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Kotzamanidis C, Malousi A, Paraskeva A, Vafeas G, Giantzi V, Hatzigiannakis E, Dalampakis P, Kinigopoulou V, Vrouhakis I, Zouboulis A, Yiangou M, Zdragas A. River waters in Greece: A reservoir for clinically relevant extended-spectrum-β-lactamases-producing Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173554. [PMID: 38823724 DOI: 10.1016/j.scitotenv.2024.173554] [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: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
In the current study, the genotypic characteristics such as antimicrobial resistance and virulence genes, and plasmid replicons and phenotypic characteristics such as biofilm formation and antimicrobial resistance of 87 extended-spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-Ec) isolated from 7 water bodies in northern Greece were investigated. Our data show a high prevalence (60.0 %) of ESBL-Ec in surface waters that exhibit high genetic diversity, suggesting multiple sources of their transmission into the aquatic environment. When evaluating the antimicrobial resistance of isolates, wide variation in their resistance profiles has been detected, with all isolates being multi-drug resistant (MDR). Regarding biofilm formation capacity and phylogenetic groups, the majority (54.0 %, 47/87) of ESBL-Ec were classified as no biofilm producers mainly assigned to phylogroup A (35.6 %; 31/87), followed by B2 (26.5 %; 23/87). PCR screening showed that a high proportion of the isolates tested positive for the blaCTX-M-1 group genes (69 %, 60/87), followed by blaTEM (55.2 %, 48/87), blaOXA (25.3 %, 22/87) and blaCTX-M-9 (17.2 %, 15/87). A subset of 28 ESBL-Ec strains was further investigated by applying whole genome sequencing (WGS), and among them, certain clinically significant sequence types were identified, such as ST131 and ST10. The corresponding in silico analysis predicted all these isolates as human pathogens, while a significant proportion of WGS-ESBL-Ec were assigned to extraintestinal pathogenic E. coli (ExPEC; 32.1 %), and urinary pathogenic E. coli (UPEC; 28.6 %) pathotypes. Comparative phylogenetic analysis, showed that the genomes of the ST131-O25:H4-H30 isolates are genetically linked to the human clinical strains. Here, we report for the first time the detection of a plasmid-mediated mobile colistin resistance gene in ESBL-Ec in Greece isolated from an environmental source. Overall, this study underlines the role of surface waters as a reservoir for antibiotic resistance genes and for presumptive pathogenic ESBL-Ec.
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Affiliation(s)
- Charalampos Kotzamanidis
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece.
| | - Andigoni Malousi
- School of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Genomics and Epigenomics Translational Research Group, Center for Interdisciplinary Research and Innovation, Thessaloniki 57001, Greece
| | - Anastasia Paraskeva
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - George Vafeas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Virginia Giantzi
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
| | - Evaggelos Hatzigiannakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Paschalis Dalampakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Vasiliki Kinigopoulou
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Ioannis Vrouhakis
- Soil & Water Resources Institute, Hellenic Agricultural Organisation-DEMETER, Sindos, Central Macedonia 57400, Greece
| | - Anastasios Zouboulis
- Department of Chemistry, Division of Chemical & Industrial Technology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Minas Yiangou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonios Zdragas
- Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation-DEMETER, Campus of Thermi, Thermi 570 01, Greece
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Tomasch J, Kopejtka K, Shivaramu S, Mujakić I, Koblížek M. On the evolution of chromosomal regions with high gene strand bias in bacteria. mBio 2024; 15:e0060224. [PMID: 38752745 PMCID: PMC11237797 DOI: 10.1128/mbio.00602-24] [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: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
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Lerminiaux N, Mitchell R, Bartoszko J, Davis I, Ellis C, Fakharuddin K, Hota SS, Katz K, Kibsey P, Leis JA, Longtin Y, McGeer A, Minion J, Mulvey M, Musto S, Rajda E, Smith SW, Srigley JA, Suh KN, Thampi N, Tomlinson J, Wong T, Mataseje L. Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021. Antimicrob Agents Chemother 2023; 67:e0086023. [PMID: 37971242 PMCID: PMC10720558 DOI: 10.1128/aac.00860-23] [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: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.
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Affiliation(s)
| | | | | | - Ian Davis
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Chelsey Ellis
- The Moncton Hospital, Moncton, New Brunswick, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Susy S. Hota
- University Health Network, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Pamela Kibsey
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Jerome A. Leis
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yves Longtin
- Jewish General Hospital, Montréal, Québec, Canada
| | | | - Jessica Minion
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sonja Musto
- Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Ewa Rajda
- McGill University Health Centre, Montréal, Québec, Canada
| | | | - Jocelyn A. Srigley
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Nisha Thampi
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Titus Wong
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - on behalf of the Canadian Nosocomial Infection Surveillance Program
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
- The Moncton Hospital, Moncton, New Brunswick, Canada
- University Health Network, Toronto, Ontario, Canada
- North York General Hospital, Toronto, Ontario, Canada
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Jewish General Hospital, Montréal, Québec, Canada
- Sinai Health, Toronto, Ontario, Canada
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
- Health Sciences Centre, Winnipeg, Manitoba, Canada
- McGill University Health Centre, Montréal, Québec, Canada
- University of Alberta Hospital, Edmonton, Alberta, Canada
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
- The Ottawa Hospital, Ottawa, Ontario, Canada
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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Messele YE, Trott DJ, Hasoon MF, Veltman T, McMeniman JP, Kidd SP, Djordjevic SP, Petrovski KR, Low WY. Phylogenetic Analysis of Escherichia coli Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates. Antibiotics (Basel) 2023; 12:antibiotics12050895. [PMID: 37237797 DOI: 10.3390/antibiotics12050895] [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: 04/06/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The similarity of commensal Escherichia coli isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic relationships among faecal Escherichia coli isolates from beef cattle (n = 37) from a single feedlot in comparison to previously analysed pig faecal (n = 45), poultry extraintestinal (n = 19), and human extraintestinal E. coli isolates (n = 40) from three previous Australian studies. Most beef cattle and pig isolates belonged to E. coli phylogroups A and B1, whereas most avian and human isolates belonged to B2 and D, although a single human extraintestinal isolate belonged to phylogenetic group A and sequence type (ST) 10. The most common E. coli sequence types (STs) included ST10 for beef cattle, ST361 for pig, ST117 for poultry, and ST73 for human isolates. Extended-spectrum and AmpC β-lactamase genes were identified in seven out of thirty-seven (18.9%) beef cattle isolates. The most common plasmid replicons identified were IncFIB (AP001918), followed by IncFII, Col156, and IncX1. The results confirm that feedlot cattle isolates examined in this study represent a reduced risk to human and environmental health with regard to being a source of antimicrobial-resistant E. coli of clinical importance.
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Affiliation(s)
- Yohannes E Messele
- The Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, Australia
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Darren J Trott
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Mauida F Hasoon
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Tania Veltman
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Joe P McMeniman
- Meat & Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
| | - Stephen P Kidd
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
- Research Centre for Infectious Disease, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kiro R Petrovski
- The Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, Australia
- The Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Wai Y Low
- The Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, Australia
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Downing T, Lee MJ, Archbold C, McDonnell A, Rahm A. Informing plasmid compatibility with bacterial hosts using protein-protein interaction data. Genomics 2022; 114:110509. [PMID: 36273742 DOI: 10.1016/j.ygeno.2022.110509] [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: 08/19/2022] [Revised: 09/23/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
The compatibility of plasmids with new host cells is significant given their role in spreading antimicrobial resistance (AMR) and virulence factor genes. Evaluating this using in vitro screening is laborious and can be informed by computational analyses of plasmid-host compatibility through rates of protein-protein interactions (PPIs) between plasmid and host cell proteins. We identified large excesses of such PPIs in eight important plasmids, including pOXA-48, using most known bacteria (n = 4363). 23 species had high rates of interactions with four blaOXA-48-positive plasmids. We also identified 48 species with high interaction rates with plasmids common in Escherichia coli. We found a strong association between one plasmid and the fimbrial adhesin operon pil, which could enhance host cell adhesion in aqueous environments. An excess rate of PPIs could be a sign of host-plasmid compatibility, which is important for AMR control given that plasmids like pOXA-48 move between species with ease.
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Affiliation(s)
- Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland; The Pirbright Institute, UK.
| | - Min Jie Lee
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Conor Archbold
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Adam McDonnell
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Alexander Rahm
- GAATI Lab, University of French Polynesia, Tahiti, French Polynesia
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