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Youngblom MA, Imhoff MR, Smyth LM, Mohamed MA, Pepperell CS. Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553882. [PMID: 37645846 PMCID: PMC10462137 DOI: 10.1101/2023.08.18.553882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists. Data summary Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics . Impact statement It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.
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Habib I, Elbediwi M, Mohamed MYI, Ghazawi A, Abdalla A, Khalifa HO, Khan M. Enumeration, antimicrobial resistance and genomic characterization of extended-spectrum β-lactamases producing Escherichia coli from supermarket chicken meat in the United Arab Emirates. Int J Food Microbiol 2023; 398:110224. [PMID: 37167788 DOI: 10.1016/j.ijfoodmicro.2023.110224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023]
Abstract
The occurrence and counts of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in retail chicken sold in the United Arab Emirates (UAE) were investigated in this study. Results indicated that 79.68 % of chicken carcasses (251/315) sampled from UAE supermarkets harbored ESBL-producing E. coli. About half (51.75 % [163/315]) of the tested samples had an ESBL-producing E. coli count range between ≥3 log10 and < 5 log10 CFU/g. The antimicrobial resistance profiles of a subset of 100 isolates showed high rates of non-susceptibility to clinically significant antibiotics, particularly ciprofloxacin (80 %) and cefepime (46 %). Moreover, 7 % of the isolates exhibited resistance to colistin, with PCR-based screening revealing the presence of the mcr-1 gene in all colistin-resistant isolates. Multiplex PCR screening identified blaCTX-M and blaTEM genes as the most frequently presented genes among the phenotypically confirmed ESBL-producing E. coli. Further whole-genome sequencing and bioinformatic analysis of 27 ESBL-producing E. coli isolates showed that the gene family blaCTX group 1 was the most prevalent, notably CTX-M-55 (55.55 % [15/27]), followed by CTX-M-15 (22.22 % [6/27]). The most common sequence types (STs) were ST359 and ST1011, with three evident clusters identified based on phylogenomic analysis, aligned with isolates from specific production companies. Analysis of plasmid incompatibility types revealed IncFIB, IncFII, Incl2, and IncX1 as the most commonly featured plasmids. The findings of this study indicate a noticeable prevalence and high counts of ESBL-producing E. coli in chicken sampled from supermarkets in the UAE. The high rates of antimicrobial resistance to clinically important antibiotics highlight the potential public health risk associated with consuming chicken contaminated with ESBL-producing E. coli. Overall, this study emphasizes the importance of continued antimicrobial resistance monitoring in the UAE food chain and calls for further exposure risk assessment of the consumption of ESBL-producing E. coli via chicken meat.
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Affiliation(s)
- Ihab Habib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; Department of Environmental Health, High Institute of Public Health, Alexandria University, Alexandria, Egypt; ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Mohammed Elbediwi
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany; Animal Health Research Institute, Agriculture Research Centre, Cairo, Egypt
| | - Mohamed-Yousif Ibrahim Mohamed
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Afra Abdalla
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates
| | - Hazim O Khalifa
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
| | - Mushtaq Khan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 1555, United Arab Emirates; Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates
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Behrens W, Kolte B, Junker V, Frentrup M, Dolsdorf C, Börger M, Jaleta M, Kabelitz T, Amon T, Werner D, Nübel U. Bacterial genome sequencing tracks the housefly-associated dispersal of fluoroquinolone- and cephalosporin-resistant Escherichia coli from a pig farm. Environ Microbiol 2023. [PMID: 36772962 DOI: 10.1111/1462-2920.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The regular use of antimicrobials in livestock production selects for antimicrobial resistance. The potential impact of this practice on human health needs to be studied in more detail, including the role of the environment for the persistence and transmission of antimicrobial-resistant bacteria. During an investigation of a pig farm and its surroundings in Brandenburg, Germany, we detected abundant cephalosporin- and fluoroquinolone-resistant Escherichia coli in pig faeces, sedimented dust, and house flies (Musca domestica). Genome sequencing of E. coli isolates revealed large phylogenetic diversity and plasmid-borne extended-spectrum beta lactamase (ESBL) genes CTX-M-1 in multiple strains. [Correction added on 28 February 2023, after first online publication: In the preceding sentence, 'and TEM-1' was previously included but has been deleted in this version.] Close genomic relationships indicated frequent transmission of antimicrobial-resistant E. coli between pigs from different herds and across buildings of the farm and suggested dust and flies as vectors for dissemination of faecal pathogens. Strikingly, we repeatedly recovered E. coli from flies collected up to 2 km away from the source, whose genome sequences were identical or closely related to those from pig faeces isolates, indicating the fly-associated transport of diverse ESBL-producing E. coli from the pig farm into urban habitation areas. The observed proximity of contaminated flies to human households poses a risk of transmission of antimicrobial-resistant enteric pathogens from livestock to man.
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Affiliation(s)
- Wiebke Behrens
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Baban Kolte
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vera Junker
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Martinique Frentrup
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Dolsdorf
- Teaching and Research Station for Animal Breeding and Husbandry (LVAT), Ruhlsdorf, Germany
| | - Maria Börger
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Megarsa Jaleta
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tina Kabelitz
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Thomas Amon
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany.,Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
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4
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dessouky YE, Elsayed SW, Abdelsalam NA, Saif NA, Álvarez-Ordóñez A, Elhadidy M. Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective. Gut Pathog 2022; 14:44. [PMID: 36471447 PMCID: PMC9721040 DOI: 10.1186/s13099-022-00517-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Campylobacteriosis represents a global public health threat with various socio-economic impacts. Among different Campylobacter species, Campylobacter jejuni (C. jejuni) is considered to be the foremost Campylobacter species responsible for most of gastrointestinal-related infections. Although these species are reported to primarily inhabit birds, its high genetic and phenotypic diversity allowed their adaptation to other animal reservoirs and to the environment that may impact on human infection. MAIN BODY A stringent and consistent surveillance program based on high resolution subtyping is crucial. Recently, different epidemiological investigations have implemented high-throughput sequencing technologies and analytical pipelines for higher resolution subtyping, accurate source attribution, and detection of antimicrobial resistance determinants among these species. In this review, we aim to present a comprehensive overview on the epidemiology, clinical presentation, antibiotic resistance, and transmission dynamics of Campylobacter, with specific focus on C. jejuni. This review also summarizes recent attempts of applying whole-genome sequencing (WGS) coupled with bioinformatic algorithms to identify and provide deeper insights into evolutionary and epidemiological dynamics of C. jejuni precisely along the farm-to-fork continuum. CONCLUSION WGS is a valuable addition to traditional surveillance methods for Campylobacter. It enables accurate typing of this pathogen and allows tracking of its transmission sources. It is also advantageous for in silico characterization of antibiotic resistance and virulence determinants, and hence implementation of control measures for containment of infection.
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Affiliation(s)
- Yara El dessouky
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7269.a0000 0004 0621 1570Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nehal Adel Abdelsalam
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7776.10000 0004 0639 9286Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Nehal A. Saif
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Avelino Álvarez-Ordóñez
- grid.4807.b0000 0001 2187 3167Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mohamed Elhadidy
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.10251.370000000103426662Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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5
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de Andrade Pereira L, de Carvalho Queiroz MM, Faria SCR, Zahner V. Ultrastructural and pathogenicity of Brevibacillus laterosporus against sinantropic muscoid dipterans. Microsc Res Tech 2021; 85:149-155. [PMID: 34331401 DOI: 10.1002/jemt.23891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/10/2022]
Abstract
Brevibacillus laterosporus has entomopathogenic potential against several orders of insects and its wide bioactivity is associated with a variety of strain-specific molecules. In order to avoid the use of synthetic insecticides, along with the need to control insect pests, microbial control has been widely used. Muscoid dipterans are known for their medical-veterinary and sanitary importance, and synanthropy. The enormous biotechnological potential of B. laterosporus has been demonstrated, but there are still few studies with muscoid dipterans. The aim of the study was to verify the mortality of B. laterosporus NRS590 on synanthropic flies and to characterize its different cell stages ultrastructurally. The flies were collected from garbage bins and the colonies were adapted to the laboratory conditions. Bioassays with neo larvae were carried out from the bacterial growth in the phases: vegetative (6 hr), sporangium (20 hr), and free spores (44 hr). An aliquot of each phase was collected for Transmission (TEM) and Scanning Electron Microscopy (SEM). The effectiveness of NRS590 was observed in the sporulation phase, where the corrected mortality was 83.3, 85.1, and 99% for Chrysomya megacephala, Chrysomya putoria, and Musca domestica, respectively. The parasporal body was observed in detail on the entire spore surface. Although our knowledge of this bacterium is growing, it remains to be determined the real virulence factors responsible for the wide entomopathogenic activity observed on muscoid dipterans. Therefore, this study can provide subsidies for the improvement of efficient and safe microbial control techniques for the environment and living beings.
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Affiliation(s)
- Lorrane de Andrade Pereira
- Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Viviane Zahner
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
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Heiden SE, Kurz MSE, Bohnert J, Bayingana C, Ndoli JM, Sendegeya A, Gahutu JB, Eger E, Mockenhaupt FP, Schaufler K. Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131. Antimicrob Resist Infect Control 2020; 9:34. [PMID: 32066506 PMCID: PMC7026959 DOI: 10.1186/s13756-020-0696-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/07/2020] [Indexed: 11/24/2022] Open
Abstract
Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics to study MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance of different MRGN including E. coli pathogenic lineage ST131 suggesting the important role of flies in disseminating highly virulent pathogens in clinical settings and beyond.
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Affiliation(s)
- Stefan E Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | | | | | | | - Jules M Ndoli
- University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Augustin Sendegeya
- University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Jean Bosco Gahutu
- University of Rwanda, Kigali, Rwanda.,University Teaching Hospital of Butare, Butare, Rwanda
| | - Elias Eger
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | | | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany.
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7
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The role of ‘filth flies’ in the spread of antimicrobial resistance. Travel Med Infect Dis 2018; 22:8-17. [DOI: 10.1016/j.tmaid.2018.02.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022]
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8
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Schets FM, Jacobs-Reitsma WF, van der Plaats RQJ, Heer LKD, van Hoek AHAM, Hamidjaja RA, de Roda Husman AM, Blaak H. Prevalence and types of Campylobacter on poultry farms and in their direct environment. JOURNAL OF WATER AND HEALTH 2017; 15:849-862. [PMID: 29215350 DOI: 10.2166/wh.2017.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To study whether broiler and layer farms contribute to the environmental Campylobacter load, environmental matrices at or close to farms, and caecal material from chickens, were examined. Similarity between Campylobacter from poultry and environment was tested based on species identification and Multilocus Sequence Typing. Campylobacter prevalence in caecal samples was 97% at layer farms (n = 5), and 93% at broiler farms with Campylobacter-positive flocks (n = 2/3). Campylobacter prevalence in environmental samples was 24% at layer farms, and 29% at broiler farms with Campylobacter-positive flocks. Campylobacter was detected in soil and surface water, not in dust and flies. Campylobacter prevalence in adjacent and remote surface waters was not significantly (P > 0.1) different. Detected species were C. coli (52%), C. jejuni (40%) and C. lari (7%) in layers, and C. jejuni (100%) in broilers. Identical sequence types (STs) were detected in caecal material and soil. A deviating species distribution in surface water adjacent to farms indicated a high background level of environmental Campylobacter. STs from layer farms were completely deviant from surface water STs. The occasional detection of identical STs in broilers, wastewater at broiler farms and surface water in the farm environment suggested a possible contribution of broiler farms to the aquatic environmental Campylobacter load.
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Affiliation(s)
- Franciska M Schets
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Wilma F Jacobs-Reitsma
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Rozemarijn Q J van der Plaats
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Lianne Kerkhof-De Heer
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Angela H A M van Hoek
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Raditijo A Hamidjaja
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Ana Maria de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
| | - Hetty Blaak
- National Institute for Public Health and the Environment (RIVM), Centre for Zoonoses and Environmental Microbiology, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, The Netherlands E-mail:
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Abstract
For several billion years, bacteria have developed mechanisms to resist antibacterial substances. In modern time, antibiotics are frequently used in veterinary and human medicine for prevention and treatment of diseases, globally still also for their growth promoting effects as feed additives. This complex situation has evolved in accelerating development and prevalence of multi-drug resistant bacteria in livestock and people. Extended-spectrum beta-lactamase (ESBL) producing bacteria are resistant to a wide range of ß-lactam antibiotics. They are currently considered as one of the main threats for the treatment of infections in humans and animals. In livestock and animal products, poultry and poultry products show the highest prevalence of ESBL-producers with CTX-M-1, TEM-52 and SHV-12 being the most common ESBL-types in poultry. Escherichia coli and Salmonella spp. are the bacteria in poultry, which carry ESBL-genes most frequently. ESBL-producing bacteria are present at every level of the poultry production pyramid and can be detected even in the meconium of newly hatched chicks. The environment close to poultry barns shows high prevalence rates of these bacteria and contributes to an ongoing infection pressure with further ESBL-types. Probiotics have been shown to successfully reduce ESBL-producers in chicken, as well as ESBL-gene transfer. Other feed additives, such as zinc and copper, increase the prevalence of ESBL-producing bacteria when fed to animals. To our best knowledge, this is the first publication presenting a comparative overview of the prevalence of ESBL-types using data from different countries. To reduce the hazard for public health from poultry carrying high numbers of ESBL-producers, preventive measurements must include the surrounding environment and avoidance of antibiotic usage at all levels of the production pyramid. The first results, of the research on the impact of feed additives on the spread of ESBL-genes, indicate the diet as a further, possible magnitude of influence.
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10
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de Vries SP, Gupta S, Baig A, Wright E, Wedley A, Jensen AN, Lora LL, Humphrey S, Skovgård H, Macleod K, Pont E, Wolanska DP, L'Heureux J, Mobegi FM, Smith DGE, Everest P, Zomer A, Williams N, Wigley P, Humphrey T, Maskell DJ, Grant AJ. Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models. Sci Rep 2017; 7:1251. [PMID: 28455506 PMCID: PMC5430854 DOI: 10.1038/s41598-017-01133-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/27/2017] [Indexed: 01/22/2023] Open
Abstract
Campylobacter is the most common cause of foodborne bacterial illness worldwide. Faecal contamination of meat, especially chicken, during processing represents a key route of transmission to humans. There is a lack of insight into the mechanisms driving C. jejuni growth and survival within hosts and the environment. Here, we report a detailed analysis of C. jejuni fitness across models reflecting stages in its life cycle. Transposon (Tn) gene-inactivation libraries were generated in three C. jejuni strains and the impact on fitness during chicken colonisation, survival in houseflies and under nutrient-rich and -poor conditions at 4 °C and infection of human gut epithelial cells was assessed by Tn-insertion site sequencing (Tn-seq). A total of 331 homologous gene clusters were essential for fitness during in vitro growth in three C. jejuni strains, revealing that a large part of its genome is dedicated to growth. We report novel C. jejuni factors essential throughout its life cycle. Importantly, we identified genes that fulfil important roles across multiple conditions. Our comprehensive screens showed which flagella elements are essential for growth and which are vital to the interaction with host organisms. Future efforts should focus on how to exploit this knowledge to effectively control infections caused by C. jejuni.
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Affiliation(s)
- Stefan P de Vries
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Srishti Gupta
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Abiyad Baig
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonnington, Leicestershire, United Kingdom
| | - Elli Wright
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Amy Wedley
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | | | - Lizeth LaCharme Lora
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Suzanne Humphrey
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Henrik Skovgård
- Department of Agroecology, University of Aarhus, Slagelse, Denmark
| | - Kareen Macleod
- University of Glasgow, Veterinary School, Glasgow, United Kingdom
| | - Elsa Pont
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Dominika P Wolanska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Joanna L'Heureux
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fredrick M Mobegi
- Department of Paediatric Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David G E Smith
- Heriot-Watt University, School of Life Sciences, Edinburgh, Scotland, United Kingdom
| | - Paul Everest
- University of Glasgow, Veterinary School, Glasgow, United Kingdom
| | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nicola Williams
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Paul Wigley
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Thomas Humphrey
- School of Medicine, Institute of Life Sciences, Swansea University, Swansea, United Kingdom
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
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Evers EG, Pielaat A, Smid JH, van Duijkeren E, Vennemann FBC, Wijnands LM, Chardon JE. Comparative Exposure Assessment of ESBL-Producing Escherichia coli through Meat Consumption. PLoS One 2017; 12:e0169589. [PMID: 28056081 PMCID: PMC5215934 DOI: 10.1371/journal.pone.0169589] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/19/2016] [Indexed: 02/06/2023] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL) and plasmidic AmpC (pAmpC) producing Escherichia coli (EEC) in food animals, especially broilers, has become a major public health concern. The aim of the present study was to quantify the EEC exposure of humans in The Netherlands through the consumption of meat from different food animals. Calculations were done with a simplified Quantitative Microbiological Risk Assessment (QMRA) model. The model took the effect of pre-retail processing, storage at the consumers home and preparation in the kitchen (cross-contamination and heating) on EEC numbers on/in the raw meat products into account. The contribution of beef products (78%) to the total EEC exposure of the Dutch population through the consumption of meat was much higher than for chicken (18%), pork (4.5%), veal (0.1%) and lamb (0%). After slaughter, chicken meat accounted for 97% of total EEC load on meat, but chicken meat experienced a relatively large effect of heating during food preparation. Exposure via consumption of filet americain (a minced beef product consumed raw) was predicted to be highest (61% of total EEC exposure), followed by chicken fillet (13%). It was estimated that only 18% of EEC exposure occurred via cross-contamination during preparation in the kitchen, which was the only route by which EEC survived for surface-contaminated products. Sensitivity analysis showed that model output is not sensitive for most parameters. However, EEC concentration on meat other than chicken meat was an important data gap. In conclusion, the model assessed that consumption of beef products led to a higher exposure to EEC than chicken products, although the prevalence of EEC on raw chicken meat was much higher than on beef. The (relative) risk of this exposure for public health is yet unknown given the lack of a modelling framework and of exposure studies for other potential transmission routes.
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Affiliation(s)
- Eric G. Evers
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Annemarie Pielaat
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Joost H. Smid
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Engeline van Duijkeren
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Francy B. C. Vennemann
- Public Health and Health Services Division, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lucas M. Wijnands
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jurgen E. Chardon
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Ter Kuile BH, Kraupner N, Brul S. The risk of low concentrations of antibiotics in agriculture for resistance in human health care. FEMS Microbiol Lett 2016; 363:fnw210. [PMID: 27609231 DOI: 10.1093/femsle/fnw210] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
The contribution of antibiotic resistance originally selected for in the agricultural sector to resistance in human pathogens is not known exactly, but is unlikely to be negligible. It is estimated that 50% to 80% of all antibiotics used are applied in agriculture and the remainder for treating infections in humans. Since dosing regimens are less controlled in agriculture than in human health care, veterinary and environmental microbes are often exposed to sublethal levels of antibiotics. Exposure to sublethal drug concentrations must be considered a risk factor for de novo resistance, transfer of antimicrobial resistant (AMR) genes, and selection for already existing resistance. Resistant zoonotic agents and commensal strains carrying AMR genes reach the human population by a variety of routes, foodstuffs being only one of these. Based on the present knowledge, short treatments with the highest dose that does not cause unacceptable side-effects may be optimal for achieving therapeutic goals while minimizing development of resistance. Novel approaches such as combination or alternating therapy are promising, but need to be explored further before they can be implemented in daily practice.
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Affiliation(s)
- Benno H Ter Kuile
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, the Netherlands
| | - Nadine Kraupner
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
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Blaak H, van Hoek AHAM, Hamidjaja RA, van der Plaats RQJ, Kerkhof-de Heer L, de Roda Husman AM, Schets FM. Distribution, Numbers, and Diversity of ESBL-Producing E. coli in the Poultry Farm Environment. PLoS One 2015; 10:e0135402. [PMID: 26270644 PMCID: PMC4536194 DOI: 10.1371/journal.pone.0135402] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022] Open
Abstract
This study aimed to discern the contribution of poultry farms to the contamination of the environment with ESBL-producing Escherichia coli and therewith, potentially to the spread of these bacteria to humans and other animals. ESBL-producing E. coli were detected at all investigated laying hen farms (n = 5) and broiler farms (n = 3) in 65% (46/71) and 81% (57/70) of poultry faeces samples, respectively. They were detected in rinse water and run-off water (21/26; 81%), other farm animals (11/14; 79%), dust (21/35; 60%), surface water adjacent to farms (20/35; 57%), soil (48/87; 55%), on flies (11/73; 15%), and in barn air (2/33; 6%). The highest prevalence and concentrations in the outdoor environment were observed in soil of free-range areas at laying hen farms (100% of samples positive, geometric mean concentration 2.4×104 cfu/kg), and surface waters adjacent to broiler farms during, or shortly after, cleaning between production rounds (91% of samples positive, geometric mean concentration 1.9×102 cfu/l). The diversity of ESBL-producing E. coli variants with respect to sequence type, phylogenetic group, ESBL-genotype and antibiotic resistance profile was high, especially on broiler farms where on average 16 different variants were detected, and the average Simpson’s Indices of diversity (SID; 1–D) were 0.93 and 0.94 among flock and environmental isolates respectively. At laying hen farms on average nine variants were detected, with SIDs of 0.63 (flock isolates) and 0.77 (environmental isolates). Sixty percent of environmental isolates were identical to flock isolates at the same farm. The highest proportions of ‘flock variants’ were observed in dust (94%), run-off gullies (82%), and barn air (67%), followed by surface water (57%), soil (56%), flies (50%) and other farm animals (35%).The introduction of ESBL-producing E. coli from poultry farms to the environment may pose a health risk if these bacteria reach places where people may become exposed.
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Affiliation(s)
- Hetty Blaak
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Angela H A M van Hoek
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Raditijo A Hamidjaja
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rozemarijn Q J van der Plaats
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lianne Kerkhof-de Heer
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ana Maria de Roda Husman
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Franciska M Schets
- Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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