi S, Yamamoto S, Fukushima Y, Nakajima C, Suzuki Y, Yokota SI, Masumori N. Sitafloxacin has a potent activity for eradication of extended spectrum β-lactamase-producing fluoroquinolone-resistant Escherichia coli forming intracellular bacterial communities in uroepithelial cells. J Infect Chemother 2020; 26:1272-1277. [PMID: 32768340 DOI: 10.1016/j.jiac.2020.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 07/19/2020] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Eradication of asymptomatic bacteriuria (ASB) before urological procedures is important to reduce the risk for infectious complications after surgery. However, the appropriate regimen for antimicrobial treatment has not been fully determined. We experienced continuous (over 10 months) isolation of extended spectrum β-lactamase (ESBL)-producing fluoroquinolone-resistant Escherichia coli from urine of an asymptomatic patient. The four isolates obtained (SMESC1 to 4) were international high-risk clones of O25b:H4-ST131-H30R, and originated from one strain, as revealed by the whole genome sequences. Although the patient received meropenem (MEPM) and fosfomycin (FOM), to which the strains were susceptible before the urological procedures, they could not be eradicated. METHODS To explore the reason for the continuous isolation even after MEPM and FOM administration, antimicrobial killing of adherent and/or intracellular bacterial communities (IBC) formed by coculture of the E. coli cells and T24 bladder epithelial cells were examined. RESULTS FOM and levofloxacin did not decrease viable E. coli cells compared with gentamicin. MEPM partly decreased them, and sitafloxacin (STFX) decreased them most potently. These observations indicate that E. coli can survive in the urinary tract under antimicrobial administration, and some antimicrobials such as FOM and MEPM cannot eradicate E. coli in uroepithelial cells. Adhesion on urinary epithelial cells and/or IBC formation might result in continuous isolation from the urinary tract and recurrence of ASB and urinary tract infections. CONCLUSIONS The present study suggests that STFX is a promising optional agent for the eradication of ESBL-producing fluoroquinolone-resistant E. coli in the urinary tract before urological procedures.
Collapse
Affiliation(s)
- Yoshiki Hiyama
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan; Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan.
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Soh Yamamoto
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Naoya Masumori
- Department of Urology, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
46
|
Denisuik AJ, Karlowsky JA, Adam HJ, Baxter MR, Lagacé-Wiens PRS, Mulvey MR, Hoban DJ, Zhanel GG. Dramatic rise in the proportion of ESBL-producing Escherichia coli and Klebsiella pneumoniae among clinical isolates identified in Canadian hospital laboratories from 2007 to 2016. J Antimicrob Chemother 2020; 74:iv64-iv71. [PMID: 31505647 DOI: 10.1093/jac/dkz289] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To assess the prevalence, antimicrobial susceptibilities and molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae infecting patients receiving care in Canadian hospitals from January 2007 to December 2016. METHODS Clinical isolates of E. coli (n = 8387) and K. pneumoniae (n = 2623) submitted to CANWARD, an ongoing Canadian national surveillance study, were tested using the CLSI reference broth microdilution method to determine their susceptibility to 15 antimicrobial agents. ESBL-producing E. coli and K. pneumoniae confirmed by the CLSI phenotypic method and putative AmpC-producing E. coli underwent PCR testing and DNA sequencing to identify resistance genes. Annual proportions of isolates harbouring ESBL and AmpC genes were assessed by the Cochran-Armitage test of trend. RESULTS The annual proportion of isolates of E. coli that were ESBL producing increased from 3.4% in 2007 to 11.1% in 2016 (P < 0.0001); >95% of ESBL-producing E. coli were susceptible to amikacin, colistin, ertapenem, meropenem and tigecycline. The proportion of isolates of K. pneumoniae that were ESBL producing increased from 1.3% in 2007 to 9.7% in 2016 (P < 0.0001); >95% of ESBL-producing K. pneumoniae were susceptible to amikacin and meropenem. CTX-M-15 was the predominant genotype in both ESBL-producing E. coli (64.2% of isolates) and ESBL-producing K. pneumoniae (51.0%). The annual proportion of isolates of E. coli that were AmpC producing [annual proportion mean 1.9% (range 0.3%-3.1%)] was unchanged from 2007 to 2016 (P > 0.5). CONCLUSIONS The prevalence of both ESBL-producing E. coli and K. pneumoniae increased significantly in Canada during the study period while the prevalence of AmpC-producing E. coli remained low and stable.
Collapse
Affiliation(s)
- Andrew J Denisuik
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Clinical Microbiology, St. Boniface Hospital/Diagnostic Services, Shared Health Manitoba, L4025-409 Taché Avenue, Winnipeg, Manitoba, Canada
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Clinical Microbiology, Health Sciences Centre/Diagnostic Services, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | - Philippe R S Lagacé-Wiens
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Clinical Microbiology, St. Boniface Hospital/Diagnostic Services, Shared Health Manitoba, L4025-409 Taché Avenue, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada.,Clinical Microbiology, Health Sciences Centre/Diagnostic Services, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada
| | | |
Collapse
|
47
|
Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence. Antimicrob Agents Chemother 2020; 64:AAC.02351-19. [PMID: 32423949 DOI: 10.1128/aac.02351-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/06/2020] [Indexed: 11/20/2022] Open
Abstract
Invasive infections due to extended-spectrum-β-lactamase- and pAmpC-producing Escherichia coli (ESBL/pAmpC-EC) are an important cause of morbidity, often caused by the high-risk clone sequence type (ST131) and isolates classified as extraintestinal pathogenic E. coli (ExPEC). The relative influence of host immunocompetence versus microbiological virulence factors in the acquisition and outcome of bloodstream infections (BSI) is poorly understood. Herein, we used whole-genome sequencing on 278 blood culture isolates of ESBL/pAmpC-EC from 260 patients with community-onset BSI collected from 2012 to 2015 in Stockholm to study the association of virulence genes, sequence types, and antimicrobial resistance with severity of disease, infection source, ESBL/pAmpC-EC BSI low-risk patients, and patients with repeated episodes. ST131 subclade C2 comprised 29% of all patients. Factors associated with septic shock in multivariable analysis were patient host factors (hematologic cancer or transplantation and reduced daily living activity), presence of the E. coli virulence factor iss (increased serum survival), absence of phenotypic multidrug resistance, and absence of the genes pap and hsp Adhesins, particularly pap, were associated with urinary tract infection (UTI) source, while isolates from post-prostate biopsy sepsis had a low overall number of virulence operons, including adhesins, and commonly belonged to ST131 clades A, B, and subclade C1, ST1193, and ST648. ST131 was associated with recurrent episodes. In conclusion, the most interesting finding is the association of iss with septic shock. Adhesins are important for UTI pathogenesis, while otherwise low-pathogenic isolates from the microbiota can cause post-prostate biopsy sepsis.
Collapse
|
48
|
Jafari A, Falahatkar S, Delpasand K, Sabati H, Sedigh Ebrahim-Saraie H. Emergence of Escherichia coli ST131 Causing Urinary Tract Infection in Western Asia: A Systematic Review and Meta-Analysis. Microb Drug Resist 2020; 26:1357-1364. [PMID: 32380906 DOI: 10.1089/mdr.2019.0312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Escherichia coli sequence type (ST) 131 is considered a high-risk pandemic clone and frequently extended-spectrum β-lactamase (ESBL)-producing clone that is strongly associated with the global dissemination of CTX-M-15 type. The emergence of ST131 has become a public health threat because this clonal group typically exhibits multiple virulence factors and antimicrobial resistance. Therefore, this study aimed to analyze the literature published on the estimation of the prevalence of clone ST131 among E. coli strains isolated from patients with urinary tract infections in western Asia. A systematic search was carried out to identify eligible articles in the Web of Science, PubMed, Scopus, Embase, and Google Scholar electronic databases from January 2010 to December 2018. Next, 13 articles meeting the inclusion criteria were selected for data extraction and analysis by Comprehensive Meta-Analysis Software. The included studies were conducted in Iran, Jordan, Kuwait, Pakistan, Saudi Arabia, Turkey, and Yemen. In all studies, the pooled prevalence of ST131 was 24.6% (95% CI: 13.5%-40.4%) in wild type isolates, 42.7% (95% CI: 32.5%-53.5%) among ESBLs-producing isolates, and 64.8% (95% CI: 36%-85.5%) among multiple-drug resistant (MDR) isolates. Moreover, the prevalence of ST131 isolates carrying CTX-M-15 type was 68% (95% CI: 48.4%-82.8%). Our study indicated the high prevalence of broadly disseminated ST131 clone among MDR and ESBLs isolates in western Asia. Moreover, O25b was the predominant ST131 clone type, which was mostly associated with CTX-M-15 type.
Collapse
Affiliation(s)
- Alireza Jafari
- Urology Research Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Siavash Falahatkar
- Urology Research Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Kourosh Delpasand
- Department of Medical Ethics, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Hoda Sabati
- Biotechnology and Biological Science Research Center, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hadi Sedigh Ebrahim-Saraie
- Razi Clinical Research Development Unit, Razi Hospital, Guilan University of Medical Sciences, Rasht, Iran
| |
Collapse
|
49
|
Ma T, Fu J, Xie N, Ma S, Lei L, Zhai W, Shen Y, Sun C, Wang S, Shen Z, Wang Y, Walsh TR, Shen J. Fitness Cost of blaNDM-5-Carrying p3R-IncX3 Plasmids in Wild-Type NDM-Free Enterobacteriaceae. Microorganisms 2020; 8:microorganisms8030377. [PMID: 32156014 PMCID: PMC7143814 DOI: 10.3390/microorganisms8030377] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/31/2022] Open
Abstract
The wide dissemination of New Delhi metallo-β-lactamase genes (blaNDM) has resulted in the treatment failure of most available β-lactam antibiotics, with IncX3-type blaNDM-5-carrying plasmids recognised as having spread worldwide. In China, bacteria carrying these plasmids are increasingly being detected from diverse samples, including hospitals, communities, livestock and poultry, and the environment, suggesting that IncX3 plasmids are becoming a vital vehicle for blaNDM dissemination. To elucidate the fitness cost of these plasmids on the bacterial host, we collected blaNDM-negative strains from different sources and tested their ability to acquire the blaNDM-5-harboring p3R-IncX3 plasmid. We then measured changes in antimicrobial susceptibility, growth kinetics, and biofilm formation following plasmid acquisition. Overall, 70.7% (29/41) of our Enterobacteriaceae recipients successfully acquired the blaNDM-5-harboring p3R-IncX3 plasmid. Contrary to previous plasmid burden theory, 75.9% (22/29) of the transconjugates showed little fitness cost as a result of plasmid acquisition, with 6.9% (2/29) of strains exhibiting enhanced growth compared with their respective wild-type strains. Following plasmid acquisition, all transconjugates demonstrated resistance to most β-lactams, while several strains showed enhanced biofilm formation, further complicating treatment and prevention measures. Moreover, the highly virulent Escherichia coli sequence type 131 strain that already harbored mcr-1 also demonstrated the ability to acquire the blaNDM-5-carrying p3R-IncX3 plasmid, resulting in further limited therapeutic options. This low fitness cost may partly explain the rapid global dissemination of blaNDM-5-harboring IncX3 plasmids. Our study highlights the growing threat of IncX3 plasmids in spreading blaNDM-5.
Collapse
Affiliation(s)
- Tengfei Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Jiani Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Ning Xie
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Shizhen Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Lei Lei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Yingbo Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Chengtao Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Shaolin Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
| | - Timothy R. Walsh
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
- Department of Medical Microbiology and Infectious Disease, Institute of Infection & Immunity, Heath Park Hospital, Cardiff CF14 4XN, UK
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.M.); (J.F.); (S.M.); (L.L.); (W.Z.); (Y.S.); (C.S.); (S.W.); (Z.S.); (T.R.W.)
- Correspondence:
| |
Collapse
|
50
|
Mastrorilli E, Petrin S, Orsini M, Longo A, Cozza D, Luzzi I, Ricci A, Barco L, Losasso C. Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. BMC Genomics 2020; 21:202. [PMID: 32131727 PMCID: PMC7057659 DOI: 10.1186/s12864-020-6588-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated from humans and the environment, but neither the reservoir nor its route of infection are clearly defined. This serovar is characterized by high genomic diversity, and molecular evidences revealed important similarities with typhoidal serovars. RESULTS 179 S. Napoli genomes as well as 239 genomes of typhoidal and non-typhoidal serovars were analyzed in a comparative genomic study. Phylogenetic analysis and draft genome characterization in terms of Multi Locus Sequence Typing (MLST), plasmid replicons, Salmonella Pathogenicity Islands (SPIs), antimicrobial resistance genes (ARGs), phages, biocide and metal-tolerance genes confirm the high genetic variability of S. Napoli, also revealing a within-serovar phylogenetic structure more complex than previously known. Our work also confirms genomic similarity of S. Napoli to typhoidal serovars (S. Typhi and S. Paratyphi A), with S. Napoli samples clustering primarily according to ST, each being characterized by specific genomic traits. Moreover, two major subclades of S. Napoli can be clearly identified, with ST-474 being biphyletic. All STs span among isolation sources and years of isolation, highlighting the challenge this serovar poses to define its epidemiology and evolution. Altogether, S. Napoli strains carry less SPIs and less ARGs than other non-typhoidal serovars and seldom acquire plasmids. However, we here report the second case of an extended-spectrum β-lactamases (ESBLs) producing S. Napoli strain and the first cases of multidrug resistant (MDR) S. Napoli strains, all isolated from humans. CONCLUSIONS Our results provide evidence of genomic plasticity of S. Napoli, highlighting genomic similarity with typhoidal serovars and genomic features typical of non-typhoidal serovars, supporting the possibility of survival in different niches, both enteric and non-enteric. Presence of horizontally acquired ARGs and MDR profiles rises concerns regarding possible selective pressure exerted by human environment on this pathogen.
Collapse
Affiliation(s)
- Eleonora Mastrorilli
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
- Present address: European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sara Petrin
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy.
| | - Alessandra Longo
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| | - Debora Cozza
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| | - Antonia Ricci
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Lisa Barco
- Istituto Zooprofilattico Sperimentale delle Venezie, Food Safety Department, Legnaro, Italy
| | - Carmen Losasso
- Istituto Zooprofilattico Sperimentale delle Venezie, Microbial Ecology Unit, Legnaro, Italy
| |
Collapse
|