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Aziz M, Davis GS, Park DE, Idris AH, Sariya S, Wang Y, Zerbonne S, Nordstrom L, Weaver B, Statham S, Johnson TJ, Campos J, Castro-Nallar E, Crandall KA, Wu Z, Liu CM, DeBiasi RL, Price LB. Pediatric urinary tract infections caused by poultry-associated Escherichia coli. Microbiol Spectr 2024; 12:e0341523. [PMID: 38864635 PMCID: PMC11218530 DOI: 10.1128/spectrum.03415-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/05/2024] [Indexed: 06/13/2024] Open
Abstract
Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children's National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E. coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.
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Affiliation(s)
- Maliha Aziz
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Gregg S Davis
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Daniel E Park
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Azza H Idris
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sanjeev Sariya
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Yashan Wang
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Sarah Zerbonne
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lora Nordstrom
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Brett Weaver
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Sally Statham
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Joseph Campos
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Keith A Crandall
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Roberta L DeBiasi
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
- Department of Pediatrics and Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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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.
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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
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Alfifi A, Christensen JP, Hounmanou YMG, Sandberg M, Dalsgaard A. Characterization of Escherichia coli and other bacteria isolated from condemned broilers at a Danish abattoir. Front Microbiol 2022; 13:1020586. [PMID: 36439808 PMCID: PMC9686377 DOI: 10.3389/fmicb.2022.1020586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/19/2022] [Indexed: 10/17/2023] Open
Abstract
Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and bla TEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need for total condemnation of carcasses with these pathological findings. A similar evaluation should be done for carcasses affected with chronic hepatitis, and minor scratches lesions.
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Affiliation(s)
- Ahmed Alfifi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Jens P. Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Marianne Sandberg
- National Food Institute, Danish Technical University, Lyngby, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
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Sadat A, Ramadan H, Elkady MA, Hammad AM, Soliman MM, Aboelenin SM, Al-Harthi HF, Abugomaa A, Elbadawy M, Awad A. Phylotypic Profiling, Distribution of Pathogenicity Island Markers, and Antimicrobial Susceptibility of Escherichia coli Isolated from Retail Chicken Meat and Humans. Antibiotics (Basel) 2022; 11:antibiotics11091197. [PMID: 36139976 PMCID: PMC9495032 DOI: 10.3390/antibiotics11091197] [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: 07/19/2022] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli (E.coli) found in retail chicken meat could be causing a wide range of infections in humans and constitute a potential risk. This study aimed to evaluate 60 E. coli isolates from retail chicken meat (n = 34) and human urinary tract infections (UTIs, n = 26) for phylogenetic diversity, presence of pathogenicity island (PAI) markers, antimicrobial susceptibility phenotypes, and antimicrobial resistance genes, and to evaluate their biofilm formation capacity. In that context, confirmed E.coli isolates were subjected to phylogrouping analysis using triplex PCR, antimicrobial susceptibility testing using the Kirby–Bauer disc diffusion method; PAI distribution was investigated by using two multiplex PCRs. Most of the chicken isolates (22/34, 64.7%) were identified as commensal E. coli (A and B1), while 12 isolates (35.3%) were classified as pathogenic virulent E. coli (B2 and D). Similarly, the commensal group dominated in human isolates. Overall, 23 PAIs were detected in the chicken isolates; among them, 39.1% (9/23) were assigned to group B1, 34.8% (8/23) to group A, 4.34% (1/23) to group B2, and 21.7% (5/23) to group D. However, 25 PAIs were identified from the human isolates. PAI IV536 was the most prevalent (55.9%, 69.2%) PAI detected in both sources. In total, 37 (61.7%) isolates of the chicken and human isolates were biofilm producers. Noticeably, 100% of E. coli isolates were resistant to penicillin and rifamycin. Markedly, all E. coli isolates displayed multiple antibiotic resistance (MAR) phenotypes, and the multiple antibiotic resistance index (MARI) among E. coli isolates ranged between 0.5 and 1. Several antibiotic resistance genes (ARGs) were identified by a PCR assay; the sul2 gene was the most prevalent (38/60, 63.3%) from both sources. Interestingly, a significant positive association (r = 0.31) between biofilm production and resistance to quinolones by the qnr gene was found by the correlation analysis. These findings were suggestive of the transmission of PAI markers and antibiotic resistance genes from poultry to humans or humans to humans through the food chain. To avoid the spread of virulent and multidrug-resistant E. coli, intensive surveillance of retail chicken meat markets is required.
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Affiliation(s)
- Asmaa Sadat
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Elkady
- Mansoura Veterinary Laboratory Branch, Microbiology Research Department, Animal Health Research Institute, Kafrelsheikh 33516, Egypt
| | - Amal Mahmoud Hammad
- Biochemistry Department, Faculty of Medicine Damietta, Al-Azhar University, Cairo 11651, Egypt
| | - Mohamed M. Soliman
- Clinical Laboratory Sciences Department, Turabah University College, Taif University, Taif 21995, Saudi Arabia
| | - Salama M. Aboelenin
- Biology Department, Turabah University College, Taif University, Al Hawiyah 21995, Saudi Arabia
| | - Helal F. Al-Harthi
- Biology Department, Turabah University College, Taif University, Al Hawiyah 21995, Saudi Arabia
| | - Amira Abugomaa
- Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed Elbadawy
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
| | - Amal Awad
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Correspondence: ; Tel.: +2-0102-127-6993
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Comparative Characteristics and Pathogenic Potential of Escherichia coli Isolates Originating from Poultry Farms, Retail Meat, and Human Urinary Tract Infection. Life (Basel) 2022; 12:life12060845. [PMID: 35743876 PMCID: PMC9225339 DOI: 10.3390/life12060845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022] Open
Abstract
The pathogenicity of many bacterial strains is determined by the acquisition of virulence genes and depends on many factors. The aim of this study was to analyse the phylogenetic background, virulence patterns, and drug susceptibility of 132 E. coli isolates tested in the context of the ExPEC (Extraintestinal Pathogenic E. coli) pathotype and the correlation of these features with bacterial isolation source: food (retail meat), poultry farms (AFEC—Avian Faecal E. coli), and patients with UTI (urinary tract infection) symptoms. The drug-susceptibility results of tested E. coli isolates obtained indicate that the resistance profile—ampicillin/tetracycline/trimethoprim+sulfamethoxazole/ciprofloxacin (AMP/TE/SXT/CIP)—was most frequently observed. The multidrug resistance (MDR) phenotype was found in 31.8% of isolates from poultry farms, 36.8% of strains isolated from food, and 20% of clinical samples. The greatest similarity of virulence profiles applied to isolates derived from poultry farms and food. Most of the AFEC from poultry farms and food-derived isolates belonged to commensals from phylogroups A and B1, while among the isolates from patients with UTI symptoms, the most common was the B2 phylogroup. The collective analysis showed similarity of the three studied groups of E. coli isolates in terms of the presented patterns of antimicrobial resistance, while the virulence profiles of the isolates studied showed great diversity. The phylogroup analysis showed no similarity between the poultry/food isolates and the UTI isolates, which had significant pathogenic potential.
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Meena PR, Priyanka P, Rana A, Raj D, Singh AP. Alarming level of single or multidrug resistance in poultry environments-associated extraintestinal pathogenic Escherichia coli pathotypes with potential to affect the One Health. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:400-411. [PMID: 35261153 DOI: 10.1111/1758-2229.13055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Prem Raj Meena
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Priyanka Priyanka
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Anuj Rana
- Department of Microbiology, College of Basic Sciences & Humanities, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Dharma Raj
- Department of Biostatistics and Bioinformatics, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, Madhya Pradesh, India
| | - Arvind Pratap Singh
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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de Mesquita Souza Saraiva M, Lim K, do Monte DFM, Givisiez PEN, Alves LBR, de Freitas Neto OC, Kariuki S, Júnior AB, de Oliveira CJB, Gebreyes WA. Antimicrobial resistance in the globalized food chain: a One Health perspective applied to the poultry industry. Braz J Microbiol 2022; 53:465-486. [PMID: 34775576 PMCID: PMC8590523 DOI: 10.1007/s42770-021-00635-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) remains a major global public health crisis. The food animal industry will face escalating challenges to increase productivity while minimizing AMR, since the global demand for animal protein has been continuously increasing and food animals play a key role in the global food supply, particularly broiler chickens. As chicken products are sources of low-cost, high-quality protein, poultry production is an important economic driver for livelihood and survival in developed and developing regions. The globalization of the food supply, markedly in the poultry industry, is aligned to the globalization of the whole modern society, with an unprecedented exchange of goods and services, and transit of human populations among regions and countries. Considering the increasing threat posed by AMR, human civilization is faced with a complex, multifaceted problem compromising its future. Actions to mitigate antimicrobial resistance are needed in all sectors of the society at the human, animal, and environmental levels. This review discusses the problems associated with antimicrobial resistance in the globalized food chain, using the poultry sector as a model. We cover critical aspects of the emergence and dissemination of antimicrobial resistance in the poultry industry and their implications to public health in a global perspective. Finally, we provide current insights using the multidisciplinary One Health approach to mitigate AMR at the human-animal-environment interface.
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Affiliation(s)
- Mauro de Mesquita Souza 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, Sao Paulo State University (FCAV-Unesp), Jaboticabal, SP, Brazil
| | - Kelvin Lim
- Veterinary Health Management Branch, National Parks Board, 6 Perahu Road, Singapore, Singapore
| | - Daniel Farias Marinho do Monte
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, SP, Brazil
| | - Patrícia Emília Naves Givisiez
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - Lucas Bocchini Rodrigues Alves
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, SP, Brazil
| | | | - Samuel Kariuki
- Kenya Medical Research Institute, Nairobi, Kenya
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH, USA
| | - Angelo Berchieri Júnior
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, SP, Brazil
| | - Celso José Bruno de 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
| | - Wondwossen Abebe Gebreyes
- Global One Health initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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Genomic analysis of the zoonotic ST73 lineage containing avian and human extraintestinal pathogenic Escherichia coli (ExPEC). Vet Microbiol 2022; 267:109372. [DOI: 10.1016/j.vetmic.2022.109372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022]
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9
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Characterization of antimicrobial resistance in chicken-source phylogroup F Escherichia coli: similar populations and resistance spectrums between E. coli recovered from chicken colibacillosis tissues and retail raw meats in Eastern China. Poult Sci 2021; 100:101370. [PMID: 34332223 PMCID: PMC8339308 DOI: 10.1016/j.psj.2021.101370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/05/2022] Open
Abstract
The extended-spectrum cephalosporin resistant E. coli from food animals transferring to community settings of humans causes a serious threat to public health. Unlike phylogroup B2 E. coli strains, the clinical significance of isolates in phylogroup F is not well revealed. Here, we report on a collection (n = 563) of phylogroup F E. coli isolates recovered from chicken colibacillosis tissues and retail raw chicken meat samples in Eastern China. There was an overlapped distribution of MLST types between chicken colibacillosis-origin and meat-source phylogroup F E. coli, including dominant STs (ST648, ST405, ST457, ST393, ST1158, etc). This study further investigated the presence of extended-spectrum β-lactamase (ESBL/pAmpC) producers in these chicken-source phylogroup F E. coli strains. The prevalence of extended-spectrum cephalosporin resistant strains in phylogroup F E. coli from chicken colibacillosis and raw meat separately accounted for 66.1 and 71.2%. The resistance genotypes and plasmid replicon types of chicken-source phylogroup F E. coli isolates were characterized by multiplex PCR. Our results revealed β-lactamase CTX-M, OXA, CMY and TEM genes were widespread in chicken-source phylogroup F E. coli, and blaCTX-M was the most predominant ESBL gene. Moreover, there was a high prevalence of non-lactamase resistance genes in these β-lactam-resistant isolates. The replicons IncB/O/K/Z, IncI1, IncN, IncFIC, IncQ1, IncX4, IncY, and p0111, associated with antibiotic-resistant large plasmids, were widespread in chicken-source phylogroup F E. coli. There was no obvious difference for the populations, resistance spectrums, and resistance genotypes between phylogroup F E. coli from chicken colibacillosis tissues and retail meats. This detail assessment of the population and resistance genotype showed chicken-source phylogroup F E. coli might hold zoonotic risk and contribute the spread of multidrug-resistant E. coli to humans.
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Innes GK, Nachman KE, Abraham AG, Casey JA, Patton AN, Price LB, Tartof SY, Davis MF. Contamination of Retail Meat Samples with Multidrug-Resistant Organisms in Relation to Organic and Conventional Production and Processing: A Cross-Sectional Analysis of Data from the United States National Antimicrobial Resistance Monitoring System, 2012-2017. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:57004. [PMID: 33978452 PMCID: PMC8114881 DOI: 10.1289/ehp7327] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND During food animal production, animals are exposed to, colonized by, and sometimes infected with bacteria that may contaminate animal products with susceptible and multidrug-resistant organisms (MDRO). The United States' Organic Foods Production Act resulted in decreased antibiotic use in some animal production operations. Some studies have reported that decreased antibiotic use is associated with reduced MDRO on meat. OBJECTIVES The aim of this study was to investigate associations of meat production and processing methods with MDRO and overall bacterial contamination of retail meats. METHODS Bacterial contamination data from 2012 to 2017 for chicken breast, ground beef, ground turkey, and pork chops were downloaded from the National Antimicrobial Resistance Monitoring System. Poisson regression models with robust variance were used to estimate associations with MDRO contamination and any contamination (adjusted for year and meat type) overall, and according to bacteria genus (Salmonella, Campylobacter, Enterococcus, Escherichia coli) and meat type. RESULTS A total of 39,349 retail meat samples were linked to 216 conventional, 123 split (conventional and organic), and three organic processing facilities. MDRO contamination was similar in conventionally produced meats processed at split vs. conventional facilities but was significantly lower in organically produced meats processed at split facilities [adjusted prevalance ratio (aPR)=0.43; 95% CI: 0.30, 0.63]. Meat processed by split vs. conventional processors had higher or similar MDRO contamination for all tested bacterial genera except Campylobacter (aPR=0.29; 95% CI: 0.13, 0.64). The prevalence of any contamination was lower in samples processed at split vs. conventional facilities for aggregated samples (aPR=0.70; 95% CI: 0.68, 0.73) and all meat types and bacterial genera. DISCUSSION Organically produced and processed retail meat samples had a significantly lower prevalence of MDRO than conventionally produced and processed samples had, whereas meat from split processors had a lower prevalence of any contamination than samples from conventional processors had. Additional studies are needed to confirm findings and clarify specific production and processing practices that might explain them. https://doi.org/10.1289/EHP7327.
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Affiliation(s)
- Gabriel K. Innes
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Keeve E. Nachman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Alison G. Abraham
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, School of Public Health University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Joan A. Casey
- Mailman School of Public Heath, Columbia University, New York, New York, USA
| | - Andrew N. Patton
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lance B. Price
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Sara Y. Tartof
- Kaiser Permanente Southern California, Pasadena, California, USA
| | - Meghan F. Davis
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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11
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Zou M, Ma PP, Liu WS, Liang X, Li XY, Li YZ, Liu BT. Prevalence and Antibiotic Resistance Characteristics of Extraintestinal Pathogenic Escherichia coli among Healthy Chickens from Farms and Live Poultry Markets in China. Animals (Basel) 2021; 11:ani11041112. [PMID: 33924454 PMCID: PMC8070349 DOI: 10.3390/ani11041112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Chicken meat has been proved to be a suspected source of extraintestinal pathogenic Escherichia coli (ExPEC), causing several diseases in humans, and bacteria in healthy chickens can contaminate chicken carcasses at the slaughter; however, reports about the prevalence and molecular characteristics of ExPEC in healthy chickens are still rare. In this study, among 926 E. coli isolates from healthy chickens in China, 22 (2.4%) were qualified as ExPEC and these ExPEC isolates were clonally unrelated. A total of six serogroups were identified in this study, with O78 being the most predominant type, and all the six serogroups had been frequently reported in human ExPEC isolates in many countries. All the 22 ExPEC isolates were multidrug-resistant and most isolates carried both blaCTX-M and fosA3 resistance genes. Notably, plasmid-borne colistin resistance gene mcr-1 was identified in six ExPEC isolates, among which two carried additional carbapenemase gene blaNDM, compromising both the efficacies of the two critically important drugs for humans, carbapenems and colistin. These results highlight that healthy chickens can serve as a potential reservoir for multidrug resistant ExPEC isolates, including mcr-1-containing ExPEC. Abstract Chicken products and chickens with colibacillosis are often reported to be a suspected source of extraintestinal pathogenic Escherichia coli (ExPEC) causing several diseases in humans. Such pathogens in healthy chickens can also contaminate chicken carcasses at the slaughter and then are transmitted to humans via food supply; however, reports about the ExPEC in healthy chickens are still rare. In this study, we determined the prevalence and characteristics of ExPEC isolates in healthy chickens in China. A total of 926 E. coli isolates from seven layer farms (371 isolates), one white-feather broiler farm (78 isolates) and 17 live poultry markets (477 isolates from yellow-feather broilers) in 10 cities in China, were isolated and analyzed for antibiotic resistance phenotypes and genotypes. The molecular detection of ExPEC among these healthy chicken E. coli isolates was performed by PCRs, and the serogroups and antibiotic resistance characteristics of ExPEC were also analyzed. Pulsed-field gel electrophoresis (PFGE) and Multilocus sequence typing (MLST) were used to analyze the genetic relatedness of these ExPEC isolates. We found that the resistance rate for each of the 15 antimicrobials tested among E. coli from white-feather broilers was significantly higher than that from brown-egg layers and that from yellow-feather broilers in live poultry markets (p < 0.05). A total of 22 of the 926 E. coli isolates (2.4%) from healthy chickens were qualified as ExPEC, and the detection rate (7.7%, 6/78) of ExPEC among white-feather broilers was significantly higher than that (1.6%, 6/371) from brown-egg layers and that (2.1%, 10/477) from yellow-feather broilers (p < 0.05). PFGE and MLST analysis indicated that clonal dissemination of these ExPEC isolates was unlikely. Serogroup O78 was the most predominant type among the six serogroups identified in this study, and all the six serogroups had been frequently reported in human ExPEC isolates in many countries. All the 22 ExPEC isolates were multidrug-resistant (MDR) and the resistance rates to ampicillin (100%) and sulfamethoxazole-trimethoprim (100%) were the highest, followed by tetracycline (95.5%) and doxycycline (90.9%). blaCTX-M was found in 15 of the 22 ExPEC isolates including 10 harboring additional fosfomycin resistance gene fosA3. Notably, plasmid-borne colistin resistance gene mcr-1 was identified in six ExPEC isolates in this study. Worryingly, two ExPEC isolates were found to carry both mcr-1 and blaNDM, compromising both the efficacies of carbapenems and colistin. The presence of ExPEC isolates in healthy chickens, especially those carrying mcr-1 and/or blaNDM, is alarming and will pose a threat to the health of consumers. To our knowledge, this is the first report of mcr-1-positive ExPEC isolates harboring blaNDM from healthy chickens.
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Affiliation(s)
- Ming Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Ping-Ping Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Wen-Shuang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Xiao Liang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
| | - Xu-Yong Li
- College of Agronomy, Liaocheng University, Liaocheng 252000, China;
| | - You-Zhi Li
- Shandong Veterinary Drug Quality Inspection Institute, Jinan 250022, China;
| | - Bao-Tao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China; (M.Z.); (P.-P.M.); (W.-S.L.); (X.L.)
- Correspondence: ; Tel.: +86-532-58957734
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12
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Avian Pathogenic Escherichia coli (APEC): An Overview of Virulence and Pathogenesis Factors, Zoonotic Potential, and Control Strategies. Pathogens 2021; 10:pathogens10040467. [PMID: 33921518 PMCID: PMC8069529 DOI: 10.3390/pathogens10040467] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis in avian species, and recent reports have suggested APEC as a potential foodborne zoonotic pathogen. Herein, we discuss the virulence and pathogenesis factors of APEC, review the zoonotic potential, provide the current status of antibiotic resistance and progress in vaccine development, and summarize the alternative control measures being investigated. In addition to the known virulence factors, several other factors including quorum sensing system, secretion systems, two-component systems, transcriptional regulators, and genes associated with metabolism also contribute to APEC pathogenesis. The clear understanding of these factors will help in developing new effective treatments. The APEC isolates (particularly belonging to ST95 and ST131 or O1, O2, and O18) have genetic similarities and commonalities in virulence genes with human uropathogenic E. coli (UPEC) and neonatal meningitis E. coli (NMEC) and abilities to cause urinary tract infections and meningitis in humans. Therefore, the zoonotic potential of APEC cannot be undervalued. APEC resistance to almost all classes of antibiotics, including carbapenems, has been already reported. There is a need for an effective APEC vaccine that can provide protection against diverse APEC serotypes. Alternative therapies, especially the virulence inhibitors, can provide a novel solution with less likelihood of developing resistance.
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13
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Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources. Antibiotics (Basel) 2021; 10:antibiotics10040351. [PMID: 33810387 PMCID: PMC8067153 DOI: 10.3390/antibiotics10040351] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.
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14
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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15
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Sanchez HM, Whitener VA, Thulsiraj V, Amundson A, Collins C, Duran-Gonzalez M, Giragossian E, Hornstra A, Kamel S, Maben A, Reynolds A, Roswell E, Schmidt B, Sevigny L, Xiong C, Jay JA. Antibiotic Resistance of Escherichia coli Isolated from Conventional, No Antibiotics, and Humane Family Owned Retail Broiler Chicken Meat. Animals (Basel) 2020; 10:ani10122217. [PMID: 33256102 PMCID: PMC7760345 DOI: 10.3390/ani10122217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary While it is well known that antibiotics administered for either therapeutic or non-therapeutic purposes in livestock farms promote the development of antibiotic resistance in bacteria through selective pressure, there are conflicting findings in the literature with regard to the influence of production strategies on antibiotic resistance in bacteria isolated from commercially-available chicken. In this work, we tested the hypothesis that there would be differences in antibiotic resistance in E. coli isolated from three categories of production methods: Conventional, No Antibiotics, and Humane Family Owned. In this work, it was found that for both ampicillin and erythromycin, there was no significant difference (p > 0.05) between Conventional and USDA-certified No Antibiotics chicken, which is in line with some previous work. The novel finding in this work is that we observed a statistically significant difference between both of the previously mentioned groups and chicken from Humane Family Owned production schemes. To our knowledge, this is the first time E. coli from Humane Family Owned chicken has been studied for antibiotic resistance. This work contributes to a better understanding of a potential strategy of chicken production for the overall benefit of human health, in line with the One Health approach implemented by the World Health Organization. Abstract The use of antibiotics for therapeutic and especially non-therapeutic purposes in livestock farms promotes the development of antibiotic resistance in previously susceptible bacteria through selective pressure. In this work, we examined E. coli isolates using the standard Kirby-Bauer disk diffusion susceptibility protocol and the CLSI standards. Companies selling retail chicken products in Los Angeles, California were grouped into three production groupings—Conventional, No Antibiotics, and Humane Family Owned. Humane Family Owned is not a federally regulated category in the United States, but shows the reader that the chicken is incubated, hatched, raised, slaughtered, and packaged by one party, ensuring that the use of antibiotics in the entire production of the chicken is known and understood. We then examined the antibiotic resistance of the E. coli isolates (n = 325) by exposing them to seven common antibiotics, and resistance was seen to two of the antibiotics, ampicillin and erythromycin. As has been shown previously, it was found that for both ampicillin and erythromycin, there was no significant difference (p > 0.05) between Conventional and USDA (United States Department of Agriculture)-certified No Antibiotics chicken. Unique to this work, we additionally found that Humane Family Owned chicken had fewer (p ≤ 0.05) antibiotic-resistant E. coli isolates than both of the previous. Although not considered directly clinically relevant, we chose to test erythromycin because of its ecological significance to the environmental antibiotic resistome, which is not generally done. To our knowledge, Humane Family Owned consumer chicken has not previously been studied for its antibiotic resistance. This work contributes to a better understanding of a potential strategy of chicken production for the overall benefit of human health, giving evidentiary support to the One Health approach implemented by the World Health Organization.
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Affiliation(s)
- Helen M. Sanchez
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Victoria A. Whitener
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Vanessa Thulsiraj
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Alicia Amundson
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Carolyn Collins
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Mckenzie Duran-Gonzalez
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Edwin Giragossian
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Allison Hornstra
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Sarah Kamel
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Andrea Maben
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Amelia Reynolds
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
| | - Elizabeth Roswell
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Benjamin Schmidt
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Lauren Sevigny
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Cindy Xiong
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
| | - Jennifer A. Jay
- Department of Civil and Environmental Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; (H.M.S.); (V.A.W.); (V.T.); (A.A.); (M.D.-G.); (A.R.)
- Institute of the Environment and Sustainability, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.C.); (E.G.); (A.H.); (S.K.); (A.M.); (E.R.); (B.S.); (L.S.); (C.X.)
- Correspondence: ; Tel.: +1-310-267-5365
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16
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Meena PR, Yadav P, Hemlata H, Tejavath KK, Singh AP. Poultry-origin extraintestinal Escherichia coli strains carrying the traits associated with urinary tract infection, sepsis, meningitis and avian colibacillosis in India. J Appl Microbiol 2020; 130:2087-2101. [PMID: 33095966 DOI: 10.1111/jam.14905] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/29/2022]
Abstract
AIM In-depth 'One Health' risk assessment of extraintestinal pathogenic Escherichia coli (ExPEC) strains carrying the traits of urinary tract infection, sepsis, meningitis and avian colibacillosis in poultry of India. METHODS AND RESULTS A total of 230 E. coli isolates were recovered from chicken samples representing the different sources (faeces vs caeca), stages (poultry farms vs retails butcher shop) or environments (rural vs urban) of poultry in India. Among all poultry-origin E. coli isolates, 49 (21·1%) strains were identified as ExPEC possessing multiple virulence determinants regardless of their association with any specific phylogenetic lineages. Of particular, potentially virulent ExPEC pathotypes, that is, uropathogenic E.coli (UPEC, 20·4%), avian pathogenic E. coli (APEC, 34·6%), septicaemia-associated E. coli (SEPEC, 47·0%) and neonatal meningitis-causing E.39 coli (NMEC, 2·0%) were also detected among all ExPEC strains. CONCLUSIONS Our study is the first to assess ExPEC strains circulating in the different settings of poultry in India and significantly demonstrates their potential ability to cause multiple extraintestinal infections both in humans and animals. SIGNIFICANCE AND IMPACT OF THE STUDY The data of our study are in favour of the possibility that poultry-origin putative virulent ExPEC pathotypes consequently constitute a threat risk to 'One Health' or for food safety and a great concern for poultry production of India.
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Affiliation(s)
- P R Meena
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - P Yadav
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - H Hemlata
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - K K Tejavath
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - A P Singh
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
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Romero-Barrios P, Deckert A, Parmley EJ, Leclair D. Antimicrobial Resistance Profiles of Escherichia coli and Salmonella Isolates in Canadian Broiler Chickens and Their Products. Foodborne Pathog Dis 2020; 17:672-678. [PMID: 32667209 PMCID: PMC7692893 DOI: 10.1089/fpd.2019.2776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global public health threat. The main purpose of this study was to evaluate AMR in generic Escherichia coli and Salmonella recovered from broiler chickens in Canada. To do this, an analysis of the antimicrobial susceptibility results was performed on a sample of generic E. coli and Salmonella isolates from the 2012 to 2013 national microbiological baseline study in broiler chicken. Of the 1135 generic E. coli isolates tested, 940 (82.8%) were resistant to at least one antimicrobial, with a large number of unique AMR profiles observed. Of the 1495 Salmonella isolates tested, 879 (58.8%) were resistant to at least one antimicrobial. Resistance was most common to aminoglycosides, β-lactams, and tetracyclines and, for generic E. coli isolates only, folate inhibitors. Differences in AMR patterns were observed across regions for both E. coli and Salmonella. For Salmonella, the levels of resistance were similar across the different sectors sampled along the food chain (e.g., slaughterhouse and retail) and the types of product sampled. There were also considerable differences in the levels and patterns of resistance among different Salmonella serovars, with most Salmonella Enteritidis isolates being susceptible to all antimicrobials tested.
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Affiliation(s)
- Pablo Romero-Barrios
- Food Safety Science Directorate, Canadian Food Inspection Agency, Ottawa, Canada
| | - Anne Deckert
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Canada
| | - E Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Canada.,Department of Population Medicine, University of Guelph, Guelph, Canada
| | - Daniel Leclair
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Canada
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Abstract
In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.
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Affiliation(s)
- Lee W. Riley
- School of Public Health, University of California, Berkeley, California 94720, USA
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19
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Zhao X, Liu Z, Zhang Y, Yuan X, Hu M, Liu Y. Prevalence and Molecular Characteristics of Avian-Origin mcr-1-Harboring Escherichia coli in Shandong Province, China. Front Microbiol 2020; 11:255. [PMID: 32153539 PMCID: PMC7044118 DOI: 10.3389/fmicb.2020.00255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
The objective of this study was to evaluate the prevalence and characteristics of avian-origin mcr-1-harbouring Escherichia coli in Shandong Province, China. During 2017—2018, a total of 668 non-duplicate E. coli isolates were separately collected from 8eight large intensive poultry farms in Shandong Province. Antimicrobial susceptibility testing for 10 antimicrobial agents commonly used in farms was performed on all E. coli isolates by the agar dilution method; the mobile colistin resistance gene (mcr-1) gene was screened by PCR, and mcr-1 positive isolates were PCR-screened for antimicrobial resistance genes and typed by multi-locus sequence typing (MLST). Among the 668 E. coli, 102 (15.3%) harbored the mcr-1 gene; high antimicrobial resistance rates were observed for ampicillin (100/102, 98.0%), followed by amoxicillin (99/102, 97.1%) and florfenicol (97/102, 95.1%), and a low level of resistance was found for amoxicillin/clavulanic acid (24/102, 23.5%). Five ESBL genes were detected, and all isolates carried blaTEM (102/102, 100%), followed by blaCTX–M (90/102, 88.2%). Four PMQR genes were detected; aac(6)-Ib-cr (40/102, 39.2%) was the most commonly isolated PMQR gene, followed by qnrA (10/102, 9.8%). Thirty-eight different kinds of STs were identified, and the dominant ST was ST93 (19/102, 18.6%), followed by ST48 (9/102, 8.8%). In summary, E. coli from poultry in Shandong could be a reservoir for the mcr-1 gene, which could pose serious risks to human public health.
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Affiliation(s)
- Xiaonan Zhao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China
| | - Zhengjie Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China
| | - Yin Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China
| | - Xiaomeng Yuan
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China.,College of Life Sciences, Shandong Normal University, Shandong, China
| | - Ming Hu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China
| | - Yuqing Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong, China
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20
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Manson AL, Van Tyne D, Straub TJ, Clock S, Crupain M, Rangan U, Gilmore MS, Earl AM. Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. Appl Environ Microbiol 2019; 85:e01559-19. [PMID: 31471308 PMCID: PMC6821970 DOI: 10.1128/aem.01559-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.
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Affiliation(s)
- Abigail L Manson
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daria Van Tyne
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Timothy J Straub
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah Clock
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael Crupain
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Urvashi Rangan
- Food Safety and Sustainability Center, Consumer Reports, Yonkers, New York, USA
| | - Michael S Gilmore
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Genomic Center for Infectious Diseases, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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21
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Johnson JR, Johnston BD, Porter S, Thuras P, Aziz M, Price LB. Accessory Traits and Phylogenetic Background Predict Escherichia coli Extraintestinal Virulence Better Than Does Ecological Source. J Infect Dis 2019; 219:121-132. [PMID: 30085181 DOI: 10.1093/infdis/jiy459] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/31/2018] [Indexed: 01/11/2023] Open
Abstract
Background The distinguishing characteristics of extraintestinal pathogenic Escherichia coli (ExPEC) strains are incompletely defined. Methods We characterized 292 diverse-source human Escherichia coli isolates (116 from fecal specimens, 79 from urine specimens [of which 39 were from patients with cystitis and 40 were from patients with pyelonephritis], and 97 from blood specimens) for phylogenetic group, sequence type complex (STc), and 49 putative extraintestinal pathogenic E. coli (ExPEC)-associated virulence genes. We then assessed these traits and ecological source as predictors of illness severity in a murine sepsis model. Results The study isolates exhibited a broad range of virulence in mice. Most of the studied bacterial characteristics corresponded significantly with experimental virulence, as did ecological source and established molecular definitions of ExPEC and uropathogenic E. coli (UPEC). Multivariable modeling identified the following bacterial traits as independent predictors of illness severity both overall and among the fecal and clinical (ie, urine and blood) isolates separately: fyuA (yersiniabactin receptor), kpsM K1 (K1 capsule), and kpsM II (group 2 capsules). Molecular UPEC status predicted virulence independently only among fecal isolates. Neither ecological source (ie, clinical vs fecal) nor molecular ExPEC status added predictive power to these traits, which accounted collectively for up to 49% of the observed variation in virulence. Conclusions Among human-source E. coli isolates, specific accessory traits and phylogenetic/clonal backgrounds predict experimental virulence in a murine sepsis model better than does ecological source.
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Affiliation(s)
- James R Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Brian D Johnston
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Stephen Porter
- Veterans Affairs Medical Center, Minneapolis, Minnesota.,University of Minnesota, Minneapolis, Minnesota
| | - Paul Thuras
- George Washington University, Washington, D. C
| | - Maliha Aziz
- George Washington University, Washington, D. C
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Gibson SB, Green SI, Liu CG, Salazar KC, Clark JR, Terwilliger AL, Kaplan HB, Maresso AW, Trautner BW, Ramig RF. Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections. Front Microbiol 2019; 10:2537. [PMID: 31781060 PMCID: PMC6861333 DOI: 10.3389/fmicb.2019.02537] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Abstract
Phage therapy requires libraries of well-characterized phages. Here we describe the generation of phage libraries for three target species: Escherichia coli, Pseudomonas aeruginosa, and Enterobacter cloacae. The basic phage characteristics on the isolation host, sequence analysis, growth properties, and host range and virulence on a number of contemporary clinical isolates are presented. This information is required before phages can be added to a phage library for potential human use or sharing between laboratories for use in compassionate use protocols in humans under eIND (emergency investigational new drug). Clinical scenarios in which these phages can potentially be used are discussed. The phages presented here are currently being characterized in animal models and are available for eINDs.
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Affiliation(s)
- Shelley B. Gibson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Carmen Gu Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Keiko C. Salazar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen L. Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Robert F. Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
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23
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Zhuge X, Jiang M, Tang F, Sun Y, Ji Y, Xue F, Ren J, Zhu W, Dai J. Avian-source mcr-1-positive Escherichia coli is phylogenetically diverse and shares virulence characteristics with E. coli causing human extra-intestinal infections. Vet Microbiol 2019; 239:108483. [PMID: 31699469 DOI: 10.1016/j.vetmic.2019.108483] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Colisepticemia caused by bloodstream infection of the extraintestinal pathogenic Escherichia coli (ExPEC) has become a serious public health problem. The recent emergence of the colistin-resistant Enterobacteriaceae, especially mcr-1-positive E. coli (MCRPEC) exerts great concern around the world. The molecular epidemiology and zoonosis risk of avian-origin MCRPEC are reported to be substantially lower. Here, we presented a system-wide analysis of emerging trends and zoonotic risk of MCRPEC recovered from avian colibacillosis in China. Our results showed the majority of avian-source MCRPEC isolates were classified as ExPECs. We also found that not only MCRPEC in phylogroups B2 and D, but also several E. coli populations in groups B1 and F possessed high virulence in the two models of avian colibacillosis and three rodent models for ExPEC-associated human infections. The high-virulent MCRPEC clones belong to ST131, as well as ST-types (such as ST48, ST117, ST162, ST501, ST648, and ST2085). Our data suggested the zoonotic risk of MCRPEC appeared to be a close association with ColV/ColBM type virulence plasmids. A comprehensive genomic analysis showed the overlapped of ColV/ColBM plasmids contents between MCRPEC isolates from humans and poultry. Identification of ColV/ColBM plasmids among human MCRPEC isolates revealed the potential transmission of avian-source mcr-1-positive ExPECs to humans. Moreover, the presence of ColV/ColBM plasmid-encoded virulence determinants, could be used as a predictive label for pathogenic MCRPEC. These findings highlighted avian-origin MCRPEC isolates could be recognized as a foodborne pathogen.
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Affiliation(s)
- Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; Center for Post-doctoral Studies of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Yu Sun
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiming Ji
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Weiyun Zhu
- Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; China Pharmaceutical University, Nanjing 211198, China; Center for Post-doctoral Studies of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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24
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Day MJ, Hopkins KL, Wareham DW, Toleman MA, Elviss N, Randall L, Teale C, Cleary P, Wiuff C, Doumith M, Ellington MJ, Woodford N, Livermore DM. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study. THE LANCET. INFECTIOUS DISEASES 2019; 19:1325-1335. [PMID: 31653524 DOI: 10.1016/s1473-3099(19)30273-7] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/13/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Extended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points. METHODS Sampling for ESBL-E coli was done between Aug 1, 2013, and Dec 15, 2014. We used selective media to seek ESBL-E coli in routinely submitted samples from human faeces, and prospectively collected samples from sewage, farm slurry, and retail foodstuffs in London, East Anglia, northwest England, Scotland, and Wales. We sequenced recovered isolates and compared these isolates with 293 bloodstream and 83 veterinary surveillance ESBL-E coli isolates from the same regions. FINDINGS 2157 (11%) of 20 243 human faeces samples contained ESBL-E coli, including 678 (17%) of 3995 in London. ESBL-E coli also were frequent in sewage and retail chicken (104 [65%] of 159 meat samples), but were rare in other meats and absent from plant-based foods (0 of 400 fruit and vegetable samples). Sequence type (ST) 131 dominated among ESBL-E coli from human blood (188 [64%] of 293 isolates), faeces (128 [36%] of 360), and sewage (14 [22%] of 65) with STs 38 and 648 also widespread; CTX-M-15 was the predominant ESBL in these lineages (319 [77%] of 416). By contrast, STs 602, 23, and 117-mostly with CTX-M-1 ESBL-dominated among food and veterinary isolates (68 [31%] of 218), with only two ST131 organisms recovered. ST10 occurred in both animals and humans, being frequent in surveillance bovines (11 [22%] of 51 cattle) and representing 15 (4%) of 360 human faecal isolates (but only three [1%] of 293 from bacteraemias); however, both human and animal ST10 isolates were diverse in serotype. INTERPRETATION Most human bacteraemias with ESBL-E coli in the UK involve internationally prevalent human-associated STs, particularly ST131; non-human reservoirs made little contribution to invasive human disease. Any interventions that seek to target food or livestock can affect the numbers of human infections caused by ESBL-E coli; prevention of the spread of resistant lineages among humans is more vital. FUNDING NIHR Policy Research.
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Affiliation(s)
- Michaela J Day
- National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- National Infection Service, Public Health England, London, UK
| | - David W Wareham
- Barts and The London School of Medicine and Dentistry, London, UK
| | | | - Nicola Elviss
- National Infection Service, Public Health England, London, UK
| | | | | | | | | | - Michel Doumith
- National Infection Service, Public Health England, London, UK
| | | | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | - David M Livermore
- National Infection Service, Public Health England, London, UK; University of East Anglia, Norwich, Norfolk, UK.
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25
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Riley LW. Differentiating Epidemic from Endemic or Sporadic Infectious Disease Occurrence. Microbiol Spectr 2019; 7:10.1128/microbiolspec.ame-0007-2019. [PMID: 31325286 PMCID: PMC10957193 DOI: 10.1128/microbiolspec.ame-0007-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Indexed: 12/19/2022] Open
Abstract
One important scope of work of epidemiology is the investigation of infectious diseases that cluster in time and place. Clusters of infectious disease may represent outbreaks or epidemics in which the cases share in common a point source exposure or an infectious agent in a chain of transmission pathways. Investigations of outbreaks of an illness can facilitate identification of a source, risk, or cause of the illness. However, most infectious disease episodes occur not as part of any apparent outbreaks but as sporadic infections. Multiple sporadic infections that occur steadily in time and place are referred to as endemic disease. How does one investigate sources and risk factors for sporadic or endemic infections? As part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, this review discusses limitations of traditional approaches and advantages of molecular epidemiology approaches to investigate sporadic and endemic infections. Using specific examples, the discussions show that most sporadic infections are actually part of unrecognized outbreaks and that what appears to be endemic disease occurrence is actually comprised of multiple small outbreaks. These molecular epidemiologic investigations have unmasked modes of transmission of infectious agents not known to cause outbreaks. They have also raised questions about the traditional ways to measure incidence and assess sources of drug-resistant infections in community settings. The discoveries made by the application of molecular microbiology methods in epidemiologic investigations have led to creation of new public health intervention strategies that have not been previously considered. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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26
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O’Brien TF, Clark A, Peters R, Stelling J. Why surveillance of antimicrobial resistance needs to be automated and comprehensive. J Glob Antimicrob Resist 2019; 17:8-15. [DOI: 10.1016/j.jgar.2018.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 08/03/2018] [Accepted: 10/07/2018] [Indexed: 10/28/2022] Open
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27
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Zhuge X, Ji Y, Tang F, Sun Y, Jiang M, Hu W, Wu Y, Xue F, Ren J, Zhu W, Dai J. Population structure and antimicrobial resistance traits of avian-origin mcr-1-positive Escherichia coli in Eastern China, 2015 to 2017. Transbound Emerg Dis 2019; 66:1920-1929. [PMID: 31059196 DOI: 10.1111/tbed.13222] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
Abstract
Recent emergence of mcr-1-positive Escherichia coli (MCRPEC) is causing serious concern around the world. Due to poultry-origin E. coli holding zoonotic potential, the improved understandings of MCRPEC population structure and antimicrobial resistance are critical to public health purposes. This study provided novel insights into the molecular epidemiology of avian-origin MCRPEC. For the mcr genes prevalence study, we analysed 1,360 E. coli recovered from avian colibacillosis in eastern China from 2015 to 2017. The mcr-1 was present in 172 (12.6%) E. coli isolates. For all of MCRPEC isolates, MICs of colistin were ≥4 mg/L. Avian-origin MCRPEC was widely distributed throughout phylogroups A, B1, B2, D, and F. Moreover, those isolates were assigned to 52 unique STs, such as ST48, ST117, ST131, and ST648, suggesting substantial horizontal dissemination of mcr-1 gene through avian-origin E. coli populations. The susceptibility of MCRPEC isolates was tested with 26 antimicrobial agents from 16 antimicrobial categories. There were high resistance rates of MCRPEC isolates against the clinically used antibiotics. All MCRPEC isolates in this study presented the multidrug-resistant (MDR) trait were even considered as extensively drug-resistant (XDR) strains. Resistance genotypes and plasmid replicon profiling showed that a majority of MCRPEC isolates contained plasmid-mediated resistance genes and exhibited the co-existence of mcr-1 with ESBLs and pAmpCs genes. Furthermore, the overlapped distribution of ST types and resistance gene contents was detected among MCRPEC isolates from humans and poultry. Besides mcr-1, our findings highlighted a significant prevalence of plasmid-mediated resistance genes among avian-origin MCRPEC isolates.
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Affiliation(s)
- Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.,Center for Post-doctoral Studies of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China
| | - Yiming Ji
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yu Sun
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wenhao Hu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yibang Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China.,Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China.,China Pharmaceutical University, Nanjing, China
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis. To date, molecular epidemiological studies have yielded numerous important insights into putative virulence factors, host-pathogen relationships, phylogenetic background, reservoirs, antimicrobial-resistant strains, clinical diagnostics, and transmission pathways of ExPEC, and have delineated areas in which further study is needed. The rapid pace of discovery of new putative virulence factors and the increasing awareness of the importance of virulence factor regulation, expression, and molecular variation should stimulate many future molecular epidemiological investigations. The growing sophistication and availability of molecular typing methodologies, and of the new computational and statistical approaches that are being developed to address the huge amounts of data that whole genome sequencing generates, provide improved tools for such studies and allow new questions to be addressed.
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Rincé A, Balière C, Hervio-Heath D, Cozien J, Lozach S, Parnaudeau S, Le Guyader FS, Le Hello S, Giard JC, Sauvageot N, Benachour A, Strubbia S, Gourmelon M. Occurrence of Bacterial Pathogens and Human Noroviruses in Shellfish-Harvesting Areas and Their Catchments in France. Front Microbiol 2018; 9:2443. [PMID: 30364306 PMCID: PMC6193098 DOI: 10.3389/fmicb.2018.02443] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/24/2018] [Indexed: 01/18/2023] Open
Abstract
During a 2-year study, the presence of human pathogenic bacteria and noroviruses was investigated in shellfish, seawater and/or surface sediments collected from three French coastal shellfish-harvesting areas as well as in freshwaters from the corresponding upstream catchments. Bacteria isolated from these samples were further analyzed. Escherichia coli isolates classified into the phylogenetic groups B2, or D and enterococci from Enterococcus faecalis and E. faecium species were tested for the presence of virulence genes and for antimicrobial susceptibility. Salmonella members were serotyped and the most abundant serovars (Typhimurium and its monophasic variants and Mbandaka) were genetically characterized by high discriminative subtyping methods. Campylobacter and Vibrio were identified at the species level, and haemolysin-producing Vibrio parahaemolyticus were searched by tdh- and trh- gene detection. Main results showed a low prevalence of Salmonella in shellfish samples where only members of S. Mbandaka were found. Campylobacter were more frequently isolated than Salmonella and a different distribution of Campylobacter species was observed in shellfish compared to rivers, strongly suggesting possible additional inputs of bacteria. Statistical associations between enteric bacteria, human noroviruses (HuNoVs) and concentration of fecal indicator bacteria revealed that the presence of Salmonella was correlated with that of Campylobacter jejuni and/or C. coli as well as to E. coli concentration. A positive correlation was also found between the presence of C. lari and the detection of HuNoVs. This study highlights the importance of simultaneous detection and characterization of enteric and marine pathogenic bacteria and human noroviruses not only in shellfish but also in catchment waters for a hazard assessment associated with microbial contamination of shellfish.
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Affiliation(s)
- Alain Rincé
- UNICAEN, U2RM, Normandie Université, Caen, France
| | - Charlotte Balière
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Dominique Hervio-Heath
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Joëlle Cozien
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Solen Lozach
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | - Sylvain Parnaudeau
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
| | | | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur,Paris, France
| | | | | | | | - Sofia Strubbia
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur,Paris, France
| | - Michèle Gourmelon
- RBE-SG2M-LSEM, Institut Français de Recherche pour l’Exploitation de la Mer, Brest, France
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Borzi MM, Cardozo MV, Oliveira ESD, Pollo ADS, Guastalli EAL, Santos LFD, Ávila FAD. Characterization of avian pathogenic Escherichia coli isolated from free-range helmeted guineafowl. Braz J Microbiol 2018; 49 Suppl 1:107-112. [PMID: 30170963 PMCID: PMC6328720 DOI: 10.1016/j.bjm.2018.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 11/24/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) isolates from apparently healthy free range helmeted guineafowl were characterized. Most of them had a high frequency of virulence associated genes, multi drug resistance and high pathogenicity. We demonstrated that helmeted guineafowl have potential to transmit antibiotic resistant APEC to other species including humans.
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Affiliation(s)
- Mariana Monezi Borzi
- UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Patologia Veterinária, Programa em Microbiologia Agrícola, Jaboticabal, SP, Brazil.
| | - Marita Vedovelli Cardozo
- UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Patologia Veterinária, Programa em Microbiologia Agrícola, Jaboticabal, SP, Brazil
| | - Elisabete Schirato de Oliveira
- UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Patologia Veterinária, Programa em Microbiologia Agrícola, Jaboticabal, SP, Brazil
| | - Andressa de Souza Pollo
- UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Medicina Veterinária Preventiva e Reprodução Animal, São Paulo, SP, Brazil
| | | | | | - Fernando Antonio de Ávila
- UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Patologia Veterinária, Programa em Microbiologia Agrícola, Jaboticabal, SP, Brazil
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