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BABINES-OROZCO L, BALBUENA-ALONSO MG, BARRIOS-VILLA E, LOZANO-ZARAIN P, MARTÍNEZ-LAGUNA Y, DEL CARMEN ROCHA-GRACIA R, CORTÉS-CORTÉS G. Antimicrobial resistance in food-associated Escherichia coli in Mexico and Latin America. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:4-12. [PMID: 38188662 PMCID: PMC10767319 DOI: 10.12938/bmfh.2023-022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/11/2023] [Indexed: 01/09/2024]
Abstract
The World Health Organization (WHO) considers antimicrobial resistance to be one of the critical global public health priorities to address. Escherichia coli is a commensal bacterium of the gut microbiota in humans and animals; however, some strains cause infections and are resistant to antibiotics. One of the most common ways of acquiring pathogenic E. coli strains is through food. This review analyzes multidrug-resistant E. coli isolated from food, emphasizing Latin America and Mexico, and the mobile genetic elements (MGEs) responsible for spreading antibiotic resistance determinants among bacteria in different environments and hosts. We conducted a systematic search of the literature published from 2015 to 2022 in open access databases and electronic repositories. The prevalence of 11 E. coli pathotypes was described, with diarrheagenic E. coli pathotypes being the most frequently associated with foodborne illness in different Latin American countries, highlighting the presence of different antibiotic resistance genes mostly carried by IncF-type plasmids or class 1 integrons. Although the global incidence of foodborne illness is high, there have been few studies in Mexico and Latin America, which highlights the need to generate updated epidemiological data from the "One Health" approach, which allows monitoring of the multidrug-resistance phenomenon in E. coli from a common perspective in the interaction of human, veterinary, and environmental health.
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Affiliation(s)
- Lorena BABINES-OROZCO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - María Guadalupe BALBUENA-ALONSO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Edwin BARRIOS-VILLA
- Departamento de Ciencias Químico Biológicas y Agropecuarias,
Unidad Regional Norte, Campus Caborca, Universidad de Sonora, Col. Eleazar Ortiz C.P.
83621 H. Caborca, Sonora, México
| | - Patricia LOZANO-ZARAIN
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Ygnacio MARTÍNEZ-LAGUNA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Rosa DEL CARMEN ROCHA-GRACIA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Gerardo CORTÉS-CORTÉS
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
- Department of Microbiology and Environmental Toxicology,
University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance. mSystems 2022; 7:e0015822. [PMID: 35469421 PMCID: PMC9238384 DOI: 10.1128/msystems.00158-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Australian silver gull is an urban-adapted species that frequents anthropogenic waste sites. The enterobacterial flora of synanthropic birds often carries antibiotic resistance genes. Whole-genome sequence analyses of 425 Escherichia coli isolates from cloacal swabs of chicks inhabiting three coastal sites in New South Wales, Australia, cultured on media supplemented with meropenem, cefotaxime, or ciprofloxacin are reported. Phylogenetically, over 170 antibiotic-resistant lineages from 96 sequence types (STs) representing all major phylogroups were identified. Remarkably, 25 STs hosted the carbapenemase gene blaIMP-4, sourced only from Five Islands. Class 1 integrons carrying blaIMP and blaOXA alongside blaCTX-M and qnrS were notable. Multiple plasmid types mobilized blaIMP-4 and blaOXA-1, and 121 isolates (28%) carried either a ColV-like (18%) or a pUTI89-like (10%) F virulence plasmid. Phylogenetic comparisons to human isolates provided evidence of interspecies transmission. Our study underscores the importance of bystander species in the transmission of antibiotic-resistant and pathogenic E. coli. IMPORTANCE By compiling various genomic and phenotypic data sets, we have provided one of the most comprehensive genomic studies of Escherichia coli isolates from the Australian silver gull, on media containing clinically relevant antibiotics. The analysis of genetic structures capturing antimicrobial resistance genes across three gull breeding colonies in New South Wales, Australia, and comparisons to clinical data have revealed a range of trackable genetic signatures that highlight the broad distribution of clinical antimicrobial resistance in more than 170 different lineages of E. coli. Conserved truncation sizes of the class 1 integrase gene, a key component of multiple-drug resistance structures in the Enterobacteriaceae, represent unique deletion events that are helping to link seemingly disparate isolates and highlight epidemiologically relevant data between wildlife and clinical sources. Notably, only the most anthropogenically affected of the three sites (Five Islands) was observed to host carbapenem resistance, indicating a potential reservoir among the sites sampled.
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Dobrindt U, Wami HT, Schmidt-Wieland T, Bertsch D, Oberdorfer K, Hof H. Compared with Cotrimoxazole Nitroxoline Seems to Be a Better Option for the Treatment and Prophylaxis of Urinary Tract Infections Caused by Multidrug-Resistant Uropathogens: An In Vitro Study. Antibiotics (Basel) 2021; 10:645. [PMID: 34071539 PMCID: PMC8230139 DOI: 10.3390/antibiotics10060645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023] Open
Abstract
The resistance of uropathogens to various antibiotics is increasing, but nitroxoline remains active in vitro against some relevant multidrug resistant uropathogenic bacteria. E. coli strains, which are among the most common uropathogens, are unanimously susceptible. Thus, nitroxoline is an option for the therapy of urinary tract infections caused by multiresistant bacteria. Since nitroxoline is active against bacteria in biofilms, it will also be effective in patients with indwelling catheters or foreign bodies in the urinary tract. Cotrimoxazole, on the other hand, which, in principle, can also act on bacteria in biofilms, is frequently inactive against multiresistant uropathogens. Based on phenotypic resistance data from a large number of urine isolates, structural characterisation of an MDR plasmid of a recent ST131 uropathogenic E. coli isolate, and publicly available genomic data of resistant enterobacteria, we show that nitroxoline could be used instead of cotrimoxazole for intervention against MDR uropathogens. Particularly in uropathogenic E. coli, but also in other enterobacterial uropathogens, the frequent parallel resistance to different antibiotics due to the accumulation of multiple antibiotic resistance determinants on mobile genetic elements argues for greater consideration of nitroxoline in the treatment of uncomplicated urinary tract infections.
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Affiliation(s)
- Ulrich Dobrindt
- Institut für Hygiene, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Haleluya T. Wami
- Institut für Hygiene, Universitätsklinikum Münster, 48149 Münster, Germany;
| | - Torsten Schmidt-Wieland
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Daniela Bertsch
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Klaus Oberdorfer
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
| | - Herbert Hof
- MVZ Labor Limbach und Kollegen, Im Breitspiel 16, 69126 Heidelberg, Germany; (T.S.-W.); (D.B.); (K.O.); (H.H.)
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4
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Zelendova M, Papagiannitsis CC, Valcek A, Medvecky M, Bitar I, Hrabak J, Gelbicova T, Barakova A, Kutilova I, Karpiskova R, Dolejska M. Characterization of the Complete Nucleotide Sequences of mcr-1-Encoding Plasmids From Enterobacterales Isolates in Retailed Raw Meat Products From the Czech Republic. Front Microbiol 2021; 11:604067. [PMID: 33519748 PMCID: PMC7843963 DOI: 10.3389/fmicb.2020.604067] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
The aim of our study was to determine complete nucleotide sequence of mcr-1-carrying plasmids from Enterobacterales isolates recovered from domestic and imported raw retailed meat and compare them with plasmids available at the GenBank sequence database. A set of 16 plasmids originating from Escherichia coli (n = 13), Klebsiella pneumoniae (n = 2), and Citrobacter braakii (n = 1) were analyzed. In our previous study, data from whole genome sequencing showed that mcr-1 gene was located on plasmids of different incompatibility groups (IncHI2, IncI2, and IncX4). The IncI2 (n = 3) and IncX4 (n = 8) plasmids harbored mcr-1.1 gene only, whereas IncHI2 sequence type 4 plasmids (n = 5) carried large multidrug resistance (MDR) regions. MDR regions of IncHI2 plasmids included additional antimicrobial resistance genes conferring resistance to β-lactams (blaTEM−1), aminoglycosides [aadA1, aadA2, and aph(6)-Id], macrolides [mef (B)], tetracycline (tetA, tetR), and sulphonamides (sul1, sul2, and sul3). Likewise, IncHI2 plasmids carried several insertion sequences including IS1, IS3, IS26, IS1326, and ISApl1. In conclusion, our findings confirmed the involvement of IncX4, IncI2, and IncHI2 plasmids in the dissemination of mcr-1.1 gene in several environmental niches, as in samples of retail meat originating from different geographical regions. In contrast to IncX4 and IncI2, IncHI2 plasmids were more diverse and carried additional genes for resistance to heavy metals and multiple antimicrobials.
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Affiliation(s)
- Marketa Zelendova
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Costas C Papagiannitsis
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia.,Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Adam Valcek
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Matej Medvecky
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Tereza Gelbicova
- Department of Bacteriology, Veterinary Research Institute, Brno, Czechia
| | - Alzbeta Barakova
- Department of Bacteriology, Veterinary Research Institute, Brno, Czechia.,Department of Experimental Biology, Faculty of Science, Masaryk University Brno, Brno, Czechia
| | - Iva Kutilova
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Renata Karpiskova
- Department of Bacteriology, Veterinary Research Institute, Brno, Czechia
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
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5
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Bogema DR, McKinnon J, Liu M, Hitchick N, Miller N, Venturini C, Iredell J, Darling AE, Roy Chowdury P, Djordjevic SP. Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups. Microb Genom 2020; 6. [PMID: 30810518 PMCID: PMC7067039 DOI: 10.1099/mgen.0.000255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequence type (ST)73 has emerged as one of the most frequently isolated extraintestinal pathogenic Escherichia coli. To examine the localized diversity of ST73 clonal groups, including their mobile genetic element profile, we sequenced the genomes of 16 multiple-drug resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia, between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccurred, over a 2 year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 clone D i2 reference genome shows high bootstrap support and clusters into four major groups that correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes, but the presence of iss, pic and several iron-acquisition operons was notable.
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Affiliation(s)
- D R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia.,The ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - J McKinnon
- The ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - M Liu
- The ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - N Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - N Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - C Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - J Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - A E Darling
- The ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - P Roy Chowdury
- The ithree Institute, University of Technology Sydney, NSW 2007, Australia
| | - S P Djordjevic
- The ithree Institute, University of Technology Sydney, NSW 2007, Australia
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6
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McKinnon J, Roy Chowdhury P, Djordjevic SP. Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature. Microb Drug Resist 2020; 26:787-793. [DOI: 10.1089/mdr.2019.0277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jessica McKinnon
- ithree Institute, University of Technology Sydney, Sydney, Australia
| | - Piklu Roy Chowdhury
- ithree Institute, University of Technology Sydney, Sydney, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
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Zingali T, Chapman TA, Webster J, Roy Chowdhury P, Djordjevic SP. Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia. Microorganisms 2020; 8:microorganisms8060896. [PMID: 32545892 PMCID: PMC7355605 DOI: 10.3390/microorganisms8060896] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/16/2023] Open
Abstract
Antibiotic resistance genes (ARGs) including those from the blaCTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.
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Affiliation(s)
- Tiziana Zingali
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia; (T.A.C.); (J.W.)
| | - John Webster
- NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia; (T.A.C.); (J.W.)
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
- Correspondence: ; Tel.: +61-2-9514-4127
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Hastak P, Cummins ML, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital. Microb Genom 2020; 6:e000371. [PMID: 32374251 PMCID: PMC7371115 DOI: 10.1099/mgen.0.000371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/03/2020] [Indexed: 11/29/2022] Open
Abstract
This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried blaCTX -M-gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII-IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.
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Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Max L. Cummins
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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Reid CJ, Blau K, Jechalke S, Smalla K, Djordjevic SP. Whole Genome Sequencing of Escherichia coli From Store-Bought Produce. Front Microbiol 2020; 10:3050. [PMID: 32063888 PMCID: PMC7000624 DOI: 10.3389/fmicb.2019.03050] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/18/2019] [Indexed: 12/22/2022] Open
Abstract
The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. Escherichia coli is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for E. coli from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant E. coli from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant E. coli from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. E. coli were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant E. coli providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection (n = 84, 70%) with multi-locus sequence types B1-ST6186 (n = 37, 31%), C-ST165 (n = 17, 14%), B1-ST58 (n = 14, 12%), B1-ST641 (n = 8, 7%), and C-ST88 (n = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS26 were also identified. Storage may affect the lineages of E. coli isolated, however further studies are needed. Our study indicates produce predominantly carry E. coli with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.
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Affiliation(s)
- Cameron J. Reid
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Khald Blau
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sven Jechalke
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Institute for Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Steven P. Djordjevic
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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10
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Zhu D, Yang Z, Xu J, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen X, Cheng A. Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands. Funct Integr Genomics 2019; 20:307-320. [PMID: 31654228 DOI: 10.1007/s10142-019-00715-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/20/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023]
Abstract
Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.
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Affiliation(s)
- Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Jinge Xu
- Guizhou Animal Husbandry and Veterinary Research Institute, Guiyang, Guizhou, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunya Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ling Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanling Yu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoyue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China.
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11
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Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production. Microorganisms 2019; 7:microorganisms7090299. [PMID: 31470501 PMCID: PMC6780720 DOI: 10.3390/microorganisms7090299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/22/2019] [Accepted: 08/25/2019] [Indexed: 12/29/2022] Open
Abstract
Knowledge of mobile genetic elements that capture and disseminate antimicrobial resistance genes between diverse environments, particularly across human-animal boundaries, is key to understanding the role anthropogenic activities have in the evolution of antimicrobial resistance. Plasmids that circulate within the Enterobacteriaceae and the Proteobacteria more broadly are well placed to acquire resistance genes sourced from separate niche environments and provide a platform for smaller mobile elements such as IS26 to assemble these genes into large, complex genomic structures. Here, we characterised two atypical Z/I1 hybrid plasmids, pSTM32-108 and pSTM37-118, hosting antimicrobial resistance and virulence associated genes within endemic pathogen Salmonella enterica serovar Typhimurium 1,4,[5],12:i:-, sourced from Australian swine production facilities during 2013. We showed that the plasmids found in S. Typhimurium 1,4,[5],12:i:- are close relatives of two plasmids identified from Escherichia coli of human and bovine origin in Australia circa 1998. The older plasmids, pO26-CRL125 and pO111-CRL115, encoded a putative serine protease autotransporter and were host to a complex resistance region composed of a hybrid Tn21-Tn1721 mercury resistance transposon and composite IS26 transposon Tn6026. This gave a broad antimicrobial resistance profile keyed towards first generation antimicrobials used in Australian agriculture but also included a class 1 integron hosting the trimethoprim resistance gene dfrA5. Genes encoding resistance to ampicillin, trimethoprim, sulphonamides, streptomycin, aminoglycosides, tetracyclines and mercury were a feature of these plasmids. Phylogenetic analyses showed very little genetic drift in the sequences of these plasmids over the past 15 years; however, some alterations within the complex resistance regions present on each plasmid have led to the loss of various resistance genes, presumably as a result of the activity of IS26. These alterations may reflect the specific selective pressures placed on the host strains over time. Our studies suggest that these plasmids and variants of them are endemic in Australian food production systems.
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12
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Smalla K, Cook K, Djordjevic SP, Klümper U, Gillings M. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiol Ecol 2019; 94:5114257. [PMID: 30277517 DOI: 10.1093/femsec/fiy195] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 09/28/2018] [Indexed: 02/01/2023] Open
Abstract
Antibiotic resistance is one of the major problems facing medical practice in the 21st century. Historical approaches to managing antibiotic resistance have often focused on individual patients, specific pathogens and particular resistance phenotypes. However, it is increasingly recognized that antibiotic resistance is a complex ecological and evolutionary problem. As such, understanding the dynamics of antibiotic resistance requires integration of data on the diverse mobile genetic elements often associated with antibiotic resistance genes, and their dissemination by various mechanisms of horizontal gene transfer between bacterial cells and environments. Most important is understanding the fate and effects of antibiotics at sub-inhibitory concentrations, and co-selection. This opinion paper identifies key knowledge gaps in our understanding of resistance phenomena, and outlines research needs that should be addressed to help us manage resistance into the future.
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Affiliation(s)
- Kornelia Smalla
- Julius Kühn-Institut Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA Agricultural Research center, 950 College Station Road, Athens GA 306052720, USA
| | - Steven P Djordjevic
- ithree institute, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007 Australia
| | - Uli Klümper
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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13
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Wyrsch ER, Reid CJ, DeMaere MZ, Liu MY, Chapman TA, Roy Chowdhury P, Djordjevic SP. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Reid CJ, Wyrsch ER, Roy Chowdhury P, Zingali T, Liu M, Darling AE, Chapman TA, Djordjevic SP. Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microb Genom 2019; 3. [PMID: 29306352 PMCID: PMC5761274 DOI: 10.1099/mgen.0.000143] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
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Affiliation(s)
- Cameron J Reid
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Ethan R Wyrsch
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tiziana Zingali
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Michael Liu
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Aaron E Darling
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Toni A Chapman
- 2NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Steven P Djordjevic
- 1The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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15
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Roy Chowdhury P, McKinnon J, Liu M, Djordjevic SP. Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS 26 Transposon in a Unique Chromosomal Location. Front Microbiol 2019; 9:3212. [PMID: 30671039 PMCID: PMC6331395 DOI: 10.3389/fmicb.2018.03212] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of blaCTX-M, blaNDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo.
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Affiliation(s)
- Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Macarthur, NSW, Australia
| | - Jessica McKinnon
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Michael Liu
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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16
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Juhas M. Genomic Islands and the Evolution of Multidrug-Resistant Bacteria. HORIZONTAL GENE TRANSFER 2019:143-153. [DOI: 10.1007/978-3-030-21862-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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17
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Reid CJ, DeMaere MZ, Djordjevic SP. Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny. Microb Genom 2018; 5. [PMID: 30303480 PMCID: PMC6487311 DOI: 10.1099/mgen.0.000225] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.
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Affiliation(s)
- Cameron J Reid
- The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Matthew Z DeMaere
- The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- The i3 institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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18
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Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
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19
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Gillings MR. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 2016; 1389:20-36. [DOI: 10.1111/nyas.13213] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Michael R. Gillings
- Genes to Geoscience Research Centre, Department of Biological Sciences Macquarie University Sydney New South Wales Australia
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20
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Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
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Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
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21
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Kubasova T, Cejkova D, Matiasovicova J, Sekelova Z, Polansky O, Medvecky M, Rychlik I, Juricova H. Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium. Genome Biol Evol 2016; 8:1661-71. [PMID: 27189997 PMCID: PMC5390554 DOI: 10.1093/gbe/evw105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.
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Affiliation(s)
- Tereza Kubasova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Darina Cejkova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | | | - Zuzana Sekelova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Ondrej Polansky
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Matej Medvecky
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Helena Juricova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
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22
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García P, Malorny B, Rodicio MR, Stephan R, Hächler H, Guerra B, Lucarelli C. Horizontal Acquisition of a Multidrug-Resistance Module (R-type ASSuT) Is Responsible for the Monophasic Phenotype in a Widespread Clone of Salmonella Serovar 4,[5],12:i:. Front Microbiol 2016; 7:680. [PMID: 27242707 PMCID: PMC4861720 DOI: 10.3389/fmicb.2016.00680] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/26/2016] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium incapable of expressing the second-phase flagellar antigen (fljAB operon), and it is recognized to be one of the most prevalent serovars causing human infections. A clonal lineage characterized by phage type DT193, PulseNet PFGE profile STYMXB.0131 and multidrug resistance to ampicillin, streptomycin, sulphonamides and tetracycline (R-type ASSuT) is commonly circulating in Europe. In this study we determined the deletions affecting the fljAB operon and the resistance region responsible for the R-type ASSuT in a strain of Salmonella enterica serovar 4,5,12:i:- DT193/STYMXB.0131, through an approach based on PCRs and Southern blot hybridization of genomic DNA. Using a set of nine specific PCRs, the prevalence of the resistance region was assessed in a collection of 144 S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains isolated from Germany, Switzerland and Italy. A 28 kb-region is embedded between the loci STM2759 and iroB, replacing the DNA located in between, including the fljAB operon. It encompasses the genes bla TEM-1, strA-strB, sul2 and tet(B) responsible for the R-type ASSuT together with genes involved in plasmid replication and orfs of unknown function characteristically located on IncH1 plasmids. Its location and internal structure is fairly conserved in S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains regardless of the isolation source or country. Hence, in the S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 clonal lineage widespread in Germany, Switzerland and Italy, a resistance region derived from IncH1 plasmids has replaced the chromosomal region encoding the second flagellar phase and is an example of the stabilization of new plasmid-derived genetic material due to integration into the bacterial chromosome.
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Affiliation(s)
- Patricia García
- Department of Functional Biology, Area of Microbiology, University of OviedoOviedo, Spain
| | - Burkhard Malorny
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
| | - M. Rosario Rodicio
- Department of Functional Biology, Area of Microbiology, University of OviedoOviedo, Spain
| | - Roger Stephan
- Vetsuisse Faculty, National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of ZurichZürich, Switzerland
| | - Herbert Hächler
- Vetsuisse Faculty, National Centre for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of ZurichZürich, Switzerland
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
| | - Claudia Lucarelli
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di SanitàRome, Italy
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and ControlStockholm, Sweden
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Tn6026 and Tn6029 are found in complex resistance regions mobilised by diverse plasmids and chromosomal islands in multiple antibiotic resistant Enterobacteriaceae. Plasmid 2015; 80:127-37. [PMID: 25917547 DOI: 10.1016/j.plasmid.2015.04.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 04/07/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
Transposons flanked by direct copies of IS26 are important contributors to the evolution of multiple antibiotic resistance. Tn6029 and Tn6026 are examples of composite transposons that have become widely disseminated on small and large plasmids with different incompatibility markers in pathogenic and commensal Escherichia coli and various serovars of Salmonella enterica. Some of the plasmids that harbour these transposons also carry combinations of virulence genes. Recently, Tn6029 and Tn6026 and derivatives thereof have been found on chromosomal islands in both established and recently emerged pathogens. While Tn6029 and Tn6026 carry genes encoding resistance to older generation antibiotics, they also provide a scaffold for the introduction of genes encoding resistance to a wide variety of clinically relevant antibiotics that are mobilised by IS26. As a consequence, Tn6029 and Tn6026 or variants are likely to increasingly feature in complex resistance regions in multiple antibiotic resistant Enterobacteriaceae that threaten the health of humans and food production animals.
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Correction: A role for Tn6029 in the evolution of the complex antibiotic resistance gene loci in genomic island 3 in enteroaggregative hemorrhagic Escherichia coli O104:H4. PLoS One 2015; 10:e0126197. [PMID: 25885569 PMCID: PMC4401760 DOI: 10.1371/journal.pone.0126197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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