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Staudacher M, Hotz JF, Kriz R, Schefberger K, Schneider L, Spettel K, Starzengruber P, Hagemann JB, Leutzendorff A, Burgmann H, Lagler H. Differences in oxazolidinone resistance mechanisms and small colony variants emergence of Staphylococcus aureus induced in an in vitro resistance development model. Emerg Microbes Infect 2024; 13:2292077. [PMID: 38055244 PMCID: PMC10849000 DOI: 10.1080/22221751.2023.2292077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Invasive Staphylococcus aureus infections are associated with a high burden of disease, case fatality rate and healthcare costs. Oxazolidinones such as linezolid and tedizolid are considered potential treatment choices for conditions involving methicillin resistance or penicillin allergies. Additionally, they are being investigated as potential inhibitors of toxins in toxin-mediated diseases. In this study, linezolid and tedizolid were evaluated in an in vitro resistance development model for induction of resistance in S. aureus. Whole genome sequencing was conducted to elucidate resistance mechanisms through the identification of causal mutations. After inducing resistance to both linezolid and tedizolid, several partially novel single nucleotide variants (SNVs) were detected in the rplC gene, which encodes the 50S ribosome protein L3 in S. aureus. These SNVs were found to decrease the binding affinity, potentially serving as the underlying cause for oxazolidinone resistance. Furthermore, in opposite to linezolid we were able to induce phenotypically small colony variants of S. aureus after induction of resistance with tedizolid for the first time in literature. In summary, even if different antibiotic concentrations were required and SNVs were detected, the principal capacity of S. aureus to develop resistance to oxazolidinones seems to differ between linezolid and tedizolid in-vivo but not in vitro. Stepwise induction of resistance seems to be a time and cost-effective tool for assessing resistance evolution. Inducted-resistant strains should be examined and documented for epidemiological reasons, if MICs start to rise or oxazolidinone-resistant S. aureus outbreaks become more frequent.
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Affiliation(s)
- Moritz Staudacher
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Angiology, Medical University of Vienna, Vienna, Austria
| | - Julian Frederic Hotz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Neurology, Evangelic Hospital Vienna, Vienna, Austria
| | - Richard Kriz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Katharina Schefberger
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisa Schneider
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Kathrin Spettel
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Peter Starzengruber
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | | | - Amelie Leutzendorff
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Heimo Lagler
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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Tadesse BT, Svetlicic E, Zhao S, Berhane N, Jers C, Solem C, Mijakovic I. Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms. Microbiol Res 2024; 283:127702. [PMID: 38552381 DOI: 10.1016/j.micres.2024.127702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark; Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark
| | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Ethiopia
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark.
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark; Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Sapula SA, Hart BJ, Siderius NL, Amsalu A, Blaikie JM, Venter H. Multidrug-resistant Stenotrophomonas maltophilia in residential aged care facilities: An emerging threat. Microbiologyopen 2024; 13:e1409. [PMID: 38682784 PMCID: PMC11057060 DOI: 10.1002/mbo3.1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Stenotrophomonas maltophilia is a multidrug-resistant (MDR), Gram-negative bacterium intrinsically resistant to beta-lactams, including last-resort carbapenems. As an opportunistic pathogen, it can cause serious healthcare-related infections. This study assesses the prevalence, resistance profiles, and genetic diversity of S. maltophilia isolated from residential aged care facilities (RACFs). RACFs are known for their overuse and often inappropriate use of antibiotics, creating a strong selective environment that favors the development of bacterial resistance. The study was conducted on 73 S. maltophilia isolates recovered from wastewater and facility swab samples obtained from three RACFs and a retirement village. Phenotypic and genotypic assessments of the isolates revealed high carbapenem resistance, exemplifying their intrinsic beta-lactam resistance. Alarmingly, 49.3% (36/73) of the isolates were non-wild type for colistin, with minimum inhibitory concentration values of > 4 mg/L, and 11.0% (8/73) were resistant to trimethoprim-sulfamethoxazole. No resistance mechanisms were detected for either antimicrobial. Genotypic assessment of known lineages revealed isolates clustering with Sm17 and Sm18, lineages not previously reported in Australia, suggesting the potential ongoing spread of MDR S. maltophilia. Lastly, although only a few isolates were biocide tolerant (2.7%, 2/73), their ability to grow in high concentrations (64 mg/L) of triclosan is concerning, as it may be selecting for their survival and continued dissemination.
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Affiliation(s)
- Sylvia A. Sapula
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Bradley J. Hart
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Naomi L. Siderius
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Anteneh Amsalu
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
- Department of Medical MicrobiologyUniversity of GondarGondarEthiopia
| | - Jack M. Blaikie
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Henrietta Venter
- Health and Biomedical Innovation, UniSA Clinical and Health SciencesUniversity of South AustraliaAdelaideSouth AustraliaAustralia
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Flatgard BM, Williams AD, Amin MB, Hobman JL, Stekel DJ, Rousham EK, Islam MA. Tracking antimicrobial resistance transmission in urban and rural communities in Bangladesh: a One Health study of genomic diversity of ESBL-producing and carbapenem-resistant Escherichia coli. Microbiol Spectr 2024:e0395623. [PMID: 38700359 DOI: 10.1128/spectrum.03956-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to global health and sustainable development goals, especially in low- and middle-income countries (LMICs). This study aimed to understand the transmission of AMR between poultry, humans, and the environment in Bangladesh using a One Health approach. We analyzed the whole genome sequences (WGS) of 117 extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) isolates, with 46 being carbapenem resistant. These isolates were obtained from human (n = 20) and poultry feces (n = 12), as well as proximal environments (wastewater) (n = 85) of three different study sites, including rural households (n = 48), rural poultry farms (n = 20), and urban wet markets (n = 49). The WGS of ESBL-Ec isolates were compared with 58 clinical isolates from global databases. No significant differences in antibiotic resistance genes (ARGs) were observed in ESBL-Ec isolated from humans with and without exposure to poultry. Environmental isolates showed higher ARG diversity than human and poultry isolates. No clonal transmission between poultry and human isolates was found, but wastewater was a reservoir for ESBL-Ec for both. Except for one human isolate, all ESBL-Ec isolates were distinct from clinical isolates. Most isolates (77.8%) carried at least one plasmid replicon type, with IncFII being the most prevalent. IncFIA was predominant in human isolates, while IncFII, Col(MG828), and p0111 were common in poultry. We observed putative sharing of ARG-carrying plasmids among isolates, mainly from wastewater. However, in most cases, bacterial isolates sharing plasmids were also clonally related, suggesting clonal spread was more probable than just plasmid transfer. IMPORTANCE Our study underscores that wastewater discharged from households and wet markets carries antibiotic-resistant organisms from both human and animal sources. Thus, direct disposal of wastewater into the environment not only threatens human health but also endangers food safety by facilitating the spread of antimicrobial resistance (AMR) to surface water, crops, vegetables, and subsequently to food-producing animals. In regions with intensive poultry production heavily reliant on the prophylactic use of antibiotics, compounded by inadequate waste management systems, such as Bangladesh, the ramifications are particularly pronounced. Wastewater serves as a pivotal juncture for the dissemination of antibiotic-resistant organisms and functions as a pathway through which strains of human and animal origin can infiltrate the environment and potentially colonize new hosts. Further research is needed to thoroughly characterize wastewater isolates/populations and understand their potential impact on interconnected environments, communities, and wildlife.
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Affiliation(s)
- Brandon M Flatgard
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Alexander D Williams
- Laboratory of Data Discovery for Health Ltd, Hong Kong Science and Technology Park, Tai Po, Hong Kong, China
- School of Public Health, University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | | | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, United Kingdom
- Department of Mathematics and Applied Mathematics, University of Johannesburg, Johannesburg, South Africa
| | - Emily K Rousham
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, United Kingdom
| | - Mohammad Aminul Islam
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Laboratory of Food Safety and One Health, icddr,b, Dhaka, Bangladesh
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Sprotte S, Brinks E, Neve H, Franz CM. Complete genome sequence of the novel virulent phage PMBT24 infecting Enterocloster bolteae from the human gut. Heliyon 2024; 10:e28813. [PMID: 38655313 PMCID: PMC11035940 DOI: 10.1016/j.heliyon.2024.e28813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
PMBT24, the first reported virulent bacteriophage infecting the anaerobic human gut bacterium Enterocloster bolteae strain MBT-21, was isolated from a municipal sewage sample and its genome was sequenced and analysed. Transmission electron microscopy revealed a phage with an icosahedral head and a long, non-contractile tail. The circularly permutated, 99,962-bp dsDNA genome of the pac-type phage has a mol% G + C content of 32.1 and comprises 173 putative ORFs. Using amino acid sequence-based phylogeny, phage PMBT24 showed similarity to other, hitherto non-published phage genomes in the databases. Our data suggested phage PMBT24 to present the type phage of a novel genus (proposed name Kielvirus) and novel family of phages (proposed name Kielviridae).
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Affiliation(s)
- Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
| | | | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Str. 1, 24103, Kiel, Germany
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6
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Kanje LE, Kumburu H, Kuchaka D, Shayo M, Juma MA, Kimu P, Beti M, van Zwetselaar M, Wadugu B, Mmbaga BT, Mkumbaye SI, Sonda T. Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:110. [PMID: 38671498 PMCID: PMC11055328 DOI: 10.1186/s12920-024-01882-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance. OBJECTIVE To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. MATERIALS AND METHODS A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion. RESULTS Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes. CONCLUSION Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.
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Affiliation(s)
- Livin E Kanje
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
| | - Happiness Kumburu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Masoud A Juma
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- State University of Zanzibar, Zanzibar, Tanzania
| | - Patrick Kimu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina T Mmbaga
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
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Nhu NTK, Phan MD, Hancock SJ, Peters KM, Alvarez-Fraga L, Forde BM, Andersen SB, Miliya T, Harris PNA, Beatson SA, Schlebusch S, Bergh H, Turner P, Brauner A, Westerlund-Wikström B, Irwin AD, Schembri MA. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 2024; 12:RP91853. [PMID: 38622998 PMCID: PMC11021048 DOI: 10.7554/elife.91853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of QueenslandBrisbaneAustralia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
| | - Patrick NA Harris
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Sanmarie Schlebusch
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers PlainsBrisbaneAustralia
| | - Haakon Bergh
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Infection Management Prevention Service, Queensland Children's HospitalBrisbaneAustralia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
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8
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Barmak SM, Mendenhall IH, Sinyavskiy YA, Berdygaliev AB, Sharmanov TS, Sultankulova GT, Tuigunov DN, Zholdybayeva EV. Whole-genome sequence and annotation of Salmonella enterica subsp. enterica strain QazSL-4. Microbiol Resour Announc 2024:e0087623. [PMID: 38624204 DOI: 10.1128/mra.00876-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024] Open
Abstract
Here, we present the whole-genome sequence of Salmonella enterica subsp. enterica strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.
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Affiliation(s)
- Sabyrkhan M Barmak
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yuriy A Sinyavskiy
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Aidar B Berdygaliev
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Turegeldy Sh Sharmanov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Gulmira T Sultankulova
- Department of Pediatric Surgery, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Dilyar N Tuigunov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Elena V Zholdybayeva
- National scientific shared laboratory of biotechnology, National Center for Biotechnology, Astana, Kazakhstan
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9
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Tóth K, Damjanova I, Laczkó L, Buzgó L, Lesinszki V, Ungvári E, Jánvári L, Hanczvikkel A, Tóth Á, Szabó D. Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary. Antibiotics (Basel) 2024; 13:363. [PMID: 38667039 PMCID: PMC11047377 DOI: 10.3390/antibiotics13040363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ivelina Damjanova
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
- HUN-REN-DE Conservation Biology Research Group, University of Debrecen, 4032 Debrecen, Hungary
| | - Lilla Buzgó
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Virág Lesinszki
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Erika Ungvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Laura Jánvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Adrienn Hanczvikkel
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ákos Tóth
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Dóra Szabó
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- HUN-REN-SE Human Microbiota Research Group, 1052 Budapest, Hungary
- Neurosurgical and Neurointervention Clinic, Semmelweis University, 1083 Budapest, Hungary
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10
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Abriouel H, Caballero Gómez N, Manetsberger J, Benomar N. Dual effects of a bacteriocin-producing Lactiplantibacillus pentosus CF-6HA, isolated from fermented aloreña table olives, as potential probiotic and antimicrobial agent. Heliyon 2024; 10:e28408. [PMID: 38560111 PMCID: PMC10981101 DOI: 10.1016/j.heliyon.2024.e28408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The probiotic potential of Lactiplantibacillus pentosus CF-6HA isolated from traditionally fermented Aloreña table olives was analyzed in vitro and in silico. Results obtained suggested that this strain can be catalogued as "talented" bacterium exhibiting bacteriocin production with antimicrobial activity against human/animal and plant pathogens, such as Pseudomonas syringae and Verticillium dahliae. The robustness, safety and probiotic potential of L. pentosus CF-6HA was confirmed by in silico analysis. In addition, a plethora of coding genes for defense and adaptability to different life styles besides functional properties were identified. In this sense, defense mechanisms of L. pentosus CF-6HA consist of 17 ISI elements, 98 transposases and 13 temperate phage regions as well as a CRISPR (clustered regularly interspaced short palindromic repeats)/cas system. Moreover, the functionality of this strain was confirmed by the presence of genes coding for secondary metabolites, exopolysaccharides and other bioactive molecules. Finally, we demonstrated the ability of L. pentosus CF-6HA to biotransform selenite to nanoparticles (SeNPs) highlighting its potential role in selenium bioremediation to be exploited in foods, agriculture and the environment; but also for the bio-enrichment of fermented foods with selenium.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Julia Manetsberger
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de La Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071-Jaén, Spain
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11
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Bacon RL, Norman KN, Nickodem CA, Vinasco JA, Gray SB, Hodo CL, Lawhon SD. Whole-genome sequences of Campylobacter coli and Campylobacter jejuni isolates from rhesus macaques ( Macaca mulatta) with and without intestinal disease. Microbiol Resour Announc 2024; 13:e0001824. [PMID: 38446060 PMCID: PMC11008214 DOI: 10.1128/mra.00018-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
Campylobacter jejuni or Campylobacter coli infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (Macaca mulatta). We report the complete genomes of 8 C. jejuni isolates and 103 C. coli isolates obtained from rhesus macaques with and without intestinal disease.
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Affiliation(s)
- Rebecca L. Bacon
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Keri N. Norman
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Colette A. Nickodem
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Javier A. Vinasco
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Stanton B. Gray
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Carolyn L. Hodo
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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12
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Recacha E, Kuropka B, Díaz-Díaz S, García-Montaner A, González-Tortuero E, Docobo-Pérez F, Rodríguez-Rojas A, Rodríguez-Martínez JM. Impact of suppression of the SOS response on protein expression in clinical isolates of Escherichia coli under antimicrobial pressure of ciprofloxacin. Front Microbiol 2024; 15:1379534. [PMID: 38659986 PMCID: PMC11039860 DOI: 10.3389/fmicb.2024.1379534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction/objective Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of Escherichia coli clinical strains. Materials and methods Five clinical isolates of E. coli carrying different chromosomally- and/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with E. coli ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the recA gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1 h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC-MS) in order to identify proteins that were differentially expressed upon deletion of recA in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software. Results The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins. Conclusion High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.
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Affiliation(s)
- Esther Recacha
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Sara Díaz-Díaz
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Andrea García-Montaner
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | | | - Fernando Docobo-Pérez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Alexandro Rodríguez-Rojas
- Division for Small Animal Internal Medicine, Department for Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jose Manuel Rodríguez-Martínez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
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13
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Timková I, Maliničová L, Nosáľová L, Kolesárová M, Lorková Z, Petrová N, Pristaš P, Kisková J. Genomic insights into the adaptation of Acinetobacter johnsonii RB2-047 to the heavy metal-contaminated subsurface mine environment. Biometals 2024; 37:371-387. [PMID: 37973678 PMCID: PMC11006771 DOI: 10.1007/s10534-023-00555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023]
Abstract
The subsurface mine environments characterized by high levels of toxic metals and low nutrient availability represent an extreme threat to bacterial persistence. In recent study, the genomic analysis of the Acinetobacter johnsonii strain RB2-047 isolated from the Rozália Gold Mine in Slovakia was performed. As expected, the studied isolate showed a high level of heavy metal tolerance (minimum inhibitory concentrations were 500 mg/L for copper and nickel, 1,500 mg/L for lead, and 250 mg/L for zinc). The RB2-047 strain also showed noticeable resistance to several antibiotics (ampicillin, kanamycin, chloramphenicol, tetracycline and ciprofloxacin). The genomic composition analysis demonstrated a low number of antibiotic and metal resistance coding genes, but a high occurrence of efflux transporter genes located on the bacterial chromosome. The experimental inhibition of efflux pumps resulted in decreased tolerance to Zn and Ni (but not to Cu and Pb) and to all antibiotics tested. In addition, the H33342 dye-accumulation assay confirmed the high efflux activity in the RB2-047 isolate. These findings showed the important role of efflux pumps in the adaptation of Acinetobacter johsonii strain RB2-047 to metal polluted mine environment as well as in development of multi-antibiotic resistance.
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Affiliation(s)
- Ivana Timková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lenka Maliničová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Lea Nosáľová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Mariana Kolesárová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Zuzana Lorková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Nikola Petrová
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
| | - Peter Pristaš
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| | - Jana Kisková
- Department of Microbiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154, Košice, Slovakia.
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14
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Hu K, Meyer F, Deng ZL, Asgari E, Kuo TH, Münch PC, McHardy AC. Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes. Brief Bioinform 2024; 25:bbae206. [PMID: 38706320 DOI: 10.1093/bib/bbae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species-antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism, Campylobacter jejuni and Enterococcus faecium phenotypes were more robustly predicted than those of Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species-antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.
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Affiliation(s)
- Kaixin Hu
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, USA
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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15
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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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16
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Li W, Lim CH, Zhao Z, Wang Y, Conway PL, Loo SCJ. In Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10244-0. [PMID: 38498111 DOI: 10.1007/s12602-024-10244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.
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Affiliation(s)
- Wenrui Li
- NTU Institute for Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, 61 Nanyang Drive, Singapore, 637335, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chiun Hao Lim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Zhongtian Zhao
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Patricia Lynne Conway
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Centre for Marine Science Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Say Chye Joachim Loo
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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17
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Lagerstrom KM, Scales NC, Hadly EA. Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts. iScience 2024; 27:109072. [PMID: 38375235 PMCID: PMC10875580 DOI: 10.1016/j.isci.2024.109072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/22/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
Human and domesticated animal waste infiltrates global freshwater, terrestrial, and marine environments, widely disseminating fecal microbes, antibiotics, and other chemical pollutants. Emerging evidence suggests that guts of wild animals are being invaded by our microbes, including Escherichia coli, which face anthropogenic selective pressures to gain antimicrobial resistance (AMR) and increase virulence. However, wild animal sources remain starkly under-represented among genomic sequence repositories. We sequenced whole genomes of 145 E. coli isolates from 55 wild and 13 domestic animal fecal samples, averaging 2 (ranging 1-7) isolates per sample, on a preserve imbedded in a human-dominated landscape in California Bay Area, USA, to assess AMR, virulence, and pan-genomic diversity. With single nucleotide polymorphism analyses we predict potential transmission routes. We illustrate the usefulness of E. coli to aid our understanding of and ability to surveil the emergence of zoonotic pathogens created by the mixing of human and wild bacteria in the environment.
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Affiliation(s)
| | - Nicholas C. Scales
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Elizabeth A. Hadly
- Department of Biology, Stanford University, Stanford, CA, USA
- Stanford Woods Institute for the Environment, Stanford University, Stanford, CA, USA
- Center for Innovation in Global Health, Stanford University, Stanford, CA, USA
- Department of Earth Systems Science, Stanford University, Stanford, CA, USA
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Kerek Á, Török B, Laczkó L, Somogyi Z, Kardos G, Bányai K, Kaszab E, Bali K, Jerzsele Á. In Vitro Microevolution and Co-Selection Assessment of Amoxicillin and Cefotaxime Impact on Escherichia coli Resistance Development. Antibiotics (Basel) 2024; 13:247. [PMID: 38534682 DOI: 10.3390/antibiotics13030247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
The global spread of antimicrobial resistance has become a prominent issue in both veterinary and public health in the 21st century. The extensive use of amoxicillin, a beta-lactam antibiotic, and consequent resistance development are particularly alarming in food-producing animals, with a focus on the swine and poultry sectors. Another beta-lactam, cefotaxime, is widely utilized in human medicine, where the escalating resistance to third- and fourth-generation cephalosporins is a major concern. The aim of this study was to simulate the development of phenotypic and genotypic resistance to beta-lactam antibiotics, focusing on amoxicillin and cefotaxime. The investigation of the minimal inhibitory concentrations (MIC) of antibiotics was performed at 1×, 10×, 100×, and 1000× concentrations using the modified microbial evolution and growth arena (MEGA-plate) method. Our results indicate that amoxicillin significantly increased the MIC values of several tested antibiotics, except for oxytetracycline and florfenicol. In the case of cefotaxime, this increase was observed in all classes. A total of 44 antimicrobial resistance genes were identified in all samples. Chromosomal point mutations, particularly concerning cefotaxime, revealed numerous complex mutations, deletions, insertions, and single nucleotide polymorphisms (SNPs) that were not experienced in the case of amoxicillin. The findings suggest that, regarding amoxicillin, the point mutation of the acrB gene could explain the observed MIC value increases due to the heightened activity of the acrAB-tolC efflux pump system. However, under the influence of cefotaxime, more intricate processes occurred, including complex amino acid substitutions in the ampC gene promoter region, increased enzyme production induced by amino acid substitutions and SNPs, as well as mutations in the acrR and robA repressor genes that heightened the activity of the acrAB-tolC efflux pump system. These changes may contribute to the significant MIC increases observed for all tested antibiotics. The results underscore the importance of understanding cross-resistance development between individual drugs when choosing clinical alternative drugs. The point mutations in the mdtB and emrR genes may also contribute to the increased activity of the mdtABC-tolC and emrAB-tolC pump systems against all tested antibiotics. The exceptionally high mutation rate induced by cephalosporins justifies further investigations to clarify the exact mechanism behind.
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Affiliation(s)
- Ádám Kerek
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Bence Török
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Levente Laczkó
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- HUN-REN-UD Conservation Biology Research Group, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Zoltán Somogyi
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
| | - Gábor Kardos
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- National Public Health Center, Albert Flórián út 2-6, H-1097 Budapest, Hungary
- Department of Gerontology, Faculty of Health Sciences, University of Debrecen, Sóstói út 2-4, H-4400 Nyíregyháza, Hungary
| | - Krisztián Bányai
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary
| | - Eszter Kaszab
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary
| | - Krisztina Bali
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István u 2, H-1078 Budapest, Hungary
| | - Ákos Jerzsele
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, H-1078 Budapest, Hungary
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Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K. Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation. Sci Rep 2024; 14:5504. [PMID: 38448687 PMCID: PMC10918076 DOI: 10.1038/s41598-024-56242-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
The gut microbiota of paediatric oncology patients undergoing a conditioning regimen before hematopoietic stem cell transplantation is recently considered to play role in febrile neutropenia. Disruption of commensal microbiota and evolution of opportune pathogens community carrying a plethora of antibiotic-resistance genes play crucial role. However, the impact, predictive role and association of patient´s gut resistome in the course of the therapy is still to be elucidated. We analysed gut microbiota composition and resistome of 18 paediatric oncology patients undergoing hematopoietic stem cell transplantation, including 12 patients developing febrile neutropenia, hospitalized at The Bone Marrow Transplantation Unit of the National Institute of Children´s disease in Slovak Republic and healthy individuals (n = 14). Gut microbiome of stool samples obtained in 3 time points, before hematopoietic stem cell transplantation (n = 16), one week after hematopoietic stem cell transplantation (n = 16) and four weeks after hematopoietic stem cell transplantation (n = 14) was investigated using shotgun metagenome sequencing and bioinformatical analysis. We identified significant decrease in alpha-diversity and nine antibiotic-resistance genes msr(C), dfrG, erm(T), VanHAX, erm(B), aac(6)-aph(2), aph(3)-III, ant(6)-Ia and aac(6)-Ii, one week after hematopoietic stem cell transplantation associated with febrile neutropenia. Multidrug-resistant opportune pathogens of ESKAPE, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli found in the gut carried the significant subset of patient's resistome. Over 50% of patients treated with trimethoprim/sulfamethoxazole, piperacillin/tazobactam and amikacin carried antibiotic-resistance genes to applied treatment. The alpha diversity and the resistome of gut microbiota one week after hematopoietic stem cell transplantation is relevant predictor of febrile neutropenia outcome after hematopoietic stem cell transplantation. Furthermore, the interindividual diversity of multi-drug resistant opportunistic pathogens with variable portfolios of antibiotic-resistance genes indicates necessity of preventive, personalized approach.
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Affiliation(s)
- Sara Sardzikova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Kristina Andrijkova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Peter Svec
- Department of Paediatric Haematology and Oncology, Children's Haematology and Oncology Clinic and Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Gabor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Viktor Bielik
- Department of Biological and Medical Science, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alexandra Kolenova
- Department of Paediatric Haematology and Oncology, Children's Haematology and Oncology Clinic and Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 DOI: 10.1093/jac/dkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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Abdullahi IN, Lozano C, Zarazaga M, Simón C, Höfle U, Sieber RN, Latorre-Fernández J, Stegger M, Torres C. Comparative genomics of Staphylococcus aureus strains from wild birds and pig farms elucidates levels of mobilomes, antibiotic pressure and host adaptation. J Glob Antimicrob Resist 2024; 36:142-150. [PMID: 38128728 DOI: 10.1016/j.jgar.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES This study characterized the resistome, mobilome and phylogenomic relatedness of Staphylococcus aureus strains previously obtained from healthy nestling storks (HNS), pigs (HP) and pig farmers (HPF) to analyse possible transmission pathways of S. aureus with implications for the spread of antimicrobial resistance. METHODS The genomic contents of 52 S. aureus strains obtained from the nasal cavity of HNS, HP and HPF in Spain were sequenced using the Illumina NextSeq platform to characterize their resistome, virulome and mobile genetic elements. The relatedness of strains was assessed by core-genome single nucleotide polymorphisms (SNPs). RESULTS The frequencies of multidrug-resistance phenotype and transposons were significantly lower in strains from HNS than in those from HP and HPF (P < 0.005). However, the presence of human immune evasion cluster genes in S. aureus strains from HNS was significantly higher than in those from HP and HPF (P < 0.005). Interestingly, the frequencies of plasmids and phages were not significantly associated with the host (P > 0.05). The phylogenetic analysis identified a cluster of all the MSSA-CC398 strains carrying φSa3 and ermT on rep13 separately from the two MRSA-CC398 strains (carrying ermT on repUS18). Highly related MRSA-CC398 strains were detected in some pigs and related farmers (<10 SNPs). CONCLUSION This study confirms high-level antibiotic selection in S. aureus in HP and HPF in comparison to HNS. Furthermore, our findings highlight the continuous transmission of MRSA-CC398 in the pig-to-human interface and MSSA-CC398 with human adaptation markers in HNS. Molecular surveillance of S. aureus using the One Health model is required to establish appropriate control strategies.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Ursula Höfle
- Spanish Wildlife Research Institute IREC (CSIC‑UCLM‑JCCM), SaBio (Health and Biotechnology) Research Group, Ciudad Real, Spain
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark; Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain.
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Choudhary A, Midha T, Gulati I, Baranwal S. Isolation, Genomic Characterization of Shigella prophage fPSFA that effectively infects multi-drug resistant Shigella isolates from the Indian Poultry Sector. Microb Pathog 2024; 188:106538. [PMID: 38184177 DOI: 10.1016/j.micpath.2024.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/08/2024]
Abstract
Because of uncontrolled use of antibiotics, emergence of multidrug-resistant Shigella species poses a huge potential of zoonotic transfer from poultry sector. With increasing resistance to current antibiotics, there is a critical need to explore antibiotic alternatives. Using a Shigella flexneri reference strain, we isolated a novel fPSFA phage after inducing with mitomycin C. The phage was found to be stable for wide ranges of temperature -20 °C-65 °C and pH 3 to 11. fPSFA shows a latent period that ranges from 20 to 30 min and generation times of 50-60 min. The genome analysis of phage reveals two major contigs of 23788 bp and 23285 bp with 50.16 % and 39.33 % G + C content containing a total of 80 CDS and 2 tRNA genes. The phage belongs to Straboviridae family and lacks any virulence or antimicrobial resistance gene, thus making it a suitable candidate for treatment of drug-resistant infections. To confirm lytic ability of novel phage, we isolated 54 multidrug-resistant Shigella species from thirty-five poultry fecal samples that shows multiple antibiotic resistance index ranging from 0.15 to 0.75 (from 3 Indian states). The fPSFA showed lytic activity against multidrug-resistant Shigella isolates (73.08 %) (MARI≥0.50). The wide host ranges of fPSFA phage demonstrate its potential to be used as a biocontrol agent.
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Affiliation(s)
- Aaina Choudhary
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Tushar Midha
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Ishita Gulati
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India
| | - Somesh Baranwal
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, VPO Ghudda, Bathinda, 151401, India.
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García-Meniño I, García V, Lumbreras-Iglesias P, Fernández J, Mora A. Fluoroquinolone resistance in complicated urinary tract infections: association with the increased occurrence and diversity of Escherichia coli of clonal complex 131, together with ST1193. Front Cell Infect Microbiol 2024; 14:1351618. [PMID: 38510968 PMCID: PMC10953827 DOI: 10.3389/fcimb.2024.1351618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Urinary tract infections (UTIs) are one of the leading causes of multidrug-resistance (MDR) spread and infection-related deaths. Escherichia coli is by far the main causative agent. We conducted a prospective study on complicated urinary tract infections (cUTIs) i) to monitor the high-risk clones that could be compromising the therapeutic management and ii) to compare the cUTI etiology with uncomplicated infections (uUTIs) occurring in the same period and health area. Methods 154 non-duplicated E. coli recovered from cUTIs in 2020 at the Hospital Universitario Central de Asturias (Spain) constituted the study collection. Results Most cUTI isolates belonged to phylogroup B2 (72.1%) and met the uropathogenic (UPEC) status (69.5%) (≥3 of chuA, fyuA, vat, and yfcV genes). MDR was exhibited by 35.7% of the isolates, similarly to data observed in the uUTI collection. A significant difference observed in cUTI was the higher level of fluoroquinolone resistance (FQR) (47.4%), where the pandemic clonal groups B2-CC131 and B2-ST1193 (CH14-64) comprised 28% of the 154 E. coli, representing 52.1% of the FQR isolates. Other prevalent FQR clones were D-ST69 (CH35-27), D-ST405 (CH37-27), and B2-ST429 (CH40-20) (three isolates each). We uncovered an increased genetic and genomic diversity of the CC131: 10 different virotypes, 8 clonotypes (CH), and 2 STs. The presence of bla CTX-M-15 was determined in 12 (7.8%) isolates (all CC131), which showed 10 different core genome (cg)STs and 2 fimH types (fimH30 and fimH602) but the same set of chromosomal mutations conferring FQR (gyrA p.S83L, gyrA p.D87N, parC p.S80I, parC p.E84V, and parE p.I529L). In addition, the plasmidome analysis revealed 10 different IncF formulae in CC131 genomes. Conclusion We proved here that non-lactose fermenting screening, together with the detection of O25b (rfbO25b), H4 (fliCH4), and H5 (fliCH5) genes, and phylogroup and clonotyping assignation, is a reasonable approach that can be easily implemented for the surveillance of emerging high-risk clones associated with FQR spread in cUTIs, such as the uncommonly reported O25b:H4-B2-ST9126-CC131 (CH1267-30). Since E. coli CC131 and ST1193 are also involved in the community uUTIs of this health area, interventions to eradicate these MDR clones, along with surveillance for other emerging ones, are essential for antibiotic use optimization programs.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Pilar Lumbreras-Iglesias
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Research and Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
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De Koster S, Xavier BB, Lammens C, Perales Selva N, van Kleef-van Koeveringe S, Coenen S, Glupczynski Y, Leroux-Roels I, Dhaeze W, Hoebe CJPA, Dewulf J, Stegeman A, Kluytmans-Van den Bergh M, Kluytmans J, Goossens H. One Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019. PLoS One 2024; 19:e0298096. [PMID: 38394276 PMCID: PMC10890735 DOI: 10.1371/journal.pone.0298096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Colistin serves as the last line of defense against multidrug resistant Gram-negative bacterial infections in both human and veterinary medicine. This study aimed to investigate the occurrence and spread of colistin-resistant Enterobacterales (ColR-E) using a One Health approach in Belgium and in the Netherlands. METHODS In a transnational research project, a total of 998 hospitalized patients, 1430 long-term care facility (LTCF) residents, 947 children attending day care centres, 1597 pigs and 1691 broilers were sampled for the presence of ColR-E in 2017 and 2018, followed by a second round twelve months later for hospitalized patients and animals. Colistin treatment incidence in livestock farms was used to determine the association between colistin use and resistance. Selective cultures and colistin minimum inhibitory concentrations (MIC) were employed to identify ColR-E. A combination of short-read and long-read sequencing was utilized to investigate the molecular characteristics of 562 colistin-resistant isolates. Core genome multi-locus sequence typing (cgMLST) was applied to examine potential transmission events. RESULTS The presence of ColR-E was observed in all One Health sectors. In Dutch hospitalized patients, ColR-E proportions (11.3 and 11.8% in both measurements) were higher than in Belgian patients (4.4 and 7.9% in both measurements), while the occurrence of ColR-E in Belgian LTCF residents (10.2%) and children in day care centres (17.6%) was higher than in their Dutch counterparts (5.6% and 12.8%, respectively). Colistin use in pig farms was associated with the occurrence of colistin resistance. The percentage of pigs carrying ColR-E was 21.8 and 23.3% in Belgium and 14.6% and 8.9% in the Netherlands during both measurements. The proportion of broilers carrying ColR-E in the Netherlands (5.3 and 1.5%) was higher compared to Belgium (1.5 and 0.7%) in both measurements. mcr-harboring E. coli were detected in 17.4% (31/178) of the screened pigs from 7 Belgian pig farms. Concurrently, four human-related Enterobacter spp. isolates harbored mcr-9.1 and mcr-10 genes. The majority of colistin-resistant isolates (419/473, 88.6% E. coli; 126/166, 75.9% Klebsiella spp.; 50/75, 66.7% Enterobacter spp.) were susceptible to the critically important antibiotics (extended-spectrum cephalosporins, fluoroquinolones, carbapenems and aminoglycosides). Chromosomal colistin resistance mutations have been identified in globally prevalent high-risk clonal lineages, including E. coli ST131 (n = 17) and ST1193 (n = 4). Clonally related isolates were detected in different patients, healthy individuals and livestock animals of the same site suggesting local transmission. Clonal clustering of E. coli ST10 and K. pneumoniae ST45 was identified in different sites from both countries suggesting that these clones have the potential to spread colistin resistance through the human population or were acquired by exposure to a common (food) source. In pig farms, the continuous circulation of related isolates was observed over time. Inter-host transmission between humans and livestock animals was not detected. CONCLUSIONS The findings of this study contribute to a broader understanding of ColR-E prevalence and the possible pathways of transmission, offering insights valuable to both academic research and public health policy development.
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Affiliation(s)
- Sien De Koster
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, HIV/STI Unit, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, ZNA Middelheim, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, GZA Ziekenhuizen, Wilrijk, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | | | - Samuel Coenen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Isabel Leroux-Roels
- Laboratory of Medical Microbiology and Infection Control Department, Ghent University Hospital, Ghent, Belgium
| | | | - Christian J. P. A. Hoebe
- Department of Social Medicine, Maastricht University, Maastricht, the Netherlands
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, Maastricht University Medical Center+, Maastricht, The Netherlands
- Living Lab Public Health, Public Health Service South Limburg, Heerlen, the Netherlands
| | - Jeroen Dewulf
- Faculty of Veterinary Medicine, Department of Internal Medicine, Reproduction and Population Medicine, Veterinary Epidemiology Unit, Ghent University, Merelbeke, Belgium
| | - Arjan Stegeman
- Faculty of Veterinary Medicine, Department of Population Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marjolein Kluytmans-Van den Bergh
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Kluytmans
- Department of Infection Control, Amphia Hospital, Breda, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, The Netherlands
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Abad-Fau A, Sevilla E, Oro A, Martín-Burriel I, Moreno B, Morales M, Bolea R. Multidrug resistance in pathogenic Escherichia coli isolates from urinary tract infections in dogs, Spain. Front Vet Sci 2024; 11:1325072. [PMID: 38585298 PMCID: PMC10996866 DOI: 10.3389/fvets.2024.1325072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/12/2024] [Indexed: 04/09/2024] Open
Abstract
Escherichia coli (E. coli) is a pathogen frequently isolated in cases of urinary tract infections (UTIs) in both humans and dogs and evidence exists that dogs are reservoirs for human infections. In addition, E. coli is associated to increasing antimicrobial resistance rates. This study focuses on the analysis of antimicrobial resistance and the presence of selected virulence genes in E. coli isolates from a Spanish dog population suffering from UTI. This collection of isolates showed an extremely high level of phenotypic resistance to 1st-3rd generation cephalosporins, followed by penicillins, fluoroquinolones and amphenicols. Apart from that, 13.46% of them were considered extended-spectrum beta-lactamase producers. An alarmingly high percentage (71.15%) of multidrug resistant isolates were also detected. There was a good correlation between the antimicrobial resistance genes found and the phenotypic resistance expressed. Most of the isolates were classified as extraintestinal pathogenic E. coli, and two others harbored virulence factors related to diarrheagenic pathotypes. A significant relationship between low antibiotic resistance and high virulence factor carriage was found, but the mechanisms behind it are still poorly understood. The detection of high antimicrobial resistance rates to first-choice treatments highlights the need of constant antimicrobial resistance surveillance, as well as continuous revision of therapeutic guidelines for canine UTI to adapt them to changes in antimicrobial resistance patterns.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
| | - Eloisa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Ainara Oro
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon, Universidad de Zaragoza, Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Mariano Morales
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
- Albéitar Laboratories, Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
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Nhu NTK, Rahman MA, Goh KGK, Kim SJ, Phan MD, Peters KM, Alvarez-Fraga L, Hancock SJ, Ravi C, Kidd TJ, Sullivan MJ, Irvine KM, Beatson SA, Sweet MJ, Irwin AD, Vukovic J, Ulett GC, Hasnain SZ, Schembri MA. A convergent evolutionary pathway attenuating cellulose production drives enhanced virulence of some bacteria. Nat Commun 2024; 15:1441. [PMID: 38383596 PMCID: PMC10881479 DOI: 10.1038/s41467-024-45176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria adapt to selective pressure in their immediate environment in multiple ways. One mechanism involves the acquisition of independent mutations that disable or modify a key pathway, providing a signature of adaptation via convergent evolution. Extra-intestinal pathogenic Escherichia coli (ExPEC) belonging to sequence type 95 (ST95) represent a global clone frequently associated with severe human infections including acute pyelonephritis, sepsis, and neonatal meningitis. Here, we analysed a publicly available dataset of 613 ST95 genomes and identified a series of loss-of-function mutations that disrupt cellulose production or its modification in 55.3% of strains. We show the inability to produce cellulose significantly enhances ST95 invasive infection in a rat model of neonatal meningitis, leading to the disruption of intestinal barrier integrity in newborn pups and enhanced dissemination to the liver, spleen and brain. Consistent with these observations, disruption of cellulose production in ST95 augmented innate immune signalling and tissue neutrophil infiltration in a mouse model of urinary tract infection. Mutations that disrupt cellulose production were also identified in other virulent ExPEC STs, Shigella and Salmonella, suggesting a correlative association with many Enterobacteriaceae that cause severe human infection. Together, our findings provide an explanation for the emergence of hypervirulent Enterobacteriaceae clones.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - M Arifur Rahman
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Kelvin G K Goh
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Seung Jae Kim
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- INRAE, Univ Montpellier, LBE, 102 Avenue des Etangs, Narbonne, 11100, France
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chitra Ravi
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Matthew J Sullivan
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Katharine M Irvine
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
- University of Queensland Centre for Clinical Research, Brisbane, Australia
- Queensland Children's Hospital, Brisbane, Australia
| | - Jana Vukovic
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Glen C Ulett
- School of Pharmacy and Medical Sciences, Griffith University, Southport, QLD, Australia.
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia.
| | - Sumaira Z Hasnain
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
- Immunopathology Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
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27
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Guzinski J, Potter J, Tang Y, Davies R, Teale C, Petrovska L. Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas. Front Microbiol 2024; 14:1244533. [PMID: 38414709 PMCID: PMC10896835 DOI: 10.3389/fmicb.2023.1244533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/04/2023] [Indexed: 02/29/2024] Open
Abstract
Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.
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Affiliation(s)
- Jaromir Guzinski
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joshua Potter
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Rob Davies
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
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Black CA, Benavides R, Bandy SM, Dallas SD, Gawrys G, So W, Moreira AG, Aguilar S, Quidilla K, Smelter DF, Reveles KR, Frei CR, Koeller JM, Lee GC. Diverse Role of blaCTX-M and Porins in Mediating Ertapenem Resistance among Carbapenem-Resistant Enterobacterales. Antibiotics (Basel) 2024; 13:185. [PMID: 38391571 PMCID: PMC10885879 DOI: 10.3390/antibiotics13020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Among carbapenem-resistant Enterobacterales (CRE) are diverse mechanisms, including those that are resistant to meropenem but susceptible to ertapenem, adding further complexity to the clinical landscape. This study investigates the emergence of ertapenem-resistant, meropenem-susceptible (ErMs) Escherichia coli and Klebsiella pneumoniae CRE across five hospitals in San Antonio, Texas, USA, from 2012 to 2018. The majority of the CRE isolates were non-carbapenemase producers (NCP; 54%; 41/76); 56% of all NCP isolates had an ErMs phenotype. Among ErMs strains, E. coli comprised the majority (72%). ErMs strains carrying blaCTX-M had, on average, 9-fold higher copies of blaCTX-M than CP-ErMs strains as well as approximately 4-fold more copies than blaCTX-M-positive but ertapenem- and meropenem-susceptible (EsMs) strains (3.7 vs. 0.9, p < 0.001). Notably, carbapenem hydrolysis was observed to be mediated by strains harboring blaCTX-M with and without a carbapenemase(s). ErMs also carried more mobile genetic elements, particularly IS26 composite transposons, than EsMs (37 vs. 0.2, p < 0.0001). MGE- ISVsa5 was uniquely more abundant in ErMs than either EsMs or ErMr strains, with over 30 more average ISVsa5 counts than both phenotype groups (p < 0.0001). Immunoblot analysis demonstrated the absence of OmpC expression in NCP-ErMs E. coli, with 92% of strains lacking full contig coverage of ompC. Overall, our findings characterize both collaborative and independent efforts between blaCTX-M and OmpC in ErMs strains, indicating the need to reappraise the term "non-carbapenemase (NCP)", particularly for strains highly expressing blaCTX-M. To improve outcomes for CRE-infected patients, future efforts should focus on mechanisms underlying the emerging ErMs subphenotype of CRE strains to develop technologies for its rapid detection and provide targeted therapeutic strategies.
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Affiliation(s)
- Cody A Black
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Raymond Benavides
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sarah M Bandy
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Steven D Dallas
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Gerard Gawrys
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Wonhee So
- College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Alvaro G Moreira
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Veterans Administration Research Center for AIDS and HIV-1 Infection and Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
| | - Samantha Aguilar
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Kevin Quidilla
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Dan F Smelter
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kelly R Reveles
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Christopher R Frei
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Jim M Koeller
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Grace C Lee
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Veterans Administration Research Center for AIDS and HIV-1 Infection and Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
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Che Hamzah AM, Chew CH, Al-Trad EI, Puah SM, Chua KH, A Rahman NI, Ismail S, Maeda T, Palittapongarnpim P, Yeo CC. Whole genome sequencing of methicillin-resistant Staphylococcus aureus clinical isolates from Terengganu, Malaysia, indicates the predominance of the EMRSA-15 (ST22-SCCmec IV) clone. Sci Rep 2024; 14:3485. [PMID: 38347106 PMCID: PMC10861583 DOI: 10.1038/s41598-024-54182-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/09/2024] [Indexed: 02/15/2024] Open
Abstract
Despite the importance of methicillin-resistant Staphylococcus aureus (MRSA) as a priority nosocomial pathogen, the genome sequences of Malaysian MRSA isolates are currently limited to a small pool of samples. Here, we present the genome sequence analyses of 88 clinical MRSA isolates obtained from the main tertiary hospital in Terengganu, Malaysia in 2016-2020, to obtain in-depth insights into their characteristics. The EMRSA-15 (ST22-SCCmec IV) clone of the clonal complex 22 (CC22) lineage was predominant with a total of 61 (69.3%) isolates. Earlier reports from other Malaysian hospitals indicated the predominance of the ST239 clone, but only two (2.3%) isolates were identified in this study. Two Indian-origin clones, the Bengal Bay clone ST772-SCCmec V (n = 2) and ST672 (n = 10) were also detected, with most of the ST672 isolates obtained in 2020 (n = 7). Two new STs were found, with one isolate each, and were designated ST7879 and ST7883. From the core genome phylogenetic tree, the HSNZ MRSA isolates could be grouped into seven clades. Antimicrobial phenotype-genotype concordance was high (> 95%), indicating the accuracy of WGS in predicting most resistances. Majority of the MRSA isolates were found to harbor more than 10 virulence genes, demonstrating their pathogenic nature.
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Affiliation(s)
- Ainal Mardziah Che Hamzah
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, 21300, Kuala Nerus, Terengganu, Malaysia.
| | - Esra'a Ibrahim Al-Trad
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
- Faculty of Allied Medical Sciences, Jadara University, Irbid, Jordan
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nor Iza A Rahman
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Toshinari Maeda
- Department of Biological Functions and Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-Ku, Kitakyushu, 808-0196, Japan
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, 20400, Kuala Terengganu, Terengganu, Malaysia.
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Ocejo M, Mugica M, Oporto B, Lavín JL, Hurtado A. Whole-genome long-read sequencing to unveil Enterococcus antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of Enterococcus lactis. Microbiol Spectr 2024; 12:e0367223. [PMID: 38230937 PMCID: PMC10846211 DOI: 10.1128/spectrum.03672-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Enterococcus faecalis (Efs) and Enterococcus faecium (Efm) are major causes of multiresistant healthcare-associated or nosocomial infections. Efm has been traditionally divided into clades A (healthcare associated) and B (community associated) but clade B has been recently reassigned to Enterococcus lactis (Elc). However, identification techniques do not routinely differentiate Elc from Efm. As part of a longitudinal study to investigate the antimicrobial resistance of Enterococcus in dairy cattle, isolates initially identified as Efm were confirmed as Elc after Oxford-Nanopore long-fragment whole-genome sequencing and genome comparisons. An Efm-specific PCR assay was developed and used to identify isolates recovered from animal feces on five farms, resulting in 44 Efs, 23 Efm, and 59 Elc. Resistance, determined by broth microdilution, was more frequent in Efs than in Efm and Elc but all isolates were susceptible to ampicillin, daptomycin, teicoplanin, tigecycline, and vancomycin. Genome sequencing analysis of 32 isolates identified 23 antimicrobial resistance genes (ARGs, mostly plasmid-located) and 2 single nucleotide polymorphisms associated with resistance to 10 antimicrobial classes, showing high concordance with phenotypic resistance. Notably, linezolid resistance in Efm was encoded by the optrA gene, located in plasmids downstream of the fexA gene. Although most Elc lacked virulence factors and genetic determinants of resistance, one isolate carried a plasmid with eight ARGs. This study showed that Elc is more prevalent than Efm in dairy cattle but carries fewer ARGs and virulence genes. However, Elc can carry multi-drug-resistant plasmids like those harbored by Efm and could act as a donor of ARGs for other pathogenic enterococcal species.IMPORTANCEEnterococcus species identification is crucial due to differences in pathogenicity and antibiotic resistance profiles. The failure of traditional methods or whole-genome sequencing-based taxonomic classifiers to distinguish Enterococcus lactis (Elc) from Enterococcus faecium (Efm) results in a biased interpretation of Efm epidemiology. The Efm species-specific real-time PCR assay developed here will help to properly identify Efm (only the formerly known clade A) in future studies. Here, we showed that Elc is prevalent in dairy cattle, and although this species carries fewer genetic determinants of resistance (GDRs) than Enterococcus faecalis (Efs) and Efm, it can carry multi-drug-resistant (MDR) plasmids and could act as a donor of resistance genes for other pathogenic enterococcal species. Although all isolates (Efs, Efm, and Elc) were susceptible to critically or highly important antibiotics like daptomycin, teicoplanin, tigecycline, and vancomycin, the presence of GDRs in MDR-plasmids is a concern since antimicrobials commonly used in livestock could co-select and confer resistance to critically important antimicrobials not used in food-producing animals.
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Affiliation(s)
- Medelin Ocejo
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Maitane Mugica
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - José Luis Lavín
- Applied Mathematics Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
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Luoto J, Keto-Timonen R, Kivistö R. Campylobacter species and genotype distribution in Finnish beef liver - Retail liver juice ideal for isolation and quantification. Int J Food Microbiol 2024; 411:110524. [PMID: 38118359 DOI: 10.1016/j.ijfoodmicro.2023.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/18/2023] [Accepted: 12/10/2023] [Indexed: 12/22/2023]
Abstract
Campylobacteriosis, primarily caused by Campylobacter jejuni and C. coli, is the main bacterial zoonosis worldwide. While poultry is recognized as the main reservoir, bovines are considered another important reservoir for Campylobacter spp. found in human infections. In contrast to chicken, retail beef is seldom contaminated by Campylobacter species. However, beef liver is recognized to be frequently contaminated and has been linked to human infections via epidemiological investigations. Our aims were to evaluate the prevalence of Campylobacter spp. inside and on the surface of beef liver pieces at retail in Finland and to analyse the population in more detail using whole genome sequencing (WGS) to assess the public health relevance. A total of 90 retail beef livers were studied using both enrichment of the external peptone-saline rinse of the liver piece and direct culture from the inside after surface sterilization. Furthermore, 46 of the livers were also studied using direct culture of retail beef liver juice collected from the bottom of the consumer package to estimate the concentration of Campylobacter species. Overall, 44 (49 %) of the samples were positive for Campylobacter species, C. jejuni, C. fetus and C. lari being identified in 42 %, 8.9 % and 1.1 % of the samples, respectively. Direct culture of retail liver juice was a sensitive and convenient method for Campylobacter spp. detection, resulting in 48 % prevalence and a mean concentration of 49 cfu/ml (maximum 335 cfu/ml). Two samples (2.2 %), containing large hepatic ducts, were positive for C. jejuni internally, representing multilocus sequence typing (MLST) sequence type ST-19 and ST-21. WGS, core genome phylogeny and core genome MLST revealed that in most cases only one clearly distinct clone of clinically relevant C. jejuni or C. fetus was isolated from a single lot of samples. However, in some cases several distinct clones were identified simultaneously even from a single liver piece. In epidemiological investigations, it is thus highly advisable to genotype multiple isolates to capture the whole diversity of Campylobacter spp. from suspected food sources. Good kitchen hygiene, avoidance of cross-contamination and thorough cooking are important for limiting the transmission of campylobacteriosis.
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Affiliation(s)
- Jenna Luoto
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Riikka Keto-Timonen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Rauni Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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Romão FT, Santos ACM, Sperandio V, Hernandes RT, Gomes TAT. Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenic Escherichia coli 1711-4 strain of serotype O51:H40. bioRxiv 2024:2024.02.01.578415. [PMID: 38352511 PMCID: PMC10862855 DOI: 10.1101/2024.02.01.578415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) is a significant cause of diarrhea in developing countries. Some aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. They can even translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of the T3SS for the efficiency of the invasion process was demonstrated, the expression of the LEE genes during the invasion and intracellular persistence remains unclear. To address this, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytes in vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression of eae and escJ increased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 hours post-infection during the persistence period. The number of pedestal-like structures formed on HeLa cells also increased during the 24-hour analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.
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Affiliation(s)
- Fabiano T. Romão
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ana C. M. Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
| | - Vanessa Sperandio
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA; Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rodrigo T. Hernandes
- Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tânia A. T. Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo, Brazil
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Strakova N, Michova H, Shagieva E, Ovesna P, Karpiskova R, Demnerova K. Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance. Folia Microbiol (Praha) 2024; 69:207-219. [PMID: 37816942 PMCID: PMC10876727 DOI: 10.1007/s12223-023-01093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‑BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.
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Affiliation(s)
- Nicol Strakova
- Veterinary Research Institute, Hudcova 296/70, Brno, Czech Republic.
| | - Hana Michova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ekaterina Shagieva
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Ovesna
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Renata Karpiskova
- Department of Public Health, Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Katerina Demnerova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
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Hernández-García M, García-Castillo M, Nieto-Torres M, Bou G, Ocampo-Sosa A, Pitart C, Gracia-Ahufinger I, Mulet X, Pascual Á, Tormo N, Oliver A, Ruiz-Garbajosa P, Cantón R. Deciphering mechanisms affecting cefepime-taniborbactam in vitro activity in carbapenemase-producing Enterobacterales and carbapenem-resistant Pseudomonas spp. isolates recovered during a surveillance study in Spain. Eur J Clin Microbiol Infect Dis 2024; 43:279-296. [PMID: 38041722 DOI: 10.1007/s10096-023-04697-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/27/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To characterize the resistance mechanisms affecting the cefepime-taniborbactam combination in a collection of carbapenemase-producing Enterobacterales (CPE) and carbapenem-resistant Pseudomonas spp. (predominantly P. aeruginosa; CRPA) clinical isolates. METHODS CPE (n = 247) and CRPA (n = 170) isolates were prospectively collected from patients admitted to 8 Spanish hospitals. Susceptibility to cefepime-taniborbactam and comparators was determined by broth microdilution. Cefepime-taniborbactam was the most active agent, inhibiting 97.6% of CPE and 67.1% of CRPA (MICs ≤ 8/4 mg/L). All isolates with cefepime-taniborbactam MIC > 8/4 mg/L (5 CPE and 52 CRPA) and a subset with MIC ≤ 8/4 mg/L (23 CPE and 24 CRPA) were characterized by whole genome sequencing. RESULTS A reduced cefepime-taniborbactam activity was found in two KPC-ST307-Klebsiella pneumoniae isolates with altered porins [KPC-62-K. pneumoniae (OmpA, OmpR/EnvZ), KPC-150-K. pneumoniae (OmpK35, OmpK36)] and one each ST133-VIM-1-Enterobacter hormaechei with altered OmpD, OmpR, and OmpC; IMP-8-ST24-Enterobacter asburiae; and NDM-5-Escherichia coli with an YRIN-inserted PBP3 and a mutated PBP2. Among the P. aeruginosa (68/76), elevated cefepime-taniborbactam MICs were mostly associated with GES-5-ST235, OXA-2+VIM-2-ST235, and OXA-2+VIM-20-ST175 isolates also carrying mutations in PBP3, efflux pump (mexR, mexZ) and AmpC (mpl) regulators, and non-carbapenemase-ST175 isolates with AmpD-T139M and PBP3-R504C mutations. Overall, accumulation of these mutations was frequently detected among non-carbapenemase producers. CONCLUSIONS The reduced cefepime-taniborbactam activity among the minority of isolates with elevated cefepime-taniborbactam MICs is not only due to IMP carbapenemases but also to the accumulation of multiple resistance mechanisms, including PBP and porin mutations in CPE and chromosomal mutations leading to efflux pumps up-regulation, AmpC overexpression, and PBP modifications in P. aeruginosa.
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Affiliation(s)
- Marta Hernández-García
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
| | - María García-Castillo
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Nieto-Torres
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Germán Bou
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario A Coruña and Instituto de Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Alain Ocampo-Sosa
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla and Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain
| | - Cristina Pitart
- Laboratorio de Microbiología, Hospital Clínic i Provincial, Barcelona, Spain
| | - Irene Gracia-Ahufinger
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- UGC de Microbiología, Hospital Universitario Reina Sofía-Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Xavier Mulet
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Son Espases and Instituto de investigación Sanitaria Illes Balears (idISBa), Palma de Mallorca, Spain
| | - Álvaro Pascual
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS) (Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla), Sevilla, Spain
| | - Nuria Tormo
- Servicio de Microbiología, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Antonio Oliver
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Son Espases and Instituto de investigación Sanitaria Illes Balears (idISBa), Palma de Mallorca, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
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Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
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Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Patel V, Patil K, Patel D, Kikani B, Madamwar D, Desai C. Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India. Environ Monit Assess 2024; 196:208. [PMID: 38279971 DOI: 10.1007/s10661-024-12380-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.
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Affiliation(s)
- Vandan Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Kishor Patil
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Dishant Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Bhavtosh Kikani
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India.
| | - Chirayu Desai
- Department of Environmental Biotechnology, Gujarat Biotechnology University (GBU), Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India.
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Leão C, Silveira L, Usié A, Gião J, Clemente L, Themudo P, Amaro A, Pista A. Genetic Diversity of Salmonella enterica subsp. enterica Serovar Enteritidis from Human and Non-Human Sources in Portugal. Pathogens 2024; 13:112. [PMID: 38392849 PMCID: PMC10892295 DOI: 10.3390/pathogens13020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the leading causes of foodborne infections associated with broilers and laying hens. Portugal has had the lowest notification rates of salmonellosis in recent years, due to the vaccinations of layer and breeder flocks and strict compliance with biosecurity measures. However, data about the genetic diversity of S. Enteritidis in Portugal are scarce. In this study, 102 S. Enteritidis isolates selected from human (n = 63) and non-human sources (n = 39) were characterized by serotyping, antimicrobial susceptibility, and whole genome sequencing. The S. Enteritidis population was mainly resistant to fluoroquinolones, and a sole isolate showed resistance to extended-spectrum cephalosporins. ST11 was the most frequent sequence type, and three novel STs from human isolates (ST9236, ST4457, and ST9995) were assigned. Several Salmonella pathogenic islands (SPI) and Putative SPI were present in the genomes, namely SPI-1, 2, 3, 4, 5, 9, 10, 12, 13, and 14, C63PI, CS54_island, and 170 virulence genes were identified. The phylogenetic analysis revealed that strains from Portugal are genetically heterogeneous regarding sample type, collection date, and genetic content. This study increases the available data, essential to a better characterization of strains in a global context.
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Affiliation(s)
- Célia Leão
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal;
| | - Ana Usié
- Department of Animal Genomics and Bioinformatics, Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal;
- MED—Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento & CHANGE–Global Change and Sustainability Institute, CEBAL, 7801-908 Beja, Portugal
| | - Joana Gião
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, 1300-477 Lisbon, Portugal
| | - Patricia Themudo
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal;
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Ko S, Kim J, Lim J, Lee SM, Park JY, Woo J, Scott-Nevros ZK, Kim JR, Yoon H, Kim D. Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure. mSystems 2024; 9:e0094323. [PMID: 38085058 PMCID: PMC10871167 DOI: 10.1128/msystems.00943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/02/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS, sbml.unist.ac.kr), a database that comprehensively includes 3,943 reported AMR gene information for 1,997 extended spectrum beta-lactamase (ESBL) and 1,946 other genes as well as a total of 27,395 predicted protein structures. These structures, which include both wild-type AMR genes and their mutants, were derived from 80,094 publicly available whole-genome sequences. In addition, we developed the rapid analysis and detection tool of antimicrobial-resistance (RADAR), a one-stop analysis pipeline to detect AMR genes across whole-genome sequencing (WGSs). By integrating BOARDS and RADAR, the AMR prevalence landscape for eight multi-drug resistant pathogens was reconstructed, leading to unexpected findings such as the pre-existence of the MCR genes before their official reports. Enzymatic structure prediction-based analysis revealed that the occurrence of mutations found in some ESBL genes was found to be closely related to the binding affinities with their antibiotic substrates. Overall, BOARDS can play a significant role in performing in-depth analysis on AMR.IMPORTANCEWhile the increasing antibiotic resistance (AMR) in pathogen has been a burden on public health, effective tools for deep understanding of AMR based on genetic or structural information remain limited. In this study, a blanket overarching antimicrobial-resistance gene database with structure information (BOARDS)-a web-based database that comprehensively collected AMR gene data with predictive protein structural information was constructed. Additionally, we report the development of a RADAR pipeline that can analyze whole-genome sequences as well. BOARDS, which includes sequence and structural information, has shown the historical landscape and prevalence of the AMR genes and can provide insight into single-nucleotide polymorphism effects on antibiotic degrading enzymes within protein structures.
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Affiliation(s)
- Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jaewon Lim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jihoon Woo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Zoe K. Scott-Nevros
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jong R. Kim
- School of Engineering and Digital Sciences, Nazarbayev University, Astan, Kazakhstan
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
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Bogri A, Jensen EEB, Borchert AV, Brinch C, Otani S, Aarestrup FM. Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations. mSystems 2024; 9:e0101823. [PMID: 38095429 PMCID: PMC10805027 DOI: 10.1128/msystems.01018-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance (AMR) is a major global health concern, further complicated by its spread via the microbiome bacterial members. While mathematical models discuss AMR transmission through the symbiotic microbiome, experimental studies are scarce. Herein, we used a gregarious cockroach, Pycnoscelus surinamensis, as an in vivo animal model for AMR transmission investigations. We explored whether the effect of antimicrobial treatment is detectable with metagenomic sequencing, and whether AMR genes can be spread and established in unchallenged (not treated with antibiotics) individuals following contact with treated donors, and under various frequencies of interaction. Gut and soil substrate microbiomes were investigated by metagenomic sequencing for bacterial community composition and resistome profiling. We found that tetracycline treatment altered the treated gut microbiome by decreasing bacterial diversity and increasing the abundance of tetracycline resistance genes. Untreated cockroaches that interacted with treated donors also had elevated tetracycline resistance. The levels of resistance differed depending on the magnitude and frequency of donor transfer. Additionally, treated donors showed signs of microbiome recovery due to their interaction with the untreated ones. Similar patterns were also recorded in the soil substrate microbiomes. Our results shed light on how interacting microbiomes facilitate AMR gene transmission to previously unchallenged hosts, a dynamic influenced by the interaction frequencies, using an in vivo model to validate theoretical AMR transmission models.IMPORTANCEAntimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.
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Affiliation(s)
- Amalia Bogri
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | | | - Asbjørn Vedel Borchert
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs., Lyngby, Denmark
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Somalou P, Ieronymaki E, Feidaki K, Prapa I, Stylianopoulou E, Spyridopoulou K, Skavdis G, Grigoriou ME, Panas P, Argiriou A, Tsatsanis C, Kourkoutas Y. Novel Wild-Type Pediococcus and Lactiplantibacillus Strains as Probiotic Candidates to Manage Obesity-Associated Insulin Resistance. Microorganisms 2024; 12:231. [PMID: 38399636 PMCID: PMC10891751 DOI: 10.3390/microorganisms12020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
As the food and pharmaceutical industry is continuously seeking new probiotic strains with unique health properties, the aim of the present study was to determine the impact of short-term dietary intervention with novel wild-type strains, isolated from various sources, on high-fat diet (HFD)-induced insulin resistance. Initially, the strains were evaluated in vitro for their ability to survive in simulated gastrointestinal (GI) conditions, for adhesion to Caco-2 cells, for bile salt hydrolase secretion, for cholesterol-lowering and cellular cholesterol-binding ability, and for growth inhibition of food-borne pathogens. In addition, safety criteria were assessed, including hemolytic activity and susceptibility to antibiotics. The in vivo test on insulin resistance showed that mice receiving the HFD supplemented with Pediococcus acidilactici SK (isolated from human feces) or P. acidilactici OLS3-1 strain (isolated from olive fruit) exhibited significantly improved insulin resistance compared to HFD-fed mice or to the normal diet (ND)-fed group.
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Affiliation(s)
- Paraskevi Somalou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | - Eleftheria Ieronymaki
- Laboratory of Clinical Chemistry, Department of Laboratory Medicine, Medical School, University of Crete, 71003 Crete, Greece; (E.I.); (C.T.)
| | - Kyriaki Feidaki
- Institute of Applied Sciences, Centre for Research and Technology, 57001 Thessaloniki, Greece; (K.F.); (A.A.)
- Department of Food Science and Nutrition, University of the Aegean, 81400 Lemnos, Greece
| | - Ioanna Prapa
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | - Electra Stylianopoulou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | - Katerina Spyridopoulou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | - George Skavdis
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | - Maria E. Grigoriou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
| | | | - Anagnostis Argiriou
- Institute of Applied Sciences, Centre for Research and Technology, 57001 Thessaloniki, Greece; (K.F.); (A.A.)
- Department of Food Science and Nutrition, University of the Aegean, 81400 Lemnos, Greece
| | - Christos Tsatsanis
- Laboratory of Clinical Chemistry, Department of Laboratory Medicine, Medical School, University of Crete, 71003 Crete, Greece; (E.I.); (C.T.)
- Institute for Molecular Biology and Biotechnology, FORTH, 71100 Heraklion, Greece
| | - Yiannis Kourkoutas
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (P.S.); (I.P.); (E.S.); (K.S.); (G.S.); (M.E.G.)
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Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L. The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection. Front Cell Infect Microbiol 2024; 14:1335450. [PMID: 38318164 PMCID: PMC10839054 DOI: 10.3389/fcimb.2024.1335450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Since the beginning of the SARS-CoV-2 pandemic in early 2020, it has been apparent that children were partially protected from both infection and the more severe forms of the disease. Many different mechanisms have been proposed to explain this phenomenon, including children's frequent exposure to other upper respiratory infections and vaccines, and which inflammatory cytokines they are more likely to produce in response to infection. Furthermore, given the presence of SARS-CoV-2 in the intestine and its ability to infect enterocytes, combined with the well described immunomodulatory capabilities of the microbiome, another potential contributing factor may be the presence of certain protective microbial members of the gut microbiota (GM). Methods We performed shotgun metagenomic sequencing and profiled both the bacteriome and virome of the GM of pediatric SARS-CoV-2 patients compared to healthy, age-matched subjects. Results We found that, while pediatric patients do share some pro-inflammatory microbial signatures with adult patients, they also possess a distinct microbial signature of protective bacteria previously found to be negatively correlated with SARS-CoV-2 infectivity and COVID-19 severity. COVID-19 was also associated with higher fecal Cytomegalovirus load, and with shifts in the relative abundances of bacteriophages in the GM. Furthermore, we address how the preventative treatment of COVID-19 patients with antibiotics, a common practice especially in the early days of the pandemic, affected the bacteriome and virome, as well as the abundances of antimicrobial resistance and virulence genes in these patients. Discussion To our knowledge, this is the first study to address the bacteriome, virome, and resistome of pediatric patients in response to COVID-19 and to preventative antibiotics use.
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Affiliation(s)
- Antonia Piazzesi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Lorenza Romani
- Infectious Diseases Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics, Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Carlsen L, Grottker M, Heim M, Knobling B, Schlauß S, Wellbrock K, Knobloch JK. High Genetic Diversity in Third-Generation Cephalosporin-Resistant Escherichia coli in Wastewater Systems of Schleswig-Holstein. Pathogens 2024; 13:90. [PMID: 38276163 PMCID: PMC10820474 DOI: 10.3390/pathogens13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
The spread of multidrug-resistant bacteria from humans or livestock is a critical issue. However, the epidemiology of resistant pathogens across wastewater pathways is poorly understood. Therefore, we performed a detailed comparison of third-generation cephalosporin-resistant Escherichia coli (3GCREC) from wastewater treatment plants (WWTPs) to analyze dissemination pathways. A total of 172 3GCREC isolated from four WWTPs were characterized via whole genome sequencing. Clonal relatedness was determined using multi-locus sequence typing (MLST) and core genome MLST. Resistance genotypes and plasmid replicons were determined. A total of 68 MLST sequence types were observed with 28 closely related clusters. Resistance genes to eight antibiotic classes were detected. In fluoroquinolone-resistant isolates, resistance was associated with three-or-more point mutations in target genes. Typing revealed high genetic diversity with only a few clonal lineages present in all WWTPs. The distribution paths of individual lines could only be traced in exceptional cases with a lack of enrichment of certain lineages. Varying resistance genes and plasmids, as well as fluoroquinolone resistance-associated point mutations in individual isolates, further corroborated the high diversity of 3GCREC in WWTPs. In total, we observed high diversity of 3GCREC inside the tested WWTPs with proof of resistant strains being released into the environment even after treatment processes.
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Affiliation(s)
- Laura Carlsen
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg–Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; (L.C.); (B.K.)
| | - Matthias Grottker
- Laboratory for Urban Water and Waste Management, Technische Hochschule Lübeck, University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany; (M.G.); (S.S.); (K.W.)
| | - Malika Heim
- Laboratory for Urban Water and Waste Management, Technische Hochschule Lübeck, University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany; (M.G.); (S.S.); (K.W.)
| | - Birte Knobling
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg–Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; (L.C.); (B.K.)
| | - Sebastian Schlauß
- Laboratory for Urban Water and Waste Management, Technische Hochschule Lübeck, University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany; (M.G.); (S.S.); (K.W.)
| | - Kai Wellbrock
- Laboratory for Urban Water and Waste Management, Technische Hochschule Lübeck, University of Applied Sciences, Mönkhofer Weg 239, 23562 Lübeck, Germany; (M.G.); (S.S.); (K.W.)
| | - Johannes K. Knobloch
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg–Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; (L.C.); (B.K.)
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Guitart-Matas J, Espunyes J, Illera L, Gonzalez-Escalona N, Ribas MP, Marco I, Migura-Garcia L. High-risk lineages of extended spectrum cephalosporinase producing Escherichia coli from Eurasian griffon vultures (Gyps fulvus) foraging in landfills in north-eastern Spain. Sci Total Environ 2024; 909:168625. [PMID: 37977396 DOI: 10.1016/j.scitotenv.2023.168625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Extended-spectrum cephalosporinase producing (ESC) E. coli are regarded as key indicator microorganisms of antimicrobial resistance (AMR), calling for a One Health integrated global surveillance strategy. Wildlife is exposed to antibiotic contaminants and/or resistant bacteria that have been released into the environment, potentially acting as reservoirs and spreaders of resistance genes as well as sentinels of anthropogenic pressure. Monitoring AMR in wildlife has become crucial in determining anthropogenic environmental impacts as well as transmission routes. In this study, we determined the occurrence and potential sources of ESC E. coli in 218 Eurasian griffon vultures (Gyps fulvus) foraging regularly on human waste disposed at a dumpsite in north-eastern Spain. Minimal inhibitory concentration for 14 different antimicrobials was performed to evaluate the phenotype of the isolates, and whole genome sequencing was carried out to investigate lineages and plasmids harbouring ESC genes. Our sequences were compared to previously published Spanish sequences of human, animal, and wildlife origin. We report a high prevalence of CTX-M-15, as well as the presence of other resistance genes such as OXA-10, CTX-M-27, and CTX-M-65 which are rarely described in European livestock, suggesting a human origin. The isolates also carried a diverse range of additional AMR genes for a broad spectrum of drug families, with the majority being multi-drug resistant. The phylogenomic analyses suggests the transmission of high-risk lineages from humans to vultures, with 49 % of our isolates matching the most common extraintestinal pathogenic E. coli (ExPEC) lineages described in humans worldwide, including ST131, ST10 and ST58. We conclude that anthropogenically altered habitats, such as landfills, are hotspots for the acquisition and spread of high-risk ESC E. coli lineages associated with hospital infections. Measures must be implemented to limit their spread into natural environments.
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Affiliation(s)
- Judith Guitart-Matas
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain
| | - Johan Espunyes
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lucia Illera
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | | | - Maria Puig Ribas
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Ignasi Marco
- Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Catalonia, Spain
| | - Lourdes Migura-Garcia
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB), Catalonia, Spain; Institute of Agrifood Research and Technology (IRTA), Animal Health Program (CReSA), WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe, Autonomous University of Barcelona (UAB), Catalonia, Spain.
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Castañeda-Meléndrez AM, Magaña-Lizárraga JA, Martínez-Valenzuela M, Clemente-Soto AF, García-Cervantes PC, Delgado-Vargas F, Bernal-Reynaga R. Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials. AIMS Microbiol 2024; 10:41-61. [PMID: 38525046 PMCID: PMC10955171 DOI: 10.3934/microbiol.2024003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/26/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common bacterial agent associated with urinary tract infections, threatening public health systems with elevated medical costs and high morbidity rates. The successful establishment of the infection is associated with virulence factors encoded in its genome, in addition to antibacterial resistance genes, which could limit the treatment and resolution of the infection. In this sense, plant extracts from the genus Echeveria have traditionally been used to treat diverse infectious diseases. However, little is known about the effects of these extracts on bacteria and their potential mechanisms of action. This study aims to sequence a multidrug-resistant UPEC isolate (UTI-U7) and assess the multilocus sequence typing (MLST), virulence factors, antimicrobial resistance profile, genes, serotype, and plasmid content. Antimicrobial susceptibility profiling was performed using the Kirby-Bauer disk diffusion. The antibacterial and anti-adherent effects of the methanol extracts (ME) of Echeveria (E. craigiana, E. kimnachii, and E. subrigida) against UTI-U7 were determined. The isolate was characterized as an O25:H4-B2-ST2279-CH40 subclone and had resistant determinants to aminoglycosides, β-lactams, fluoroquinolones/quinolones, amphenicols, and tetracyclines, which matched with the antimicrobial resistance profile. The virulence genes identified encode adherence factors, iron uptake, protectins/serum resistance, and toxins. Identified plasmids belonged to the IncF group (IncFIA, IncFIB, and IncFII), alongside several prophage-like elements. After an extensive genome analysis that confirmed the pathogenic status of UTI-U7 isolate, Echeveria extracts were tested to determine their antibacterial effects; as an extract, E. subrigida (MIC, 5 mg/mL) displayed the best inhibitory effect. However, the adherence between UTI-U7 and HeLa cells was unaffected by the ME of the E. subrigida extract.
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Affiliation(s)
| | | | | | | | | | | | - Rodolfo Bernal-Reynaga
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico-Biológicas. Universidad Autónoma de Sinaloa. Ciudad Universitaria, Culiacán, Sinaloa, México
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Frey E, Stapleton GS, Nichols MC, Gollarza LM, Birhane M, Chen JC, McCullough A, Carleton HA, Trees E, Hise KB, Tolar B, Francois Watkins L. Antimicrobial resistance in multistate outbreaks of nontyphoidal Salmonella infections linked to animal contact-United States, 2015-2018. J Clin Microbiol 2024; 62:e0098123. [PMID: 38084949 PMCID: PMC10793259 DOI: 10.1128/jcm.00981-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/01/2023] [Indexed: 01/18/2024] Open
Abstract
Animal contact is an established risk factor for nontyphoidal Salmonella infections and outbreaks. During 2015-2018, the U.S. Centers for Disease Control and Prevention (CDC) and other U.S. public health laboratories began implementing whole-genome sequencing (WGS) of Salmonella isolates. WGS was used to supplement the traditional methods of pulsed-field gel electrophoresis for isolate subtyping, outbreak detection, and antimicrobial susceptibility testing (AST) for the detection of resistance. We characterized the epidemiology and antimicrobial resistance (AMR) of multistate salmonellosis outbreaks linked to animal contact during this time period. An isolate was considered resistant if AST yielded a resistant (or intermediate, for ciprofloxacin) interpretation to any antimicrobial tested by the CDC or if WGS showed a resistance determinant in its genome for one of these agents. We identified 31 outbreaks linked to contact with poultry (n = 23), reptiles (n = 6), dairy calves (n = 1), and guinea pigs (n = 1). Of the 26 outbreaks with resistance data available, we identified antimicrobial resistance in at least one isolate from 20 outbreaks (77%). Of 1,309 isolates with resistance information, 247 (19%) were resistant to ≥1 antimicrobial, and 134 (10%) were multidrug-resistant to antimicrobials from ≥3 antimicrobial classes. The use of resistance data predicted from WGS increased the number of isolates with resistance information available fivefold compared with AST, and 28 of 43 total resistance patterns were identified exclusively by WGS; concordance was high (>99%) for resistance determined by AST and WGS. The use of predicted resistance from WGS enhanced the characterization of the resistance profiles of outbreaks linked to animal contact by providing resistance information for more isolates.
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Affiliation(s)
- Erin Frey
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - G. Sean Stapleton
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Megin C. Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren M. Gollarza
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Meseret Birhane
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica C. Chen
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andre McCullough
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC Inc., Atlanta, Georgia, USA
| | - Heather A. Carleton
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelley B. Hise
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Beth Tolar
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Louise Francois Watkins
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Smith AB, Specker JT, Hewlett KK, Scoggins TR, Knight M, Lustig AM, Li Y, Evans KM, Guo Y, She Q, Christopher MW, Garrett TJ, Moustafa AM, Van Tyne D, Prentice BM, Zackular JP. Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection. mBio 2024; 15:e0165623. [PMID: 38078767 PMCID: PMC10790701 DOI: 10.1128/mbio.01656-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.
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Affiliation(s)
- Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharine K. Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Troy R. Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Montana Knight
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail M. Lustig
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yanhong Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tsinghua University School of Medicine, Beijing, China
| | - Kirsten M. Evans
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Qianxuan She
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Timothy J. Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Ahmed M. Moustafa
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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47
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Wiull K, Hagen LH, Rončević J, Westereng B, Boysen P, Eijsink VGH, Mathiesen G. Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2. Microb Cell Fact 2024; 23:19. [PMID: 38212746 PMCID: PMC10782763 DOI: 10.1186/s12934-024-02296-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins. RESULTS Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences. CONCLUSION All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.
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Affiliation(s)
- Kamilla Wiull
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Jelena Rončević
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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48
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Collis RM, Biggs PJ, Burgess SA, Midwinter AC, Brightwell G, Cookson AL. Impact of systemic antimicrobial therapy on the faecal microbiome in symptomatic dairy cows. PLoS One 2024; 19:e0296290. [PMID: 38180967 PMCID: PMC10769045 DOI: 10.1371/journal.pone.0296290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024] Open
Abstract
Antimicrobial resistance is a global threat to human and animal health, with the misuse and overuse of antimicrobials suggested as the main drivers of resistance. Antimicrobial therapy can alter the bacterial community composition and the faecal resistome in cattle. Little is known about the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the presence of disease. Therefore, this study aimed to assess the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the pastoral farm environment, by analysing faecal samples from cattle impacted by several different clinically-defined conditions and corresponding antimicrobial treatments. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during antimicrobial treatment but, in many cases, the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Perturbations in the microbiome composition and the ability of the microbiome to recover were specific at the individual animal level, highlighting that the animal is the main driver of variation. Other factors such as disease severity, the type and duration of antimicrobial treatment and changes in environmental factors may also impact the bovine faecal microbiome. AmpC-producing Escherichia coli were isolated from faeces collected during and post-treatment with ceftiofur from one cow while no third-generation cephalosporin resistant E. coli were isolated from the untreated cow samples. This isolation of genetically similar plasmid-mediated AmpC-producing E. coli has implications for the development and dissemination of antibiotic resistant bacteria and supports the reduction in the use of critically important antimicrobials.
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Affiliation(s)
- Rose M. Collis
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J. Biggs
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Sara A. Burgess
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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49
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Metcalf R, Messer LF, White HL, Ormsby MJ, Matallana-Surget S, Quilliam RS. Evidence of interspecific plasmid uptake by pathogenic strains of Klebsiella isolated from microplastic pollution on public beaches. J Hazard Mater 2024; 461:132567. [PMID: 37741206 DOI: 10.1016/j.jhazmat.2023.132567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Microplastic beads are becoming a common feature on beaches, and there is increasing evidence that such microplastics can become colonised by potential human pathogens. However, whether the concentrations and pathogenicity of these pathogens pose a public health risk are still unclear. Therefore, the aim of this study was to determine realistic environmental concentrations of potential pathogens colonising microplastic beads, and quantify the expression of virulence and antimicrobial resistance genes (ARGs). Microplastic beads were collected from beaches and a culture-dependent approach was used to determine the concentrations of seven target bacteria (Campylobacter spp.; E. coli; intestinal enterococci; Klebsiella spp.; Pseudomonas aeruginosa; Salmonella spp.; Vibrio spp.). All seven target bacteria were detected without the need for a pre-enrichment step; urban sites had higher bacterial concentrations, whilst polymer type had no influence on bacterial concentrations. Klebsiella was the most abundant target bacteria and possessed virulence and ARGs, some of which were present on plasmids from other species, and showed pathogenicity in a Galleria melonella infection model. Our findings demonstrate how pathogen colonised microplastic beads can pose a heightened public health risk at the beach, and highlights the urgency for improved monitoring and enforcement of regulations on the release of microplastics into the environment.
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Affiliation(s)
- Rebecca Metcalf
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | - Lauren F Messer
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Hannah L White
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Sabine Matallana-Surget
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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50
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Silva BA, do Amarante VS, Xavier RGC, Colombo SA, da Silva TF, Brenig B, Aburjaile FF, de Carvalho Azevedo VA, Silva ROS. Characterization of ESBL/AmpC-producing extraintestinal Escherichia coli (ExPEC) in dogs treated at a veterinary hospital in Brazil. Res Vet Sci 2024; 166:105106. [PMID: 38086217 DOI: 10.1016/j.rvsc.2023.105106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 01/01/2024]
Abstract
The clinical aspects and lineages involved in Extraintestinal pathogenic Escherichia coli (ExPEC) infections in dogs remain largely unknown. In this study, we investigated the antimicrobial resistance and molecular structures of ExPECs isolated from infected dogs in Brazil. Samples were obtained from dogs (n = 42) with suspected extraintestinal bacterial infections. Phylogroup B2 was predominant (65.1%). No association was observed between the site of infection, phylogroups, or virulence factors. Almost half of the isolates (44.2%) were MDR, and 20.9% were extended-spectrum β-lactamase (ESBL)-positive. E. coli isolates that were resistant to fluoroquinolones (27.9%) were more likely to be MDR. The CTX-M-15 enzyme was predominant among the ESBL-producing strains, and seven sequence types were identified, including the high-risk clones ST44 and ST131. Single SNPs analysis confirmed the presence of two clonal transmissions. The present study showed a high frequency of ExPECs from phylogroup B2 infecting various sites and a high frequency of ESBL-producing strains that included STs frequently associated with human infection. This study also confirmed the nosocomial transmission of ESBL-producing E. coli, highlighting the need for further studies on the prevention and diagnosis of nosocomial infections in veterinary settings.
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Affiliation(s)
- Brendhal Almeida Silva
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | - Victor Santos do Amarante
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | - Rafael Gariglio Clark Xavier
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | - Salene Angelini Colombo
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | - Tales Fernando da Silva
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Flavia Figueira Aburjaile
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil
| | | | - Rodrigo Otávio Silveira Silva
- Veterinary School, Federal University of Minas Gerais, Antônio Carlos Avenue, 6627, Belo Horizonte 31.270-901, MG, Brazil.
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