1
|
Furlan JPR, Ramos MS, Sellera FP, Gonzalez IHL, Ramos PL, Stehling EG. Gram-negative bacterial diversity and evidence of international clones of multidrug-resistant strains in zoo animals. Integr Zool 2024; 19:417-423. [PMID: 37984552 DOI: 10.1111/1749-4877.12790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Enterobacterales and Pseudomonas aeruginosa have been colonizing or infecting wild hosts and antimicrobial-resistant strains are present in mammals and birds. Furthermore, international high-risk clones of multidrug-resistant Escherichia coli are identified and the implications of multidrug-resistant Gram-negative bacteria in zoo animals are discussed.
Collapse
Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Irys Hany Lima Gonzalez
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
2
|
Aydin A, Suleymanoglu AA, Abdramanov A, Paulsen P, Dumen E. Detection of Extended Spectrum ß-Lactamase-Producing Escherichia coli with Biofilm Formation from Chicken Meat in Istanbul. Foods 2024; 13:1122. [PMID: 38611426 PMCID: PMC11011584 DOI: 10.3390/foods13071122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Antimicrobial resistance is one of the major public health problems worldwide. This study aimed to detect the presence of extended-spectrum β-lactamase-(ESBL-)producing Escherichia (E.) coli in chicken meat in Istanbul, Türkiye. Raw chicken meat samples (n = 208) were collected from different sale points and analyzed for ESBL-producing E. coli. In total, 101 (48.5%) isolates were confirmed as E. coli by PCR, of which 80/101 (79.2%) demonstrated multiple antibiotic resistance. Resistance against amoxicillin-clavulanic acid was most frequent (87.1%). Eighteen isolates (17.8%) demonstrated phenotypical ESBL resistance, as assessed by the double disc synergy test (DDST). Isolates were tested for the presence of β-lactamase genes and mobilized colistin-resistant genes. The blaTEM group was most frequently detected (97.02%), followed by blaCTX m (45.5%), blaSHV (9.9%), and blaOXA-2 (0.9%). However, mcr genes and blaNDM,blaKPC, blaVIM, and blaOXA-48 genes were not found in any isolate. E. coli strains were tested for biofilm formation in six different media [Nutrient broth, LB broth, Tryptone Soya broth (TSB), TSB containing 1% sucrose, TSB containing 0.6% yeast extract, and BHI]. Biofilm formation by E. coli isolates (44/101, 43.5%) was highest in TSB with 1% sucrose. It is worth noting that all biofilm-producing isolates were found to harbor the blaTEM-1 gene, which can indicate a high level of antibiotic resistance. This is the first report about ESBL-producing E. coli in poultry meat, the exposure of consumers in Istanbul metropolitan areas, and the ability of E. coli from this region to produce biofilms.
Collapse
Affiliation(s)
- Ali Aydin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, İstanbul University-Cerrahpaşa, 34320 Istanbul, Türkiye; (A.A.S.); (E.D.)
| | - Ali Anil Suleymanoglu
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, İstanbul University-Cerrahpaşa, 34320 Istanbul, Türkiye; (A.A.S.); (E.D.)
| | - Abzal Abdramanov
- Department of Veterinary Sanitary Examination and Hygiene, Kazakh National Agrarian Research University, 050010 Almaty, Kazakhstan;
| | - Peter Paulsen
- Unit for Food Hygiene and Technology, Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Emek Dumen
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, İstanbul University-Cerrahpaşa, 34320 Istanbul, Türkiye; (A.A.S.); (E.D.)
| |
Collapse
|
3
|
Gentile N, Carrasquer F, Marco-Fuertes A, Marin C. Backyard poultry: exploring non-intensive production systems. Poult Sci 2024; 103:103284. [PMID: 38056053 PMCID: PMC10749279 DOI: 10.1016/j.psj.2023.103284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023] Open
Abstract
The concept of backyard poultry historically encompassed "food-producing animals." Nevertheless, a recent shift in livestock production paradigms within developed countries is evident, as backyard poultry owners now raise their birds for purposes beyond self-consumption, raising animals in a familiar way, and fostering emotional bonds with them. Because backyard animals are frequently privately owned, and the resulting products are typically not marketed, very little information is available about the demographic profile of backyard owners and information on flocks' characteristics, husbandry, and welfare. Thus, this review aims to clarify the characteristics of backyard poultry, highlighting the prevalent infectious diseases and the zoonotic risk to which farmers are exposed. According to the FAO, there are different types of poultry production systems: intensive, sub-intensive, and extensive. The system conditions, requirements, and the resulting performance differ extensively due to the type of breed, feeding practices, prevalence of disease, prevention and control of diseases, flock management, and the interactions among all these factors. The presence and transmission of infectious diseases in avian species is a problem that affects both the animals themselves and public health. Bacterial (Escherichia coli, Salmonella, Campylobacter, and Mycoplasma), parasitic (helminths, louses, and mites), and viral (Avian influenza, Newcastle, Marek, Infectious Bronchitis, Gumboro, Infectious Laringotracheitis, and Fowlpox) are the most important pathogens involved in backyard poultry health. In addition, Avian influenza, Salmonella, Campylobacter, and E. coli, could be a risk for backyard farmers and/or backyard-derived products consumers. Thus, proper biosecurity implementation measures are mandatory to control them. While the principles and practices of on-farm biosecurity may be well-versed among commercial farmers, hobbyists, and backyard farmers might not be familiar with the necessary steps to protect their flocks from infectious diseases and curb their transmission. This sector represents the fourth category of poultry farming, characterized by the lowest biosecurity standards. Consequently, it is imperative to address the legal status of backyard poultry, educate owners about biosecurity measures, and promote proper veterinary care and disease control.
Collapse
Affiliation(s)
- Nicla Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy; Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Alfara del Patriarca, Valencia, Spain
| | - Fernando Carrasquer
- H&N International GmbH, 27472 Cuxhaven, Germany; Institute of Science and Animal Technology, Universitat Politècnica de Valencia, 46022 Valencia, Spain
| | - Ana Marco-Fuertes
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Alfara del Patriarca, Valencia, Spain
| | - Clara Marin
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Alfara del Patriarca, Valencia, Spain.
| |
Collapse
|
4
|
Allegretti YH, Yamaji R, Adams-Sapper S, Riley LW. Genetic features of antimicrobial drug-susceptible extraintestinal pathogenic Escherichia coli pandemic sequence type 95. Microbiol Spectr 2024; 12:e0418922. [PMID: 38059630 PMCID: PMC10783064 DOI: 10.1128/spectrum.04189-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/13/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Despite the increasing prevalence of antibiotic-resistant Escherichia coli strains that cause urinary tract and bloodstream infections, a major pandemic lineage of extraintestinal pathogenic E. coli (ExPEC) ST95 has a comparatively low frequency of drug resistance. We compared the genomes of 1,749 ST95 isolates to identify genetic features that may explain why most strains of ST95 resist becoming drug-resistant. Identification of such genomic features could contribute to the development of novel strategies to prevent the spread of antibiotic-resistant genes and devise new measures to control antibiotic-resistant infections.
Collapse
Affiliation(s)
| | | | | | - Lee W. Riley
- University of California Berkeley, Berkeley, California, USA
| |
Collapse
|
5
|
Zurita J, Sevillano G, Paz Y Miño A, Haro N, Larrea-Álvarez M, Alcocer I, Ortega-Paredes D. Dominance of ST131, B2, blaCTX-M-15, and papA-papC-kpsMII-uitA among ESBL Escherichia coli isolated from bloodstream infections in Quito, Ecuador: a 10-year surveillance study (2009-2019). J Appl Microbiol 2023; 134:lxad269. [PMID: 37974051 DOI: 10.1093/jambio/lxad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/21/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
AIMS This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years. METHODS AND RESULTS Isolates were collected from January 2009 to December 2019 and those testing for E. coli were included. Antibiotic susceptibility was tested using the VITEK® system. Selected isolates were further characterized by amplification of marker genes (virulence traits, phylogroups, and sequence types). A total of 166 ESBL-producing E. coli were recovered. The blaCTX-M-15 allele was the most abundant. Most of the isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin. No resistance to carbapenems was registered. More than 80% of bacteria were classified as extraintestinal pathogenic E. coli (ExPEC), and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and bacteria predominantly belonged to ST131. CONCLUSIONS There was an increase in the ExPEC ESBL-E coli in bloodstream infections and the relationship between the isolates found in these infections during these 10 years.
Collapse
Affiliation(s)
- Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito 170521, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Ariane Paz Y Miño
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Nathalí Haro
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Marco Larrea-Álvarez
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
| | - Iliana Alcocer
- Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - David Ortega-Paredes
- Facultad de Ciencias Médicas Enrique Ortega Moreira, Carrera de Medicina, Universidad Espíritu Santo, Km 2.5 vía a Samborondón 0901952, Ecuador
- Unidad de Investigación en Enfermedades Transmitidas por Alimentos y Resistencia a los, Antimicrobianos (UNIETAR), Facultad de Veterinaria, Universidad Central del Ecuador, Quito 170129, Ecuador
- Laboratorio de Referencia de E. coli, Department of Microbiology and Parasitology, Veterinary Faculty, University of Santiago de Compostela, Lugo 15782, Spain
| |
Collapse
|
6
|
Mwenifumbo M, Cookson AL, Zhao S, Fayaz A, Browne AS, Benschop J, Burgess SA. The characterisation of antimicrobial resistant Escherichia coli from dairy calves. J Med Microbiol 2023; 72. [PMID: 37578342 DOI: 10.1099/jmm.0.001742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli.Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli.Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.
Collapse
Affiliation(s)
- Merning Mwenifumbo
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
- Present address: Faculty of Veterinary Medicine, Lilongwe University of Agriculture & Natural Resources, Lilongwe, Malawi
| | - Adrian L Cookson
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
- Food Systems Integrity, Hopkirk Research Institute, cnr University & Library Rds, AgResearch Ltd, Palmerston North 4442, New Zealand
| | - Shengguo Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ahmed Fayaz
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
| | - A Springer Browne
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
| | - Jackie Benschop
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
| | - Sara A Burgess
- School of Veterinary Science, Hopkirk Research Institute, cnr University & Library Rds Massey University, Palmerston North 4442, New Zealand
| |
Collapse
|
7
|
Sartori L, Sellera FP, Fuga B, Sano E, Monte DFM, Cardoso B, Côrtes LDA, Lincopan N. Phylogenomic Analysis of CTX-M-15-Positive Escherichia coli from Companion Animal Reveals Intercontinental Dissemination of ST90 Within a One Health Framework. Microb Drug Resist 2023. [PMID: 37155698 DOI: 10.1089/mdr.2022.0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
The global dissemination of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli has been considered a critical issue within a One Health framework. The aim of this study was to perform a genomic investigation of an ESBL-producing E. coli strain belonging to the globally spread sequence type/clonal complex ST90/CC23, isolated from gastrointestinal tract of a dog, in Brazil. Besides CTX-M-15 ESBL, this E. coli isolate carried mutations conferring resistance to human and veterinary fluoroquinolones (GyrA [Ser83Leu, Asp87Asn], ParC [Ser80Ile] and ParE [Ser458Ala]), and resistance determinants to disinfectants and pesticides. Noteworthy, phylogenomic analysis revealed that this multidrug E. coli strain clustered with ST90 lineages isolated from human, dog, and livestock in Brazil. The phylogenetic tree also revealed that this E. coli strain shares a common ancestor with isolates from the United States, Russia, Germany, and China, highlighting the potential global spreading of this clone. In summary, we report genomic data of CTX-M-15-positive E.coli ST90 colonizing a pet. Colonization of companion animals by critical resistant pathogens highlights the need for close monitoring to better understand the epidemiology and genetic factors contributing for successful adaptation of global clones at the human-animal interface.
Collapse
Affiliation(s)
- Luciana Sartori
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel F M Monte
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
8
|
Ribeiro J, Silva V, Monteiro A, Vieira-Pinto M, Igrejas G, Reis FS, Barros L, Poeta P. Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli. Animals (Basel) 2023; 13:1362. [PMID: 37106925 PMCID: PMC10135345 DOI: 10.3390/ani13081362] [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: 02/23/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.
Collapse
Affiliation(s)
- Jessica Ribeiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Madalena Vieira-Pinto
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Veterinary Science, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filipa S. Reis
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| |
Collapse
|
9
|
Alvarado-Martinez Z, Tabashsum Z, Aditya A, Suh G, Wall M, Hshieh K, Biswas D. Purified Plant-Derived Phenolic Acids Inhibit Salmonella Typhimurium without Alteration of Microbiota in a Simulated Chicken Cecum Condition. Microorganisms 2023; 11:microorganisms11040957. [PMID: 37110380 PMCID: PMC10144919 DOI: 10.3390/microorganisms11040957] [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: 02/16/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (ST) remains a predominant zoonotic pathogen because of its colonization in poultry, survivability in the environment, and increasing antibiotic-resistance pattern. Plant-derived phenolics, gallic acid (GA), protocatechuic acid (PA), and vanillic acids (VA) have demonstrated antimicrobial activity in vitro; therefore, this study collected chicken cecal fluid and supplemented it with these phenolics to evaluate their potential for eliminating ST and mod-ulating the microbiota of complex environments. ST was quantified through plating, while micro-biome analysis was performed through pair-end 16S-rRNA gene sequencing. CFU/mL of ST in cecal fluid with GA was significantly reduced by 3.28 and 2.78 log at 24 h and 48 h, while PA only had a slight numerical decrease. VA significantly reduced ST by 4.81 and 5.20 log at 24 h and 48 h. Changes in relative abundance of major phyla were observed at 24 h for samples with GA and VA as Firmicute levels increased 8.30% and 20.90%, while Proteobacteria decreased 12.86% and 18.48%, respectively. Significant changes in major genre were observed in Acinetobacter (3.41% for GA) and Escherichia (13.53% for VA), while Bifidobacterium increased (3.44% for GA) and Lactobacillus remained unchanged. Results suggest that phenolic compounds exert different effects on certain pathogens, while supporting some commensal bacteria.
Collapse
Affiliation(s)
- Zabdiel Alvarado-Martinez
- Biological Sciences Program-Molecular and Cellular Biology, University of Maryland-College Park, College Park, MD 20742, USA
| | - Zajeba Tabashsum
- Biological Sciences Program-Molecular and Cellular Biology, University of Maryland-College Park, College Park, MD 20742, USA
| | - Arpita Aditya
- Department of Animal and Avian Sciences, University of Maryland-College Park, College Park, MD 20742, USA
| | - Grace Suh
- Department of Biology, University of Maryland-College Park, College Park, MD 20742, USA
| | - Matthew Wall
- Department of Biology, University of Maryland-College Park, College Park, MD 20742, USA
| | - Katherine Hshieh
- Department of Biology, University of Maryland-College Park, College Park, MD 20742, USA
| | - Debabrata Biswas
- Biological Sciences Program-Molecular and Cellular Biology, University of Maryland-College Park, College Park, MD 20742, USA
- Department of Animal and Avian Sciences, University of Maryland-College Park, College Park, MD 20742, USA
- Center for Food Safety and Security Systems, University of Maryland-College Park, College Park, MD 20742, USA
| |
Collapse
|
10
|
Al-Mustapha AI, Alada SA, Raufu IA, Lawal AN, Eskola K, Brouwer MS, Adetunji V, Heikinheimo A. Co-occurrence of antibiotic and disinfectant resistance genes in extensively drug-resistant Escherichia coli isolated from broilers in Ilorin, North Central Nigeria. J Glob Antimicrob Resist 2022; 31:337-344. [PMID: 36375754 DOI: 10.1016/j.jgar.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The occurrence of multidrug-resistant (MDR) bacteria in poultry poses the public health threat of zoonotic transmission to humans. Hence, this study assessed the occurrence of drug-resistant Escherichia coli in broilers in the largest live bird market in Kwara State, Nigeria in December 2020. METHODS Presumptive E. coli isolates were isolated using the European Union Reference Laboratory guideline of 2017 and confirmed via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Broth microdilution was performed on confirmed E. coli isolates to determine the minimum inhibitory concentration. Five extensively drug-resistant (XDR) isolates were selected for Illumina whole genome sequencing to predict the resistome, phylotype, sequence type, serotype, and diversity of mobile genetic elements in these isolates. RESULTS Of the 181 broiler caecal samples, 73 E. coli isolates were obtained, of which 67 (82.0%) and 37 (50.6%) were determined as MDR (resistant to at least three classes of antibiotics) and XDR (resistant to at least five classes of antibiotics), respectively. Whole genome sequencing revealed diverse sequence types, phylogroups, and serotypes (ST165/B1 - O80:H19, ST115/A - Unknown: H7, ST901/B1 - O109:H4, ST4087/F - O117:H42, and ST8324/A - O127:H42). The XDR E. coli isolates encoded resistance to fluoroquinolones, fosfomycin, sulfamethoxazole, ampicillin and cephalosporins, trimethoprim, aminoglycosides, chloramphenicol, tetracycline, and macrolides. Mutations in the gyrA gene conferring resistance to fluoroquinolones were also detected. There was a positive correlation between phenotypic resistance patterns and the antibiotic resistance genes that were detected in the sequenced isolates. The XDR isolates also harbored two disinfectant resistance genes (qacE and sitABCD) that conferred resistance to hydrogen peroxide and quaternary ammonium compounds, respectively. The genome of the XDR isolates harbored several mobile genetic elements and virulence-associated genes, which were conserved in all sequenced XDR isolates. CONCLUSIONS This is the first report of co-carriage of antibiotic resistance genes and disinfectant resistance genes in E. coli isolated from broilers in Ilorin, Nigeria. Our findings suggest that poultry are potential carriers of clonally diverse, pathogenic, MDR/XDR E. coli, which may have detrimental zoonotic potentials on human health.
Collapse
Affiliation(s)
- Ahmad Ibrahim Al-Mustapha
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Kwara State, Nigeria; Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Oyo State, Nigeria; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland.
| | - Shafi Abdullah Alada
- Veterinary Microbiology Laboratory, University of Ilorin Veterinary Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Ibrahim Adisa Raufu
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Kwara State, Nigeria
| | - Adedeji Nurudeen Lawal
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Kwara State, Nigeria; Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Katarina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Michael Sm Brouwer
- Department of Bacteriology and Host-Pathogen Reaction, Wageningen University and Research, Lelystad, The Netherlands
| | - Victoria Adetunji
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Oyo State, Nigeria
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
| |
Collapse
|
11
|
Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO, Adeyemo AT, Adeyemo AT, Bejide OS, Underwood A, Argimón S, Abrudan M, Egwuenu A, Ihekweazu C, Aanensen DM, Okeke IN. An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals. Microb Genom 2022; 8:mgen000863. [PMID: 36748556 PMCID: PMC9837563 DOI: 10.1099/mgen.0.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016-2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.
Collapse
Affiliation(s)
- Ayorinde O. Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Adeyemi T. Adeyemo
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Osun State, Nigeria
| | - Abolaji T. Adeyemo
- Department of Medical Microbiology and Parasitology, University of Osun Teaching Hospital, Osogbo, Osun State, Nigeria
| | - Oyeniyi S. Bejide
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| |
Collapse
|
12
|
A One Health Genomic Investigation of Gentamicin Resistance in Escherichia coli from Human and Chicken Sources in Canada, 2014 to 2017. Antimicrob Agents Chemother 2022; 66:e0067722. [PMID: 36165686 PMCID: PMC9578425 DOI: 10.1128/aac.00677-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated whether gentamicin resistance (Genr) in Escherichia coli isolates from human infections was related to Genr E. coli in chicken and whether resistance may be due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Genr E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Genr gene was different in human and chicken sources; however, both sources carried aac(3)-IId, aac(3)-VIa, and aac(3)-IVa. Forty-one percent of human clinical isolates of Genr E. coli contained a blaCTX-M extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Genr isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Genr and spectinomycin resistance (Specr) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Genr and Specr genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Genr isolates and plasmids were mostly different in chickens and humans.
Collapse
|
13
|
Bastidas-Caldes C, Romero-Alvarez D, Valdez-Vélez V, Morales RD, Montalvo-Hernández A, Gomes-Dias C, Calvopiña M. Extended-Spectrum Beta-Lactamases Producing Escherichia coli in South America: A Systematic Review with a One Health Perspective. Infect Drug Resist 2022; 15:5759-5779. [PMID: 36204394 PMCID: PMC9531622 DOI: 10.2147/idr.s371845] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Carlos Bastidas-Caldes
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
- Doctoral Program in Public and Animal Health, Faculty of Veterinary Medicine, University of Extremadura, Cáceres, Spain
- Correspondence: Carlos Bastidas-Caldes, One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, 170124, Ecuador, Tel +593 983 174949, Email
| | - Daniel Romero-Alvarez
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, The University of Kansas, Lawrence, KS, USA
| | - Victor Valdez-Vélez
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Roberto D Morales
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Andrés Montalvo-Hernández
- One Health Research Group, Faculty of Engineering and Applied Sciences, Universidad de las Américas, Quito, Ecuador
| | - Cicero Gomes-Dias
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Manuel Calvopiña
- One Health Reserch Group, Faculty of Medicine, Universidad de las Américas, Quito, Ecuador
| |
Collapse
|
14
|
Highly Virulent and Multidrug-Resistant Escherichia coli Sequence Type 58 from a Sausage in Germany. Antibiotics (Basel) 2022; 11:antibiotics11081006. [PMID: 35892394 PMCID: PMC9331442 DOI: 10.3390/antibiotics11081006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Studies have previously described the occurrence of multidrug-resistant (MDR) Escherichia coli in human and veterinary medical settings, livestock, and, to a lesser extent, in the environment and food. While they mostly analyzed foodborne E. coli regarding phenotypic and sometimes genotypic antibiotic resistance and basic phylogenetic classification, we have limited understanding of the in vitro and in vivo virulence characteristics and global phylogenetic contexts of these bacteria. Here, we investigated in-depth an E. coli strain (PBIO3502) isolated from a pork sausage in Germany in 2021. Whole-genome sequence analysis revealed sequence type (ST)58, which has an internationally emerging high-risk clonal lineage. In addition to its MDR phenotype that mostly matched the genotype, PBIO3502 demonstrated pronounced virulence features, including in vitro biofilm formation, siderophore secretion, serum resilience, and in vivo mortality in Galleria mellonella larvae. Along with the genomic analysis indicating close phylogenetic relatedness of our strain with publicly available, clinically relevant representatives of the same ST, these results suggest the zoonotic and pathogenic character of PBIO3502 with the potential to cause infection in humans and animals. Additionally, our study highlights the necessity of the One Health approach while integrating human, animal, and environmental health, as well as the role of meat products and food chains in the putative transmission of MDR pathogens.
Collapse
|
15
|
Harrison L, Tyson GH, Strain E, Lindsey RL, Strockbine N, Ceric O, Fortenberry GZ, Harris B, Shaw S, Tillman G, Zhao S, Dessai U. Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human Illness. Foods 2022; 11:foods11131975. [PMID: 35804790 PMCID: PMC9265580 DOI: 10.3390/foods11131975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) cause urinary tract and potentially life-threatening invasive infections. Unfortunately, the origins of ExPEC are not always clear. We used genomic data of E. coli isolates from five U.S. government organizations to evaluate potential sources of ExPEC infections. Virulence gene analysis of 38,032 isolates from human, food animal, retail meat, and companion animals classified the subset of 8142 non-diarrheagenic isolates into 40 virulence groups. Groups were identified as low, medium, and high relative risk of containing ExPEC strains, based on the proportion of isolates recovered from humans. Medium and high relative risk groups showed a greater representation of sequence types associated with human disease, including ST-131. Over 90% of food source isolates belonged to low relative risk groups, while >60% of companion animal isolates belonged to medium or high relative risk groups. Additionally, 18 of the 26 most prevalent antimicrobial resistance determinants were more common in high relative risk groups. The associations between antimicrobial resistance and virulence potentially limit treatment options for human ExPEC infections. This study demonstrates the power of large-scale genomics to assess potential sources of ExPEC strains and highlights the importance of a One Health approach to identify and manage these human pathogens.
Collapse
Affiliation(s)
- Lucas Harrison
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
- Correspondence: (L.H.); (U.D.)
| | - Gregory H. Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.L.L.); (N.S.)
| | - Nancy Strockbine
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.L.L.); (N.S.)
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Gamola Z. Fortenberry
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
| | - Beth Harris
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, IA 50010, USA;
| | - Sheryl Shaw
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
| | - Glenn Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Athens, GA 30605, USA;
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
- Correspondence: (L.H.); (U.D.)
| |
Collapse
|
16
|
Belas A, Marques C, Menezes J, da Gama LT, Cavaco-Silva P, Pomba C. ESBL/ pAmpC-Producing Escherichia coli Causing Urinary Tract Infections in Non-Related Companion Animals and Humans. Antibiotics (Basel) 2022; 11:antibiotics11050559. [PMID: 35625203 PMCID: PMC9137695 DOI: 10.3390/antibiotics11050559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) caused by Escherichia coli are frequently diagnosed in humans and companion animals. Extended-spectrum beta-lactamase (ESBL)- and cephalosporinase (pAmpC)-producing Escherichia coli are worldwide-disseminated and frequently multidrug-resistant, hence leading to treatment failure and public health concerns. This study aimed to characterize and compare ESBL/pAmpC-producing E. coli strains causing community-acquired UTI in companion animals and non-related humans. Third-generation cephalosporin (3GC)-resistant E. coli (companion animals n = 35; humans n = 85) isolated from patients with UTI were tested against 14 antimicrobials following CLSI guidelines. PCR-based assays were used to detect the major E. coli phylogenetic groups, pathogenicity associated-islands (PAIs), virulence genes, and ESBLs/pAmpC resistance genes. ESBL/pAmpC-producing E. coli isolates were typed by multi-locus sequence typing (MLST) and PCR. E. coli strains from companion animals and humans shared two MDR high-risk clonal lineages: ST131 and ST648. To the best of our knowledge, this study reports the first description of E. coli ST131 clade C1-M27 and the clonal lineage ST131 clade A in humans with community-acquired UTI in Portugal. Considering that companion animals with UTI are generally treated at home by the owners, measures should be implemented to avoid the spread of multidrug-resistant high-risk clones to humans and their household environment.
Collapse
Affiliation(s)
- Adriana Belas
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Cátia Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Juliana Menezes
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Luís Telo da Gama
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Patrícia Cavaco-Silva
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Caparica, Portugal;
- Technophage, 1649-028 Lisboa, Portugal
| | - Constança Pomba
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Correspondence:
| |
Collapse
|
17
|
Pellegrini MC, Okada E, González Pasayo RA, Ponce AG. Prevalence of Escherichia coli strains in horticultural farms from Argentina: antibiotic resistance, biofilm formation, and phylogenetic affiliation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:23225-23236. [PMID: 34802078 DOI: 10.1007/s11356-021-17523-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Escherichia coli is the bacteria most commonly used as an indicator of fecal contamination in agricultural environments. Moreover, E. coli is categorized as a priority pathogen due to its widespread antibiotic resistance. This study aimed to characterize E. coli strains isolated from 10 horticultural farms. Isolates were obtained from samples of vegetable crops (n = 62), the surrounding soil (n = 62), poultry litter (n = 8), and groundwater (n = 6). Phyllo-grouping assignment was performed on the total of E. coli isolates. Antibiograms and quantification of the minimal inhibitory concentration (MIC) were performed with antibiotics commonly used in humans. Biofilm formation capacity was studied by quantifying cells attached to culture tubes. Overall, 21 E. coli isolates were obtained. Three phylogenetic groups (A, B1, and C) and two Escherichia clade IV and IV-V were identified in the collection by polymerase chain reaction. Sixty-seven percent of the E. coli isolates were resistant to amoxicillin-clavulanic acid and/or ampicillin. Amoxicillin MIC values ranged from 11.9 to >190.5 µg/mL and ampicillin MIC values ranged from 3 to >190.5 µg/mL. All the E. coli isolates, resistant and non-resistant, had biofilm forming capacity. The presence of phenotypic resistance on fresh produce and environmental matrices could present significant opportunities for contamination that result in health risks for consumers. To the authors' best knowledge, this is the first environmental assessment of resistant E. coli occurrence in horticultural farms in South America.
Collapse
Affiliation(s)
- María Celeste Pellegrini
- Grupo de Investigación en Ingeniería en Alimentos (GIIA), Instituto de Ciencia y Tecnología de alimentos y ambiente (INCITAA, CIC-UNMDP), Facultad de Ingeniería, Universidad Nacional de Mar del Plata, Av. Juan B. Justo 4302, B7602AYL Mar del, Plata, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, CABA, Argentina.
| | - Elena Okada
- Instituto Nacional de Tecnología Agropecuaria (INTA) Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce, Ruta 226 Km 73.5, 7620, Balcarce, Argentina
| | - Ramón Alejandro González Pasayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible (IPADS, CONICET-INTA), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Alejandra Graciela Ponce
- Grupo de Investigación en Ingeniería en Alimentos (GIIA), Instituto de Ciencia y Tecnología de alimentos y ambiente (INCITAA, CIC-UNMDP), Facultad de Ingeniería, Universidad Nacional de Mar del Plata, Av. Juan B. Justo 4302, B7602AYL Mar del, Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, CABA, Argentina
| |
Collapse
|
18
|
Sonnevend Á, Alali WQ, Mahmoud SA, Ghazawi A, Bharathan G, Melegh S, Rizvi TA, Pál T. Molecular Characterization of MCR-1 Producing Enterobacterales Isolated in Poultry Farms in the United Arab Emirates. Antibiotics (Basel) 2022; 11:antibiotics11030305. [PMID: 35326769 PMCID: PMC8944778 DOI: 10.3390/antibiotics11030305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
Data on the prevalence of MCR-producing Enterobacterales of animal origin are scarce from the Arabian Peninsula. We investigated the presence and variety of such strains from fecal specimens of poultry collected in four farms in the United Arab Emirates. Colonies from ten composite samples per farm grown on colistin-supplemented plates were PCR-screened for alleles of the mcr gene. Thirty-nine isolates selected based on species, colony morphology, and plasmid profile were subjected to whole genome sequencing. The panel of their resistance and virulence genes, MLST and cgMLST were established. Transferability and incompatibility types of the MCR-plasmids were determined. mcr-1.1 positive strains were identified in 36 of the 40 samples. Thirty-four multi-drug resistant Escherichia coli of 16 different sequence types, two Escherichia albertii, two Klebsiella pneumoniae and one Salmonella minnesota were identified. Beyond various aminoglycoside, tetracycline, and co-trimoxazole resistance genes, seven of them also carried ESBL genes and one blaCMY-2. Six IncHI2, 26 IncI2 and 4 IncX4 MCR-plasmids were mobilized, in case of the IncHI2 plasmids co-transferring ampicillin, chloramphenicol and tetracycline resistance. The diversity of mcr-1 positive strains suggest a complex local epidemiology calling for a coordinated surveillance including animals, retail meat and clinical cases.
Collapse
Affiliation(s)
- Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Walid Q. Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Safat, Kuwait City 13110, Kuwait;
| | - Sara A. Mahmoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Greeshma Bharathan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
| | - Tahir A. Rizvi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Tibor Pál
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Correspondence:
| |
Collapse
|
19
|
Saraiva MMS, Silva NMV, Ferreira VA, Moreira Filho ALB, Givisiez PEN, Freitas Neto OC, Berchieri Júnior A, Gebreyes WA, Oliveira CJB. Residual concentrations of antimicrobial growth promoters in poultry litter favour plasmid conjugation among Escherichia coli. Lett Appl Microbiol 2022; 74:831-838. [PMID: 35138674 DOI: 10.1111/lam.13671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Considering that plasmid conjugation is a major driver for the dissemination of antimicrobial resistance in bacteria, this study aimed to investigate the effects of residual concentrations of antimicrobial growth promoters (AGPs) in poultry litter on the frequencies of IncFII-FIB plasmid conjugation among Escherichia coli organisms. A 2x5 factorial trial was performed in vitro, using two types of litter materials (sugarcane bagasse and wood shavings) and five treatments of litter: non-treated (CON), herbal alkaloid sanguinarine (SANG), and AGPs monensin (MON), lincomycin (LCM), and virginiamycin (VIR). E. coli H2332 and E. coli J62 were used as donor and recipient strains, respectively.The presence of residues of monensin, lincomycin and virginiamycin increased the frequency of plasmid conjugation among E. coli in both types of litter materials. On the contrary, sanguinarine significantly reduced the frequency of conjugation among E. coli in sugarcane bagasse litter. The conjugation frequencies were significantly higher in wood shavings compared to sugarcane bagasse only in the presence of AGPs. Considering that the presence of AGPs in the litter can increase the conjugation of IncFII-FIB plasmids carrying antimicrobial resistance genes, the real impact of this phenomenon on the dissemination of antimicrobial resistant bacteria in the poultry production chain must be investigated.
Collapse
Affiliation(s)
- M M S Saraiva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - N M V Silva
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Instituto Federal do Sertão Pernambucano - Campus Petrolina
| | - V A Ferreira
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - A L B Moreira Filho
- Department of Animal Science, Center for Human, Social and Agricultural Sciences, Federal University of Paraiba (CCHSA/UFPB), Bananeiras, PB, Brazil
| | - P E N Givisiez
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - O C Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - A Berchieri Júnior
- Department of Pathology, Theriogenology and One Health, Laboratory of Ornithopathology, São Paulo State University (FCAV/Unesp), Jaboticabal, SP, Brazil
| | - W A Gebreyes
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - C J B Oliveira
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil.,Global One health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| |
Collapse
|
20
|
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58. Nat Commun 2022; 13:683. [PMID: 35115531 PMCID: PMC8813906 DOI: 10.1038/s41467-022-28342-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
Collapse
|
21
|
Foster-Nyarko E, Pallen MJ. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6522174. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Corresponding author: Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail:
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
| |
Collapse
|
22
|
Cordeiro-Moura JR, Kraychete GB, Longo LGDA, Corrêa LL, da Silva NMV, Campana EH, Oliveira CJB, Picão RC. Description and comparative genomic analysis of a mcr-1-carrying Escherichia coli ST683/CC155 recovered from touristic coastal water in Northeastern Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105196. [PMID: 34954103 DOI: 10.1016/j.meegid.2021.105196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/01/2021] [Accepted: 12/19/2021] [Indexed: 02/07/2023]
Abstract
Polymyxin resistance is an emerging health issue aggravated by mcr dissemination among Enterobacterales recovered from various sources. Commensal Escherichia coli plays a key role in the spread of antimicrobial resistance in community settings and is likely to spread silently. It may transfer resistance genes to pathogenic bacteria in the gastrointestinal tract and the environment, and may cause difficult-to-treat infections, especially in immunocompromised patients. Unraveling actors disseminating resistance to last-resort antimicrobials might support the future development of control measures. Here we report the occurrence of a commensal ST683/CC155 colistin-resistant mcr-1.1-harboring E. coli (JP24) obtained from touristic coastal water. JP24's genome was sequenced and comparatively analyzed with other genomes from ST683/CC155 isolated worldwide and with mcr-carrying isolates recovered from various sources in Brazil. Besides mcr-1, JP24 carried blaCTX-M-8, tet(A), tet(34), dfrA12, sul2, sul3, aph(3')-Ia, aph(3')-IIa, aadA1, aadA2, cmlA1, Inu(G), mef(B) and mdf(a). mcr-1 and blaCTX-M-8 were transferable by IncX4 and IncI1/Iγ plasmids, respectively. Tree-based phylogeny of the ST683/CC155 isolates core genome revealed two larger clades. E. coli JP24 was grouped into a subclade together with an isolate from Thailand (ERR4221036), both carrying mcr-1. The core genome-based tree of the isolates carrying mcr-1 from Brazil revealed proximity with E. coli ECEST9 recovered from a mangrove also located in Northeastern Brazil. Accessory genome-based tree clustered most environmental isolates apart from the clinical ones and remained JP24 closer to ECEST9. High sequence conservation was observed between mcr-1-harboring plasmids detected in different species and reservoirs in Brazil and other countries. In addition to recreational coastal waters being potential sources for community exposure to antimicrobial-resistant bacteria, our findings reinforce a more prominent role of horizontal gene transfer, other than clonal expansion, in mcr dissemination in the community.
Collapse
Affiliation(s)
- Jhonatha Rodrigo Cordeiro-Moura
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luís Guilherme de Araújo Longo
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Laís Lisboa Corrêa
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Núbia Michelle Vieira da Silva
- Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Eloiza Helena Campana
- Laboratório de Microbiologia Clínica (LMC), Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Celso José Bruno Oliveira
- Laboratório de Avaliação de Produtos de Origem Animal (LAPOA), Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Renata Cristina Picão
- Laboratório de Investigação em Microbiologia Médica (LIMM), Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil..
| |
Collapse
|
23
|
Feng J, Xiang Q, Ma J, Zhang P, Li K, Wu K, Su M, Li R, Hurley D, Bai L, Wang J, Yang Z. Characterization of Carbapenem-Resistant Enterobacteriaceae Cultured From Retail Meat Products, Patients, and Porcine Excrement in China. Front Microbiol 2021; 12:743468. [PMID: 35002997 PMCID: PMC8734966 DOI: 10.3389/fmicb.2021.743468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence and dissemination of carbapenem-resistant Enterobacteriaceae (CRE) is a growing concern to animal and public health. However, little is known about the spread of CRE in food and livestock and its potential transmission to humans. To identify CRE strains from different origins and sources, 53 isolates were cultured from 760 samples including retail meat products, patients, and porcine excrement. Antimicrobial susceptibility testing was carried out, followed by phylogenetic typing, whole-genome sequencing, broth mating assays, and plasmids analyses. Forty-three Escherichia coli, nine Klebsiella pneumoniae, and one Enterobacter cloacae isolates were identified, each exhibiting multidrug-resistant phenotypes. Genetically, the main sequence types (STs) of E. coli were ST156 (n = 7), ST354 (n = 7), and ST48 (n = 7), and the dominant ST of K. pneumoniae is ST11 (n = 5). blaNDM–5 (n = 40) of E. coli and blaKPC–2 (n = 5) were the key genes that conferred carbapenem resistance phenotypes in these CRE strains. Additionally, the mcr-1 gene was identified in 17 blaNDM-producing isolates. The blaNDM–5 gene from eight strains could be transferred to the recipients via conjugation assays. Two mcr-1 genes in the E. coli isolates could be co-transferred along with the blaNDM–5 genes. IncF and IncX3 plasmids have been found to be predominantly associated with blaNDM gene in these strains. Strains isolated in our study from different sources and regions tend to be concordant and overlap. CRE strains from retail meat products are a reservoir for transition of CRE strains between animals and humans. These data also provide evidence of the dissemination of CRE strains and carbapenem-resistant genes between animal and human sources.
Collapse
Affiliation(s)
- Jie Feng
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qian Xiang
- Department of Healthcare Associated Infection Control, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiangang Ma
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Pei Zhang
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Kun Li
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Ke Wu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Mengru Su
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Ruichao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Daniel Hurley
- UCD-Centre for Food Safety, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Li Bai
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
- *Correspondence: Li Bai,
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Juan Wang,
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Zengqi Yang,
| |
Collapse
|
24
|
Ponomarenko GV, Kovalenko VL, Balatskiy YO, Ponomarenko OV, Paliy AP, Shulyak SV. Bactericidal efficiency of preparation based on essential oils used in aerosol disinfection in the presence of poultry. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
A disinfectant was created for aerosol disinfection of premises in the presence of poultry, which will help reduce microbial contamination of premises, increase survival, weight of poultry and economic efficiency of meat production in general. The preparation based on essential oils can be used for disinfection in the presence of poultry and at the same time exhibits a therapeutic and prophylactic effect on respiratory infections. This disinfectant has a colloidal solution of silver (Ag), benzalkonium chloride and essential oils of thyme, fir and eucalyptus. The preparation based on essential oils contains (per 100 g): benzalkonium chloride – 16.0 g; thyme oil – up to 2.0 g; eucalyptus oil – up to 2.0 g; fir oil – up to 2.0 g; colloidal solution of silver (Ag) – 20–30 mg; distilled water - up to 100 cm3. Aerosol sanitation of indoor air was carried out with 0.3% solution of preparation in the period before housing poultry and once a day from the 20th to the 35th day of growing broilers with aerosol cold mist generator Dyna-Fog Tornado (model 2897, construction type – ULV-electric spray gnerator, manufacturer – Curtis Dyna-Fog, Ltd., USA) at a dose of 50.0 cm3 per 1 m3 at an exposure of 60 minutes. The size of the aerosol particles is 20 μm. On days 1, 4, 8, 11, 15, 28, 37, and 42, the chickens were weighed, and the blood was taken for examination. Blood was examined to study the number of red blood cells, hemoglobin content, the bactericidal activity of blood serum, phagocyte activity of leukocytes, lysozyme activity of blood serum. According to the results of the research, the technological modes of air disinfection of poultry premises in the presence of broiler chickens were substantiated during the use of preparation, which contains nanoparticles (NP) of silver, benzalkonium chloride and essential oils. The optimal mode of aerosol treatment of poultry houses using a 0.3% solution preparation based on essential oils is 50 mL/m3 of a room with a 60-minute exposure. The use of air disinfection in the presence of chickens during broiler rearing and one treatment per day from 20 to 35 days of the chickens’ growth reduced the microbial pollution of indoor air. Thus, the concentration of microbial cells in the room where the chickens were kept was 230.2 ± 15.6 thousand microbial cell/m3. Sixty minutes after disinfection, the concentration decreased to 1.4 ± 0.4 thousand microbial cell/m3. In addition, the bodyweight of chickens at 6 weeks increased by 449.4 ± 16.3 g (15.9%) compared with the controls. The method and mode of air treatment did not adversely affect the development of the internal organs of the poultry and their physiological state, which is confirmed by studies of the morphological parameters of the chicken blood. The data obtained indicate a positive effect of the developed methods and modes of aerosol air treatment with the preparation based on essential oils on the growth and development of broilers.
Collapse
|
25
|
Giufrè M, Mazzolini E, Cerquetti M, Brusaferro S. Extended-spectrum β-lactamase-producing Escherichia coli from extraintestinal infections in humans and from food-producing animals in Italy: a 'One Health' study. Int J Antimicrob Agents 2021; 58:106433. [PMID: 34525400 DOI: 10.1016/j.ijantimicag.2021.106433] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/30/2021] [Accepted: 08/28/2021] [Indexed: 11/26/2022]
Abstract
Recently, Escherichia coli producing extended-spectrum β-lactamases (ESBLs) have become a serious public-health problem, and food-producing animals (FPAs) have been suggested as a potential reservoir/source. This study aimed to compare ESBL-producing E. coli isolates from different sources. ESBL-producing E. coli isolates were collected from humans (n = 480) and FPAs (n = 445) in Italy (2016-2017). Isolates were screened for the presence of ESBL and carbapenemase genes and were classified according to phylogenetic group and MLST genotyping. The genes mcr-1 to -5 were searched for in colistin-resistant isolates. CTX-M was the most frequent ESBL type both in human and animal isolates. CTX-M-15 prevailed in humans (75.0%) and cattle (51.1%) but not in poultry (36.6%). CTX-M-1 was common (58.3%) in pigs. SHV-type and CMY-2-like were found in FPAs, especially in poultry (17.0% and 29.9%, respectively). Additionally, 29 isolates were mcr-1 carriers (3 from humans and 26 from FPAs). No carbapenemase genes were detected. Human isolates mostly belonged to phylogroup B2 (76.5%). Animal isolates were distributed among groups A (35.7%), B1 (26.1%) and C (12.4%). Few animal isolates (almost all from poultry) were classified into group B2 (4.3%). Most human isolates (83.4%) belonged to the pandemic ST131 clone and frequently carried CTX-M-15 (75.9%). ST131 was rarely detected in FPAs (three isolates from poultry). Nineteen STs were shared in both sources, with ST10, ST410 and ST69 being more frequently detected. Potential exchange of ESBL genes from animals to humans is feasible, underlying the need for strict monitoring based on a 'One Health' approach.
Collapse
Affiliation(s)
- Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
| | - Elena Mazzolini
- Department of Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy
| | - Silvio Brusaferro
- Istituto Superiore di Sanità, Rome, Italy; Department of Medicine, University of Udine and Clinical Risk Management and Performance Assessment Unit, Udine Healthcare and University Integrated Trust, Udine, Italy
| | | |
Collapse
|
26
|
Savin M, Bierbaum G, Kreyenschmidt J, Schmithausen RM, Sib E, Schmoger S, Käsbohrer A, Hammerl JA. Clinically Relevant Escherichiacoli Isolates from Process Waters and Wastewater of Poultry and Pig Slaughterhouses in Germany. Microorganisms 2021; 9:microorganisms9040698. [PMID: 33800539 PMCID: PMC8066038 DOI: 10.3390/microorganisms9040698] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli is frequently associated with multiple antimicrobial resistances and a major cause of bacterial extraintestinal infections in livestock and humans. However, data on the epidemiology of (i) multidrug-resistant (MDR) and (ii) extraintestinal pathogenic E. coli (ExPEC) in poultry and pig slaughterhouses in Germany is currently lacking. Selected E. coli isolates (n = 71) with phenotypic resistance to cephalosporins from two poultry and two pig slaughterhouses expressing high MDR rates (combined resistance to piperacillin, cefotaxime and/or ceftazidime, and ciprofloxacin) of 51.4% and 58.3%, respectively, were analyzed by whole-genome sequencing. They constituted a reservoir for 53 different antimicrobial resistance determinants and were assigned various sequence types, including high-risk clones involved in human infections worldwide. An ExPEC pathotype was detected in 17.1% and 5.6% of the isolates from poultry and pig slaughterhouses, respectively. Worryingly, they were recovered from scalding water and eviscerators, indicating an increased risk for cross-contaminations. Uropathogenic E. coli (UPEC) were detected in the effluent of an in-house wastewater treatment plant (WWTP) of a poultry slaughterhouse, facilitating their further dissemination into surface waters. Our study provides important information on the molecular characteristics of (i) MDR, as well as (ii) ExPEC and UPEC regarding their clonal structure, antimicrobial resistance and virulence factors. Based on their clinical importance and pathogenic potential, the risk of slaughterhouse employees’ exposure cannot be ruled out. Through cross-contamination, these MDR E. coli pathotypes may be introduced into the food chain. Moreover, inadequate wastewater treatment may contribute to the dissemination of UPEC into surface waters, as shown for other WWTPs.
Collapse
Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, 53113 Bonn, Germany;
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
- Correspondence: (M.S.); (J.A.H.)
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53113 Bonn, Germany;
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, 53113 Bonn, Germany;
- Department of Fresh Produce Logistics, Hochschule Geisenheim University, 65366 Geisenheim, Germany
| | - Ricarda Maria Schmithausen
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
| | - Esther Sib
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, 53113 Bonn, Germany; (R.M.S.); (E.S.)
| | - Silvia Schmoger
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
| | - Annemarie Käsbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
- Department for Farm Animals and Veterinary Public Health and Epidemiology, Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (S.S.); (A.K.)
- Correspondence: (M.S.); (J.A.H.)
| |
Collapse
|
27
|
Jackson N, Borges CA, Tarlton NJ, Resendez A, Milton AK, de Boer TR, Butcher CR, Murthy N, Riley LW. A rapid, antibiotic susceptibility test for multidrug-resistant, Gram-negative bacterial uropathogens using the biochemical assay, DETECT. J Microbiol Methods 2021; 182:106160. [PMID: 33548393 DOI: 10.1016/j.mimet.2021.106160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022]
Abstract
The increasing prevalence of extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases among Enterobacterales threatens our ability to treat urinary tract infections (UTIs). These organisms are resistant to most β-lactam antibiotics and are frequently multidrug-resistant (MDR). Consequently, they are often resistant to antibiotics used to empirically treat UTIs. The lack of rapid diagnostic and antibiotic susceptibility tests (AST) makes clinical management of UTIs caused by such organisms difficult, as standard culture and susceptibility assays require several days. We have adapted a biochemical detection assay, termed dual-enzyme trigger-enabled cascade technology (DETECT) for rapid detection of resistance (time-to-result of 3 h) to other antibiotics commonly used in treatment of UTIs. DETECT is activated by the presence of CTX-M and pAmpC β-lactamases. In this proof-of-concept study, the adapted DETECT assay (AST-DETECT) has been performed on pure-cultures of Klebsiella pneumoniae and Escherichia coli (48 isolates) expressing ESBL or pAmpC β-lactamases to perform AST for ciprofloxacin (sensitivity 96.9%, specificity 100%, accuracy 97.9%) nitrofurantoin (sensitivity 95.7%, specificity 91.7%, accuracy 94%) and trimethoprim/sulfamethoxazole (sensitivity 83.3%, specificity 100%, accuracy 89.4%). These results suggest that AST-DETECT may be adapted as a potential diagnostic platform to rapidly detect multidrug-resistant E. coli and K. pneumoniae that cause UTI.
Collapse
Affiliation(s)
- Nicole Jackson
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| | - Clarissa A Borges
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Nicole J Tarlton
- Department of Microbiology, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Angel Resendez
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | | | - Tara R de Boer
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Cheyenne R Butcher
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Lee W Riley
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
28
|
Salinas L, Loayza F, Cárdenas P, Saraiva C, Johnson TJ, Amato H, Graham JP, Trueba G. Environmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:27007. [PMID: 33617318 PMCID: PMC7899495 DOI: 10.1289/ehp7729] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human-animal interfaces exist. OBJECTIVES This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS). METHODS We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs. RESULTS A total of 264 3GCR-EC isolates from children (n=21), dogs (n=20), and chickens (n=18) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes (n=14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 and blaCTX-M-65, which were found in isolates from children, dogs, and chickens. DISCUSSION This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum β-lactamase) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child-animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729.
Collapse
Affiliation(s)
- Liseth Salinas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Fernanda Loayza
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Paúl Cárdenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Carlos Saraiva
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Mid Central Research & Outreach Center, Willmar, Minnesota, USA
| | - Heather Amato
- Environmental Health Sciences Division, University of California, Berkeley, California, USA
| | - Jay P. Graham
- Environmental Health Sciences Division, University of California, Berkeley, California, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| |
Collapse
|
29
|
Singleton DA, Ball C, Rennie C, Coxon C, Ganapathy K, Jones PH, Welchman D, Tulloch JSP. Backyard poultry cases in UK small animal practices: Demographics, health conditions and pharmaceutical prescriptions. Vet Rec 2021; 188:e71. [PMID: 33835557 PMCID: PMC8638672 DOI: 10.1002/vetr.71] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/12/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Backyard poultry ownership is of keen interest in the United Kingdom. However, despite this, little is known about veterinary care engagement and outcomes of visits in this group of species. METHODS This study described and characterised veterinary practice-visiting backyard poultry, utilising electronic health record data supplied by veterinary practices voluntarily participating in the Small Animal Veterinary Surveillance Network between 1st April 2014 and 31st March 2019. RESULTS In total, 4424 recorded poultry consultations originating from 197 veterinary practices (352 sites) were summarised. Chicken consultation (n = 3740) peak incidence was in early summer (April-June), relative to all recorded species. More chickens resided in rural (incident rate ratio = 2.5, confidence interval [CI] 2.3-2.6, p <0.001) or less deprived areas. Non-specific clinical signs were commonly recorded (17.6% of chicken consultations, CI 15.9-19.2), as were those indicative of advanced disease. This latter finding was reflected in prescribed management strategies, with euthanasia comprising 29.8% (CI 27.0-32.6) of consultations. Antimicrobials were commonly prescribed (33.0% of consultations, CI 29.8-36.2), 43.8% of which included antimicrobials considered 'highest priority critically important' by the World Health Organisation. CONCLUSION Our findings indicate a need to tailor antimicrobial prescription guidance to the backyard poultry setting. In addition, late presentation of disease, vague clinical descriptions in clinical narratives and high euthanasia rates show that disease identification, management and knowledge of poultry health and welfare among owners and veterinary surgeons can be improved.
Collapse
Affiliation(s)
- David A Singleton
- Infection, Veterinary and Ecological Sciences, University of Liverpool, Cheshire, UK
| | - Christopher Ball
- Infection, Veterinary and Ecological Sciences, University of Liverpool, Cheshire, UK
| | - Cameron Rennie
- Infection, Veterinary and Ecological Sciences, University of Liverpool, Cheshire, UK
| | - Charlotte Coxon
- International Disease Monitoring and Risk Assessment (EU Exit), Animal and Plant Health Agency, Addlestone, UK
| | - Kannan Ganapathy
- Infection, Veterinary and Ecological Sciences, University of Liverpool, Cheshire, UK
| | - Phil H Jones
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Addlestone, UK
| | - David Welchman
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Winchester, UK
| | - John S P Tulloch
- Infection, Veterinary and Ecological Sciences, University of Liverpool, Cheshire, UK
| |
Collapse
|
30
|
Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
Collapse
Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
| |
Collapse
|
31
|
Liao N, Borges CA, Rubin J, Hu Y, Ramirez HA, Chen J, Zhou B, Zhang Y, Zhang R, Jiang J, Riley LW. Prevalence of β-Lactam Drug-Resistance Genes in Escherichia coli Contaminating Ready-to-Eat Lettuce. Foodborne Pathog Dis 2020; 17:739-742. [PMID: 33112663 DOI: 10.1089/fpd.2020.2792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thirty-four Escherichia coli isolates from 91 ready-to-eat lettuce packages, obtained from local supermarkets in Northern California, were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found 15 distinct sequence types (STs). Six of these genotypes (ST1198, ST2625, ST2432, ST2819, ST4600, and ST5143) have been reported as pathogens found in human samples. Twenty-six (76%) E. coli isolates were resistant to ampicillin, 17 (50%) to ampicillin/sulbactam, 8 (23%) to cefoxitin, and 7 (20%) to cefuroxime. blaCTX-M was the most prevalent β-lactamase gene, identified in eight (23%) isolates. We identified a class A broad-spectrum β-lactamase SED-1 gene, blaSED, reported by others in Citrobacter sedlakii isolated from bile of a patient. This study found that fresh lettuce carries β-lactam drug-resistant E. coli, which might serve as a reservoir for drug-resistance genes that could potentially be transmitted to pathogens that cause human infections.
Collapse
Affiliation(s)
- Ningbo Liao
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Yuan Hu
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Hector A Ramirez
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Jiang Chen
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Biao Zhou
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ronghua Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianmin Jiang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| |
Collapse
|
32
|
Bhardwaj DK, Taneja NK, Dp S, Chakotiya A, Patel P, Taneja P, Sachdev D, Gupta S, Sanal MG. Phenotypic and genotypic characterization of biofilm forming, antimicrobial resistant, pathogenic Escherichia coli isolated from Indian dairy and meat products. Int J Food Microbiol 2020; 336:108899. [PMID: 33160121 DOI: 10.1016/j.ijfoodmicro.2020.108899] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
Escherichia coli are commensal gastrointestinal microflora of humans, but few strains may cause food-borne diseases. Present study aimed to identify antimicrobial resistant (AMR), biofilm-forming E. coli from Indian dairy and meat products. A total of 32 E. coli isolates were identified and evaluated for biofilm-formation. EMC17, an E. coli isolate was established as a powerful biofilm-former that attained maximum biofilm-formation within 96 h on glass and stainless-steel surfaces. Presence and expression of virulence-associated genes (adhesins, invasins and polysaccharides) and ability to adhere and invade human liver carcinoma HepG2 cell lines implicates EMC17 to be pathotype belonging to Extra-intestinal Pathogenic E. coli (ExPEC). Antibiotic profiling of EMC17 identified it as multi-drug resistant (MDR) strain, possessing extended spectrum β-lactamases (ESBL's) and biofilm phenotype. Early production of quorum sensing molecules (AHLs) alongside EPS production facilitated early onset of biofilm formation by EMC17. Furthermore, the biofilm-forming genes of EMC17 were significantly upregulated 3-27 folds in the biofilm-state. This study showed prevalence of MDR, biofilm-forming, pathogenic E. coli in Indian dairy and meat products that potentially serve as reservoirs for transmission of antimicrobial-resistant (AMR) genes of bacteria from food to humans and pose serious food safety threat.
Collapse
Affiliation(s)
| | - Neetu Kumra Taneja
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India.
| | - Shivaprasad Dp
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Ankita Chakotiya
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Praveen Patel
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Pankaj Taneja
- Department of Life Sciences, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Divya Sachdev
- Department of Basic and Applied Sciences, NIFTEM, Sonipat 131028, Haryana, India
| | - Sarita Gupta
- Institute of Liver and Biliary Sciences, Vasant Kunj, New Delhi, India
| | | |
Collapse
|
33
|
Mourand G, Le Devendec L, Delannoy S, Fach P, Keita A, Amelot M, Jaunet H, Dia MEH, Kempf I. Variations of the Escherichia coli population in the digestive tract of broilers. Avian Pathol 2020; 49:678-688. [PMID: 32835506 DOI: 10.1080/03079457.2020.1814201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We explored the between-group and temporal variations in the intestinal Escherichia coli populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) E. coli (2.72 log10 CFU of a bla CMY-2- and 2.55 log10 CFU of a bla CTX-M-carrying E. coli). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant E. coli populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (iroN, iutA, iss, ompT, hlyF, vat, frzorf4 , and fyuA) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to bla CTX-M-positive strains, bla CMY-positive strains persisted up to Day 42, but represented only a minor fraction of the total E. coli population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between E. coli isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. RESEARCH HIGHLIGHTS Temporal variations in the intestinal E. coli populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.
Collapse
Affiliation(s)
- Gwenaëlle Mourand
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Laëtitia Le Devendec
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Sabine Delannoy
- ANSES - French Agency for Food, Environmental and Occupational Health & Safety Food Research Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - Patrick Fach
- ANSES - French Agency for Food, Environmental and Occupational Health & Safety Food Research Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - Alassane Keita
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Michel Amelot
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | | | | | - Isabelle Kempf
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| |
Collapse
|
34
|
de Carvalho MPN, Fernandes MR, Sellera FP, Lopes R, Monte DF, Hippólito AG, Milanelo L, Raso TF, Lincopan N. International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil. Transbound Emerg Dis 2020; 67:1804-1815. [PMID: 32239649 PMCID: PMC7540485 DOI: 10.1111/tbed.13558] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 12/22/2022]
Abstract
CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli clones have been increasingly reported worldwide. In this regard, although discussions of transmission routes of these bacteria are in evidence, molecular data are lacking to elucidate the epidemiological impacts of ESBL producers in wild animals. In this study, we have screened 90 wild animals living in a surrounding area of São Paulo, the largest metropolitan city in South America, to monitor the presence of multidrug-resistant (MDR) Gram-negative bacteria. Using a genomic approach, we have analysed eight ceftriaxone-resistant E. coli. Resistome analyses revealed that all E. coli strains carried blaCTX-M -type genes, prevalent in human infections, besides other clinically relevant resistance genes to aminoglycosides, β-lactams, phenicols, tetracyclines, sulphonamides, trimethoprim, fosfomycin and quinolones. Additionally, E. coli strains belonged to international sequence types (STs) ST38, ST58, ST212, ST744, ST1158 and ST1251, and carried several virulence-associated genes. Our findings suggest spread and adaptation of international clones of CTX-M-producing E. coli beyond urban settings, including wildlife from shared environments.
Collapse
Affiliation(s)
| | - Miriam R. Fernandes
- Department of Clinical and Toxicological AnalysisSchool of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Fábio P. Sellera
- Department of Internal MedicineSchool of Veterinary Medicine and Animal ScienceUniversity of São PauloSão PauloBrazil
| | - Ralf Lopes
- Department of MicrobiologyInstituto de Ciências BiomédicasUniversidade de São PauloSão PauloBrazil
| | - Daniel F. Monte
- Department of Food and Experimental NutritionFaculty of Pharmaceutical SciencesFood Research CenterUniversity of São PauloSão PauloBrazil
| | - Alícia G. Hippólito
- Department of Veterinary Surgery and AnesthesiologySchool of Veterinary Medicine and Animal ScienceUniversidade Estadual Paulista (UNESP)BotucatuBrazil
| | - Liliane Milanelo
- Reception Center for WildlifeEcological Park TietêSão PauloBrazil
| | - Tânia F. Raso
- Department of PathologySchool of Veterinary Medicine and Animal ScienceUniversity of São PauloSão PauloBrazil
| | - Nilton Lincopan
- Department of Clinical and Toxicological AnalysisSchool of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
- Department of MicrobiologyInstituto de Ciências BiomédicasUniversidade de São PauloSão PauloBrazil
| |
Collapse
|
35
|
Tarlton NJ, Petrovic DF, Frazee BW, Borges CA, Pham EM, Milton AK, Jackson N, deBoer TR, Murthy N, Riley LW. A Dual Enzyme-Based Biochemical Test Rapidly Detects Third-Generation Cephalosporin-Resistant CTX-M-Producing Uropathogens in Clinical Urine Samples. Microb Drug Resist 2020; 27:450-461. [PMID: 32830997 DOI: 10.1089/mdr.2020.0128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria (GNB) are increasingly identified as the cause of both community and healthcare-associated urinary tract infections (UTIs), with CTX-Ms being the most common ESBLs identified. CTX-M-producing GNB are resistant to most β-lactam antibiotics and are frequently multidrug-resistant, which limits treatment options. Rapid diagnostic tests that can detect ESBL-producing GNB, particularly CTX-M producers, in the urine of patients with UTIs are needed. Results from such a test could direct the selection of appropriate antimicrobial therapy at the point-of-care (POC). In this study, we show that a chromogenic, dual enzyme-mediated amplification system (termed DETECT [dual-enzyme trigger-enabled cascade technology]) can identify CTX-M-producing GNB from unprocessed urine samples in 30 minutes. We first tested DETECT against a diverse set of recombinant β-lactamases and β-lactamase-producing clinical isolates to elucidate its selectivity. We then tested DETECT with 472 prospectively collected clinical urine samples submitted for urine culture to a hospital clinical microbiology laboratory. Of these, 118 (25%) were consistent with UTI, 13 (11%) of which contained ESBL-producing GNB. We compared DETECT results in urine against a standard phenotypic method to detect ESBLs, and polymerase chain reaction and sequencing for CTX-M genes. DETECT demonstrated 90.9% sensitivity and 97.6% specificity (AUC, 0.937; 95% confidence interval, 0.822-1.000), correctly identifying 10 of 11 urine samples containing a clinically significant concentration of CTX-M-producing GNB (including Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis). Our results demonstrate the clinical potential of DETECT to deliver diagnostic information at the POC, which could improve initial antibiotic selection.
Collapse
Affiliation(s)
- Nicole J Tarlton
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Danka-Florence Petrovic
- Department of Laboratory Medicine and Pathology, Highland Hospital, Alameda Health System, Oakland, California, USA
| | - Bradley W Frazee
- Department of Emergency Medicine, Highland Hospital, Alameda Health System, Oakland, California, USA
| | - Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Emily M Pham
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Aubrianne K Milton
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Nicole Jackson
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Tara R deBoer
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| |
Collapse
|
36
|
Zhou Y, Li Y, Zhang L, Wu Z, Huang Y, Yan H, Zhong J, Wang LJ, Abdullah HM, Wang HH. Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry. Front Microbiol 2020; 11:1319. [PMID: 32733394 PMCID: PMC7358366 DOI: 10.3389/fmicb.2020.01319] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023] Open
Abstract
Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with bla CMY-2 + Escherichia coli, 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and Lactobacillus rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially Escherichia/Shigella. However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with bla CMY-2 + E. coli, oral Amp also led to the increase of Proteobacteria, dominated by Klebsiella and Escherichia/Shigella, and a reduction of Firmicutes. Specifically within Firmicutes, Enterococcus, Clostridium, etc. were enriched but Lactobacillus was diminished. The fecal resistome including Ampr genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted bla CMY-2 + gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Ampr- or multidrug resistance-encoding genes other than bla CMY-2 +. These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.
Collapse
Affiliation(s)
- Yang Zhou
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Li
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Lu Zhang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Zuowei Wu
- College of Veterinary Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Ying Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Yan
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Jiang Zhong
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ju Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Hafiz M Abdullah
- Department of Animal Science Poultry Facility, OARDC, Wooster, OH, United States
| | - Hua H Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
37
|
Fuentes-Castillo D, Navas-Suárez PE, Gondim MF, Esposito F, Sacristán C, Fontana H, Fuga B, Piovani C, Kooij R, Lincopan N, Catão-Dias JL. Genomic characterization of multidrug-resistant ESBL-producing Escherichia coli ST58 causing fatal colibacillosis in critically endangered Brazilian merganser (Mergus octosetaceus). Transbound Emerg Dis 2020; 68:258-266. [PMID: 32544292 PMCID: PMC8246901 DOI: 10.1111/tbed.13686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Even though antimicrobial‐resistant bacteria have begun to be detected in wildlife, raising important issues related to their transmission and persistence of clinically important pathogens in the environment, little is known about the role of these bacteria on wildlife health, especially on endangered species. The Brazilian merganser (Mergus octosetaceus) is one of the most threatened waterfowl in the world, classified as Critically Endangered by the International Union for Conservation of Nature. In 2019, a fatal case of sepsis was diagnosed in an 8‐day‐old Brazilian merganser inhabiting a zoological park. At necropsy, major gross lesions were pulmonary and hepatic congestion. Using microbiologic and genomic methods, we identified a multidrug‐resistant (MDR) extended‐spectrum β‐lactamase (ESBL) CTX‐M‐8‐producing Escherichia coli (designed as PMPU strain) belonging to the international clone ST58, in coelomic cavity, oesophagus, lungs, small intestine and cloaca samples. PMPU strain harboured a broad resistome against antibiotics (cephalosporins, tetracyclines, aminoglycosides, sulphonamides, trimethoprim and quinolones), domestic/hospital disinfectants and heavy metals (arsenic, mercury, lead, copper and silver). Additionally, the virulence of E. coli PMPU strain was confirmed using a wax moth (Galleria mellonella) infection model, and it was supported by the presence of virulence genes encoding toxins, adherence factors, invasins and iron acquisition systems. Broad resistome and virulome of PMPU contributed to therapeutic failure and death of the animal. In brief, we report for the first time a fatal colibacillosis by MDR ESBL‐producing E. coli in critically endangered Brazilian merganser, highlighting that besides colonization, critical priority pathogens are threatening wildlife. E. coli ST58 clone has been previously reported in humans, food‐producing animals, wildlife and environment, supporting broad adaptation and persistence at human–animal–environment interface.
Collapse
Affiliation(s)
- Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Pedro Enrique Navas-Suárez
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Carlos Sacristán
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, University of São Paulo, São Paulo, Brazil
| | | | | | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, University of São Paulo, São Paulo, Brazil
| | - José Luiz Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
38
|
Wyrsch ER, Chowdhury PR, Wallis L, Cummins ML, Zingali T, Brandis KJ, Djordjevic SP. Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis ( Threskiornis spinicollis) nesting on inland wetlands. Microb Genom 2020; 6:e000385. [PMID: 32519939 PMCID: PMC7371105 DOI: 10.1099/mgen.0.000385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/18/2020] [Indexed: 12/23/2022] Open
Abstract
Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of Escherichia coli that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of E. coli recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS26, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found E. coli ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ST6241, and a novel phylogroup D strain, ST10208. Notably, the ST58 strain hosted significant virulence gene carriage. The sequences of two plasmids hosting putative virulence-associated factors with incompatibility groups I1 and Y, an extrachromosomal integrative/conjugative element, and a variant of a large Escherichia phage of the family Myoviridae, were additionally characterized. We identified multiple epidemiologically relevant gene signatures that link the ibis isolates to sequences from international sources, plus novel variants of IS26 across different sequence types and in different contexts.
Collapse
Affiliation(s)
- Ethan R. Wyrsch
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Louise Wallis
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Max L. Cummins
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Tiziana Zingali
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Kate J. Brandis
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, 2052 NSW, Australia
| | - Steven P. Djordjevic
- ithree institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|