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Gharbi M, Tiss R, Chaouch M, Hamrouni S, Maaroufi A. Emergence of Plasmid-Mediated Quinolone Resistance (PMQR) Genes in Campylobacter coli in Tunisia and Detection of New Sequence Type ST13450. Antibiotics (Basel) 2024; 13:527. [PMID: 38927193 PMCID: PMC11200561 DOI: 10.3390/antibiotics13060527] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The aim of this study is to investigate the occurrence of plasmid mediated quinolone resistance (PMQR) determinants in Campylobacter coli isolates collected from broilers, laying hens and poultry farm environments. One hundred and thirty-nine C. coli isolates were isolated from broilers (n = 41), laying hens (n = 53), eggs (n = 4) and the environment (n = 41) of 23 poultry farms located in northeastern of Tunisia. Antimicrobial susceptibility testing was performed on all isolates according to the recommendation of the European Committee on Antimicrobial Susceptibility Testing guidelines. The detection of PMQR genes: qnrA, qnrB, qnrC, qnrD, qnrS, qepA, and aac(6)-Ib gene was performed using polymerase chain reaction (PCR) and specific primers. aac(6')-Ib amplicons were further analyzed by digestion with BtsCI to identify the aac(6')-Ib-cr variant. Mutations in GyrA and the occurrence of RE-CmeABC efflux pump were determined by mismatch amplification mutation assay (MAMA) PCR and PCR, respectively. In addition, eleven isolates were selected to determine their clonal lineage by MLST. The 139 C. coli isolates were resistant to ciprofloxacin, and 86 (61.8%) were resistant to nalidixic acid. High rates of resistance were also observed toward erythromycin (100%), azithromycin (96.4%), tetracycline (100%), chloramphenicol (98.56%), ampicillin (66.1%), amoxicillin-clavulanic acid (55.39%), and kanamycin (57.55%). However, moderate resistance rates were observed for gentamicin (9.35%) and streptomycin (22.3%). All quinolone-resistant isolates harbored the Thr-86-Ile amino acid substitution in GyrA, and the RE-CmeABC efflux pump was detected in 40.28% of isolates. Interestingly, the qnrB, qnrS, qepA, and aac(6')-Ib-cr were detected in 57.7%, 61.15%, 21.58%, and 10% of isolates, respectively. The eleven isolates studied by MLST belonged to a new sequence type ST13450. This study described for the first time the occurrence of PMQR genes in C. coli isolates in Tunisia and globally.
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Affiliation(s)
- Manel Gharbi
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia; (R.T.); (S.H.); (A.M.)
| | - Rihab Tiss
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia; (R.T.); (S.H.); (A.M.)
| | - Melek Chaouch
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (LR16IPT06), Pasteur Institute of Tunis, Tunis 1002, Tunisia;
- Laboratory of BioInformatics, BioMathematics and BioStatistics (LR16IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia
| | - Safa Hamrouni
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia; (R.T.); (S.H.); (A.M.)
| | - Abderrazak Maaroufi
- Group of Bacteriology and Biotechnology Development, Laboratory of Epidemiology and Veterinary Microbiology, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis 1002, Tunisia; (R.T.); (S.H.); (A.M.)
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022. EFSA J 2024; 22:e8583. [PMID: 38419967 PMCID: PMC10900121 DOI: 10.2903/j.efsa.2024.8583] [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] [Indexed: 03/02/2024] Open
Abstract
This report by the European Food Safety Authority and the European Centre for Disease prevention and Control, provides an overview of the main findings of the 2021-2022 harmonised Antimicrobial Resistance (AMR) monitoring in Salmonella spp., Campylobacter jejuni and C. coli from humans and food-producing animals (broilers, laying hens and fattening turkeys, fattening pigs and cattle under one year of age) and relevant meat thereof. For animals and meat thereof, AMR data on indicator commensal Escherichia coli, presumptive extended-spectrum beta-lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-/carbapenemase (CP)-producing E. coli, and the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) are also analysed. Generally, resistance levels differed greatly between reporting countries and antimicrobials. Resistance to commonly used antimicrobials was frequently found in Salmonella and Campylobacter isolates from humans and animals. In humans, increasing trends in resistance to one of two critically antimicrobials (CIA) for treatment was observed in poultry-associated Salmonella serovars and Campylobacter, in at least half of the reporting countries. Combined resistance to CIA was however observed at low levels except in some Salmonella serovars and in C. coli from humans and animals in some countries. While CP-producing Salmonella isolates were not detected in animals in 2021-2022, nor in 2021 for human cases, in 2022 five human cases of CP-producing Salmonella were reported (four harbouring bla OXA-48 or bla OXA-48-like genes). The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, bla NDM-5 and bla VIM-1 genes) in fattening pigs, cattle under 1 year of age, poultry and meat thereof by a limited number of MSs (5) in 2021 and 2022, requires a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC-producers in E. coli) showed an encouraging progress in reducing AMR in food-producing animals in several EU MSs over the last 7 years.
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Woyda R, Oladeinde A, Endale D, Strickland T, Plumblee Lawrence J, Abdo Z. Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter. Microbiol Spectr 2023; 11:e0323623. [PMID: 37882583 PMCID: PMC10871742 DOI: 10.1128/spectrum.03236-23] [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: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Campylobacter is a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat. Campylobacter is common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity of Campylobacter strains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show that Campylobacter jejuni and Campylobacter coli differ in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiating Campylobacter strains.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research Laboratory, USDA, Tifton, Georgia, USA
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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Hull DM, Harrel E, Harden L, Thakur S. Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019. Food Microbiol 2023; 116:104348. [PMID: 37689422 DOI: 10.1016/j.fm.2023.104348] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 09/11/2023]
Abstract
Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.
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Affiliation(s)
- Dawn M Hull
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Erin Harrel
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Lyndy Harden
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Pathobiology and Population Health, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA.
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Deforet F, Jehanne Q, Bénéjat L, Aptel J, Prat R, Desbiolles C, Ducournau A, Jauvain M, Bonnet R, Vandenesch F, Lemoine J, Lehours P. Combined genomic-proteomic approach in the identification of Campylobacter coli amoxicillin-clavulanic acid resistance mechanism in clinical isolates. Front Microbiol 2023; 14:1285236. [PMID: 38029165 PMCID: PMC10666280 DOI: 10.3389/fmicb.2023.1285236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Aminopenicillins resistance among Campylobacter jejuni and Campylobacter coli strains is associated with a single mutation in the promoting region of a chromosomal beta-lactamase blaOXA61, allowing its expression. Clavulanic acid is used to restore aminopenicillins activity in case of blaOXA61 expression and has also an inherent antimicrobial activity over Campylobacter spp. Resistance to amoxicillin-clavulanic acid is therefore extremely rare among these species: only 0.1% of all Campylobacter spp. analyzed in the French National Reference Center these last years (2017-2022). Material and methods Whole genome sequencing with bioinformatic resistance identification combined with mass spectrometry (MS) was used to identify amoxicillin-acid clavulanic resistance mechanism in Campylobacters. Results A G57T mutation in blaOXA61 promoting region was identified in all C. jejuni and C. coli ampicillin resistant isolates and no mutation in ampicillin susceptible isolates. Interestingly, three C. coli resistant to both ampicillin and amoxicillin-clavulanic acid displayed a supplemental deletion in the promoting region of blaOXA61 beta-lactamase, at position A69. Using MS, a significant difference in the expression of BlaOXA61 was observed between these three isolates and amoxicillin-clavulanic acid susceptible C. coli. Conclusion A combined genomics/proteomics approach allowed here to identify a rare putative resistance mechanism associated with amoxicillin-clavulanic acid resistance for C. coli.
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Affiliation(s)
- Francis Deforet
- Institut des Sciences Analytiques, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Jehanne
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Lucie Bénéjat
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Johanna Aptel
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Roxane Prat
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Chloé Desbiolles
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Astrid Ducournau
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
| | - Marine Jauvain
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, Université de Bordeaux, Bordeaux, France
| | - Richard Bonnet
- Laboratoire Associé CNR de la Résistance aux Antibiotiques, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Jérôme Lemoine
- Institut des Sciences Analytiques, Université Claude Bernard Lyon 1, Lyon, France
| | - Philippe Lehours
- Bacteriology Department, CHU de Bordeaux, National Reference Center for Campylobacters and Helicobacters, Bordeaux, France
- Bordeaux Institute of Oncology, BRIC U1312, INSERM, Université de Bordeaux, Bordeaux, France
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Yanestria SM, Effendi MH, Tyasningsih W, Mariyono M, Ugbo EN. First report of phenotypic and genotypic (bla OXA-61) beta-lactam resistance in Campylobacter jejuni from broilers in Indonesia. Vet World 2023; 16:2210-2216. [PMID: 38152271 PMCID: PMC10750733 DOI: 10.14202/vetworld.2023.2210-2216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/03/2023] [Indexed: 12/29/2023] Open
Abstract
Background and Aim Campylobacter is a zoonotic bacterium that is a major source of foodborne diseases. In humans, most cases of campylobacteriosis are caused by Campylobacter jejuni. Poultry is the main reservoir of Campylobacter for humans, because Campylobacter is part of the normal flora of the digestive tract of poultry. Antimicrobial resistance to several antibiotics in Campylobacter isolated from humans and food animals has increased rapidly. Beta-lactam is an antibiotic with a high prevalence of resistance in Campylobacter. This study aimed to investigate phenotypic and genotypic (blaOXA-61) beta-lactam resistance in C. jejuni from broilers in Indonesia. Materials and Methods A total of 100 samples of broiler intestinal contents were obtained from 10 broiler farms in Pasuruan Regency, Indonesia. Campylobacter jejuni was identified using conventional and polymerase chain reaction (PCR)-based methods. Phenotypic detection of beta-lactam resistance was performed using an antimicrobial susceptibility test with antibiotic disks of aztreonam, ampicillin, and amoxicillin-clavulanic acid. Genotypic detection by PCR was performed using the blaOXA-61 gene, which encodes beta-lactamase. Results Campylobacter jejuni was identified in 23% of the samples. Phenotypically, 100% (23/23) and 73.9% (17/23) C. jejuni isolates had high resistance to aztreonam and ampicillin, respectively, but all isolates were susceptible to amoxicillin-clavulanic acid. Genotypically, all isolates carried blaOXA-61, indicated by the presence of a 372-bp PCR product. Conclusion Campylobacter jejuni is highly resistant to beta-lactams and is a serious threat to human health. Resistance to beta-lactams should be monitored because beta-lactamase genes can be transferred between bacteria. Public awareness must also be increased on the importance of using antibiotics rationally in humans and animals.
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Affiliation(s)
- Sheila Marty Yanestria
- Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya 60115, East Java, Indonesia
| | - Mustofa Helmi Effendi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya 60115, East Java, Indonesia
| | - Wiwiek Tyasningsih
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya 60115, East Java, Indonesia
| | - Mariyono Mariyono
- Bacteriology Laboratory, Balai Besar Veteriner Wates, Jl. Yogyakarta-Wates No. Km. 27, Wates, Yogyakarta 55651, Central Java, Indonesia
| | - Emmanuel Nnabuike Ugbo
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Enugu - Abakaliki Rd, 481101, Abakaliki, Ebonyi, Nigeria
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El-Saadony MT, Saad AM, Yang T, Salem HM, Korma SA, Ahmed AE, Mosa WFA, Abd El-Mageed TA, Selim S, Al Jaouni SK, Zaghloul RA, Abd El-Hack ME, El-Tarabily KA, Ibrahim SA. Avian campylobacteriosis, prevalence, sources, hazards, antibiotic resistance, poultry meat contamination, and control measures: a comprehensive review. Poult Sci 2023; 102:102786. [PMID: 37454641 PMCID: PMC10371856 DOI: 10.1016/j.psj.2023.102786] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 07/18/2023] Open
Abstract
Avian campylobacteriosis is a vandal infection that poses human health hazards. Campylobacter is usually colonized in the avian gut revealing mild signs in the infected birds, but retail chicken carcasses have high contamination levels of Campylobacter spp. Consequently, the contaminated avian products constitute the main source of human infection with campylobacteriosis and result in severe clinical symptoms such as diarrhea, abdominal pain, spasm, and deaths in sensitive cases. Thus, the current review aims to shed light on the prevalence of Campylobacter in broiler chickens, Campylobacter colonization, bird immunity against Campylobacter, sources of poultry infection, antibiotic resistance, poultry meat contamination, human health hazard, and the use of standard antimicrobial technology during the chicken processing of possible control strategies to overcome such problems.
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Affiliation(s)
- Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed M Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Tao Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, China
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Sameh A Korma
- Department of Food Science, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, Saudi Arabia
| | - Walid F A Mosa
- Plant Production Department (Horticulture-Pomology), Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Taia A Abd El-Mageed
- Department of Soils and Water, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72388, Saudi Arabia
| | - Soad K Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Rashed A Zaghloul
- Department Agricultural Microbiology, Faculty of Agriculture, Benha University, Moshtohor, Qaluybia, 13736, Egypt
| | - Mohamed E Abd El-Hack
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Salam A Ibrahim
- Food Microbiology and Biotechnology Laboratory, Carver Hall, College of Agriculture and Environmental Sciences, North Carolina A & T State University, Greensboro, NC, 27411-1064
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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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Concha-Toloza M, Lopez-Cantillo M, Molina-Mora JA, Collado L. Genomic Characterization of Antibiotic-Resistant Campylobacterales Isolated from Chilean Poultry Meat. Antibiotics (Basel) 2023; 12:antibiotics12050917. [PMID: 37237819 DOI: 10.3390/antibiotics12050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Due to the lack of knowledge about Campylobacterales in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of Campylobacter, Arcobacter and Helicobacter in 382 samples of chicken meat purchased in Valdivia, Chile. The samples were analyzed using three isolation protocols. Resistance to four antibiotics was evaluated by phenotypic methods. Genomic analyses were performed on selected resistant strains to detect resistance determinants and their genotypes. A total of 59.2% of the samples were positive. Arcobacter butzleri (37.4%) was the most prevalent species, followed by Campylobacter jejuni (19.6%), C. coli (11.3%), A. cryaerophilus (3.7%) and A. skirrowii (1.3%). Helicobacter pullorum (14%) was detected by PCR in a subset of samples. Campylobacter jejuni was resistant to ciprofloxacin (37.3%) and tetracycline (20%), while C. coli and A. butzleri were resistant to ciprofloxacin (55.8% and 2.8%), erythromycin (16.3% and 0.7%) and tetracycline (4.7% and 2.8%), respectively. Molecular determinants were consistent with phenotypic resistance. The genotypes of C. jejuni (CC-21, CC-48, CC-49, CC-257, CC-353, CC-443, CC-446 and CC-658) and C. coli (CC-828) coincided with genotypes of Chilean clinical strains. These findings suggest that besides C. jejuni and C. coli, chicken meat could play a role in the transmission of other pathogenic and antibiotic-resistant Campylobacterales.
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Affiliation(s)
- Macarena Concha-Toloza
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Mónica Lopez-Cantillo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021. EFSA J 2023; 21:e07867. [PMID: 36891283 PMCID: PMC9987209 DOI: 10.2903/j.efsa.2023.7867] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Antimicrobial resistance (AMR) data on zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs) and reporting countries, jointly analysed by EFSA and ECDC and presented in a yearly EU Summary Report. This report provides an overview of the main findings of the 2020-2021 harmonised AMR monitoring in Salmonella spp., Campylobacter jejuni and C. coli in humans and food-producing animals (broilers, laying hens and turkeys, fattening pigs and bovines under 1 year of age) and relevant meat thereof. For animals and meat thereof, indicator E. coli data on the occurrence of AMR and presumptive Extended spectrum β-lactamases (ESBL)-/AmpC β-lactamases (AmpC)-/carbapenemases (CP)-producers, as well as the occurrence of methicillin-resistant Staphylococcus aureus are also analysed. In 2021, MSs submitted for the first time AMR data on E. coli isolates from meat sampled at border control posts. Where available, monitoring data from humans, food-producing animals and meat thereof were combined and compared at the EU level, with emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to selected and critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting ESBL-/AmpC-/carbapenemase phenotypes. Resistance was frequently found to commonly used antimicrobials in Salmonella spp. and Campylobacter isolates from humans and animals. Combined resistance to critically important antimicrobials was mainly observed at low levels except in some Salmonella serotypes and in C. coli in some countries. The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, and bla NDM-5 genes) in pigs, bovines and meat thereof by a limited number of MSs (4) in 2021, requests a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC- producers) showed that encouraging progress have been registered in reducing AMR in food-producing animals in several EU MSs over the last years.
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Bunduruș IA, Balta I, Ștef L, Ahmadi M, Peț I, McCleery D, Corcionivoschi N. Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates. Antibiotics (Basel) 2023; 12:antibiotics12020402. [PMID: 36830312 PMCID: PMC9952398 DOI: 10.3390/antibiotics12020402] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.
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Affiliation(s)
- Iulia Adelina Bunduruș
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Igori Balta
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Lavinia Ștef
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Mirela Ahmadi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Ioan Peț
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - David McCleery
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
| | - Nicolae Corcionivoschi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
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Woyda R, Oladeinde A, Endale D, Strickland T, Lawrence JP, Abdo Z. Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors of Campylobacter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526821. [PMID: 36778422 PMCID: PMC9915665 DOI: 10.1101/2023.02.02.526821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Campylobacter infections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir for Campylobacter. Here, we characterized the genetic diversity of Campylobacter species detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed on Campylobacter jejuni (n = 39) and Campylobacter coli (n = 5) isolates. All C. jejuni isolates were susceptible to all antibiotics tested while C. coli (n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates' flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3 C. jejuni isolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates' multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected for Campylobacter strains that are less likely to colonize the chicken host.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research Laboratory, USDA, Tifton, GA, 31793
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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Abstract
PURPOSE OF REVIEW Campylobacter is a major foodborne pathogen that infects the human intestinal tract. This review discusses the current status of antibiotic resistance, transmission of antibiotic resistance genes, and strategies to combat the global Campylobacter epidemic. RECENT FINDINGS Over the past 18 months, articles on Campylobacter antibiotic resistance have been published in ∼39 countries. Antibiotic-resistant Campylobacter have been detected in humans, livestock, poultry, wild animals, the environment, and food. Campylobacter spp. are resistant to a wide spectrum of antimicrobial agents, including the antibiotics quinolones, macrolides, tetracyclines, aminoglycosides, and chloramphenicols. Multidrug resistance is a globally emerging problem. Continuous antibiotic pressure promotes the spread of drug-resistant Campylobacter spp. Additionally, Campylobacter is well adapted to acquiring foreign drug resistance genes, including ermB, optrA, fexA, and cfrC, which are usually acquired from gram-positive bacteria. SUMMARY The widespread use of antibiotics has caused a global epidemic of drug-resistant Campylobacter infections. Many countries are actively reducing the use of antibiotics and adopting alternatives in the livestock and poultry industries to control the spread of drug-resistant Campylobacter spp.
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Antibiotic Resistance in Bacteria—A Review. Antibiotics (Basel) 2022; 11:antibiotics11081079. [PMID: 36009947 PMCID: PMC9404765 DOI: 10.3390/antibiotics11081079] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background: A global problem of multi-drug resistance (MDR) among bacteria is the cause of hundreds of thousands of deaths every year. In response to the significant increase of MDR bacteria, legislative measures have widely been taken to limit or eliminate the use of antibiotics, including in the form of feed additives for livestock, but also in metaphylaxis and its treatment, which was the subject of EU Regulation in 2019/6. Numerous studies have documented that bacteria use both phenotypis and gentic strategies enabling a natural defence against antibiotics and the induction of mechanisms in increasing resistance to the used antibacterial chemicals. The mechanisms presented in this review developed by the bacteria have a significant impact on reducing the ability to combat bacterial infections in humans and animals. Moreover, the high prevalence of multi-resistant strains in the environment and the ease of transmission of drug-resistance genes between the different bacterial species including commensal flora and pathogenic like foodborne pathogens (E. coli, Campylobacter spp., Enterococcus spp., Salmonella spp., Listeria spp., Staphylococcus spp.) favor the rapid spread of multi-resistance among bacteria in humans and animals. Given the global threat posed by the widespread phenomenon of multi-drug resistance among bacteria which are dangerous for humans and animals, the subject of this study is the presentation of the mechanisms of resistance in most frequent bacteria called as “foodborne pathoges” isolated from human and animals. In order to present the significance of the global problem related to multi-drug resistance among selected pathogens, especially those danger to humans, the publication also presents statistical data on the percentage range of occurrence of drug resistance among selected bacteria in various regions of the world. In addition to the phenotypic characteristics of pathogen resistance, this review also presents detailed information on the detection of drug resistance genes for specific groups of antibiotics. It should be emphasized that the manuscript also presents the results of own research i.e., Campylobacter spp., E. coli or Enetrococcus spp. This subject and the presentation of data on the risks of drug resistance among bacteria will contribute to initiating research in implementing the prevention of drug resistance and the development of alternatives for antimicrobials methods of controlling bacteria.
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