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Cooper AL, Wong A, Tamber S, Blais BW, Carrillo CD. Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database. Microorganisms 2024; 12:709. [PMID: 38674654 PMCID: PMC11051753 DOI: 10.3390/microorganisms12040709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.
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Affiliation(s)
- Ashley L. Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A0K9, Canada;
| | - Burton W. Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Catherine D. Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON K1A 0C6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
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Garcia-Fernandez A, Janowicz A, Marotta F, Napoleoni M, Arena S, Primavilla S, Pitti M, Romantini R, Tomei F, Garofolo G, Villa L. Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy. Front Microbiol 2024; 14:1293666. [PMID: 38260875 PMCID: PMC10800408 DOI: 10.3389/fmicb.2023.1293666] [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: 09/13/2023] [Accepted: 12/07/2023] [Indexed: 01/24/2024] Open
Abstract
Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by Campylobacter jejuni and Campylobacter coli, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin Campylobacter spp. strains (102 C. jejuni and 31 C. coli) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in C. jejuni and ST-828 CC in C. coli. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and tet(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in C. coli exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with C. jejuni exhibiting a higher abundance compared to C. coli. Notably, specific C. jejuni sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct C. jejuni lineages. Campylobacter spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among Campylobacter spp. The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.
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Affiliation(s)
| | - Anna Janowicz
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Francesca Marotta
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Maira Napoleoni
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Primavilla
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Monica Pitti
- Centro di Riferimento per la Tipizzazione delle Salmonelle, CeRTiS, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Turin, Italy
| | - Romina Romantini
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | | | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Yan R, M'ikanatha NM, Nachamkin I, Hudson LK, Denes TG, Kovac J. Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania. Food Microbiol 2023; 116:104349. [PMID: 37689423 DOI: 10.1016/j.fm.2023.104349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 09/11/2023]
Abstract
Poultry is the primary source of Campylobacter infections and severe campylobacteriosis cases are treated with macrolides and fluoroquinolones. However, these drugs are less effective against antimicrobial-resistant strains. Here, we investigated the prevalence of phenotypic antimicrobial resistance and associated resistance genetic determinants in Campylobacter isolates collected from human clinical (N = 123) and meat (N = 80) sources in Pennsylvania in 2017 and 2018. Our goal was to assess potential differences in the prevalence of antimicrobial resistance in Campylobacter isolated from human and poultry meat sources in Pennsylvania and to assess the accuracy of predicting antimicrobial resistance phenotypes based on resistance genotypes. We whole genome sequenced isolates and identified genetic resistance determinants using the National Antimicrobial Resistance Monitoring System Campylobacter AMR workflow v2.0 in GalaxyTrakr. Phenotypic antimicrobial susceptibility testing was carried out using the E-Test and Sensititre CAMPYCMV methods for human clinical and poultry meat isolates, respectively, and the results were interpreted using the EUCAST epidemiological cutoff values. The 193 isolates were represented by 85 MLST sequence types and 23 clonal complexes, suggesting high genetic diversity. Resistance to erythromycin was confirmed in 6% human and 4% meat isolates. Prevalence of ciprofloxacin resistance was significantly higher in human isolates as compared to meat isolates. A good concordance was observed between phenotypic resistance and the presence of the corresponding known resistance genetic determinants.
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Affiliation(s)
- Runan Yan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Irving Nachamkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
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Zhang L, Fang S, Hong W, Shen Z, Li S, Fang W. Differences in pathogenic community assembly processes and their interactions with bacterial communities in river and lake ecosystems. ENVIRONMENTAL RESEARCH 2023; 236:116847. [PMID: 37558117 DOI: 10.1016/j.envres.2023.116847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Pathogenic bacterial infections caused by water quality degradation are one of the most widespread environmental problems. Clarifying the structure of pathogens and their assembly mechanisms in lake ecosystems is vital to prevent the infestation of waterborne pathogens and maintain human health. However, the composition and assembly mechanisms of pathogenic bacterial communities in river and lake ecosystems are still poorly understood. In this study, we collected 17 water and 17 sediment samples from Lake Chaohu and its 11 inflow rivers. Sequencing of 16S rRNA genes was used to study bacterial pathogen communities. The results of the study showed that there was a significant difference (P < 0.05) in the composition of the pathogen community between riverine and lake habitats. Acinetobacter (36.49%) was the dominant bacterium in the river, whereas Flavobacterium (21.6%) was the most abundant bacterium in the lake. Deterministic processes (i.e., environmental filtering and species interaction) drove the assembly of pathogenic bacterial communities in the lake habitat, while stochastic processes shaped river pathogenic bacterial communities. Spearman correlation analysis showed that the α-diversity of bacterial communities was linearly and negatively linked to the relative abundance of pathogens. Having a higher bacterial community diversity had a suppressive effect on pathogen abundance. In addition, co-occurrence network analysis showed that bacterial communities were tightly linked to pathogenic bacteria. Pseudomonas aeruginosa and Salmonella enterica were identified as keystone species in an inflow water sampling network (W_FR), reducing the complexity of the network. These results provide a reference for assessments of water quality safety and pathogenic bacteria posing risks to human health in large freshwater lakes.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China.
| | - Shuqi Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wenqing Hong
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Zhen Shen
- Nanjing Institute of Geography and Limnology Chinese Academy of Sciences, Nanjing, 210008, China
| | - Shuo Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou, 239000, China
| | - Wangkai Fang
- School of Earth and Environment, Anhui University of Science & Technology, Huainan, 232000, China
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Xiao J, Cheng Y, Zhang W, Lu Q, Guo Y, Hu Q, Wen G, Shao H, Luo Q, Zhang T. Genetic characteristics, antimicrobial susceptibility, and virulence genes distribution of Campylobacter isolated from local dual-purpose chickens in central China. Front Cell Infect Microbiol 2023; 13:1236777. [PMID: 37743858 PMCID: PMC10517862 DOI: 10.3389/fcimb.2023.1236777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Food-borne antibiotic-resistant Campylobacter poses a serious threat to public health. To understand the prevalence and genetic characteristics of Campylobacter in Chinese local dual-purpose (meat and eggs) chickens, the genomes of 30 Campylobacter isolates, including 13 C. jejuni and 17 C. coli from Jianghan-chickens in central China, were sequenced and tested for antibiotic susceptibility. The results showed that CC-354 and CC-828 were the dominant clonal complexes of C. jejuni and C. coli, respectively, and a phylogenetic analysis showed that three unclassified multilocus sequence types of C. coli were more closely genetically related to C. jejuni than to other C. coli in this study. Of the six antibiotics tested, the highest resistance rates were to ciprofloxacin and tetracycline (100%), followed by lincomycin (63.3%), erythromycin (30.0%), amikacin (26.7%), and cefotaxime (20.0%). The antibiotic resistance rate of C. coli was higher than that of C. jejuni. The GyrA T86I mutation and 15 acquired resistance genes were detected with whole-genome sequencing (WGS). Among those, the GyrA T86I mutation and tet(O) were most prevalent (both 96.7%), followed by the blaOXA-type gene (90.0%), ant(6)-Ia (26.7%), aac(6')-aph(3'') (23.3%), erm(B) (13.3%), and other genes (3.3%). The ciprofloxacin and tetracycline resistance phenotypes correlated strongly with the GyrA T86I mutation and tet(O)/tet(L), respectively, but for other antibiotics, the correlation between genes and resistance phenotypes were weak, indicating that there may be resistance mechanisms other than the resistance genes detected in this study. Virulence gene analysis showed that several genes related to adhesion, colonization, and invasion (including cadF, porA, ciaB, and jlpA) and cytolethal distending toxin (cdtABC) were only present in C. jejuni. Overall, this study extends our knowledge of the epidemiology and antibiotic resistance of Campylobacter in local Chinese dual-purpose chickens.
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Affiliation(s)
- Jia Xiao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yiluo Cheng
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenting Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qin Lu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yunqing Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qiao Hu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guoyuan Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qingping Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Hubei Hongshan Laboratory, Wuhan, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
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Dias TS, Panzenhagen P, Figueira ADA, Costa GA, Rossi DA, de Melo RT, Pereira VLDA, de Aquino MHC. Genomic characterisation of Campylobacter jejuni Cj26: A high-level ciprofloxacin/erythromycin-resistant strain isolated from a poultry carcass in southern Brazil. J Glob Antimicrob Resist 2023; 34:1-4. [PMID: 37290693 DOI: 10.1016/j.jgar.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/12/2023] [Accepted: 05/20/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVES The draft genome sequence of Campylobacter jejuni (Cj26) was analysed to investigate genetic mechanisms of antimicrobial resistance, virulence-associated genes, and phylogenetic context. METHODS Antimicrobial resistance was assessed by agar dilution and disk diffusion. Cj26 was sequenced using NovaSeq 6000 technology. The genome was assembled and annotated. Resistance genes and chromosomal mutations were analysed using the Center for Genomic Epidemiology services, and the multilocus sequence type, SVR-flaA, and porA were determined. The virulome was determined using the Virulence Factor Database. Plasmid detection and assembly were performed using Unicycler v0.5.0 software. To infer the core genome phylogeny, prokka v1.14.5 was employed in conjunction with IQtree v2.0.3. RESULTS The Cj26 strain showed a high level of resistance to ciprofloxacin (32 µg/mL) and erythromycin (>128 µg/mL) and resistance to tetracycline and ampicillin. Multilocus sequence typing revealed that the strain belonged to sequence type 353. The substitutions Tre-86-Ile in gyrA and A2075G in 23s RNA were detected, along with the genes tetO, aph(3')-III, ant(6)-Ia, and blaOXA 460. A consistent relationship among accessory and core genes was identified. When compared to other sequence type 353 genomes from Brazil, Cj26 clustered with strains that had more antimicrobial resistance genes than the other clusters. CONCLUSION This report provides insight into the antimicrobial resistance determinants found in a C. jejuni strain and offers a valuable resource for further studies on Campylobacter genomics and antimicrobial resistance.
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Affiliation(s)
- Thomas Salles Dias
- Postgraduate Program in Veterinary Medicine (Veterinary Hygiene and Processing Technology of Animal Products), Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil.
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Brazil
| | - Arthur de Almeida Figueira
- Postgraduate Program in Veterinary Medicine (Veterinary Hygiene and Processing Technology of Animal Products), Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil
| | - Gisllany Alves Costa
- Postgraduate Program in Veterinary Medicine (Veterinary Hygiene and Processing Technology of Animal Products), Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil
| | - Daise Aparecida Rossi
- Laboratory of Molecular Epidemiology, Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Roberta Torres de Melo
- Laboratory of Molecular Epidemiology, Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Virginia Léo de Almeida Pereira
- Postgraduate Program in Veterinary Medicine (Veterinary Hygiene and Processing Technology of Animal Products), Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil; Department of Preventive Veterinary Medicine, Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil
| | - Maria Helena Cosendey de Aquino
- Postgraduate Program in Veterinary Medicine (Veterinary Hygiene and Processing Technology of Animal Products), Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil; Department of Preventive Veterinary Medicine, Faculdade de Veterinária, Universidade Federal Fluminense, Niteroi, Brazil
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7
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dos Santos AMP, Panzenhagen P, Ferrari RG, de Jesus ACS, Portes AB, Ochioni AC, Rodrigues DDP, Conte-Junior CA. Genomic Characterization of Salmonella Isangi: A Global Perspective of a Rare Serovar. Antibiotics (Basel) 2023; 12:1309. [PMID: 37627729 PMCID: PMC10451742 DOI: 10.3390/antibiotics12081309] [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: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Salmonella Isangi is an infrequent serovar that has recently been reported in several countries due to nosocomial infections. A considerable number of reports indicate Salmonella Isangi multidrug resistance, especially to cephalosporins, which could potentially pose a risk to public health worldwide. Genomic analysis is an excellent tool for monitoring the emergence of microorganisms and related factors. In this context, the aim of this study was to carry out a genomic analysis of Salmonella Isangi isolated from poultry in Brazil, and to compare it with the available genomes from the Pathogen Detection database and Sequence Read Archive. A total of 142 genomes isolated from 11 different countries were investigated. A broad distribution of extended-spectrum beta-lactamase (ESBL) genes was identified in the Salmonella Isangi genomes examined (blaCTX-M-15, blaCTX-M-2, blaDHA-1, blaNDM-1, blaOXA-10, blaOXA-1, blaOXA-48, blaSCO-1, blaSHV-5, blaTEM-131, blaTEM-1B), primarily in South Africa. Resistome analysis revealed predicted resistance to aminoglycoside, sulfonamide, macrolide, tetracycline, trimethoprim, phenicol, chloramphenicol, and quaternary ammonium. Additionally, PMQR (plasmid-mediated quinolone resistance) genes qnr19, qnrB1, and qnrS1 were identified, along with point mutations in the genes gyrAD87N, gyrAS83F, and gyrBS464F, which confer resistance to ciprofloxacin and nalidixic acid. With regard to plasmids, we identified 17 different incompatibility groups, including IncC, Col(pHAD28), IncHI2, IncHI2A, IncM2, ColpVC, Col(Ye4449), Col156, IncR, IncI1(Alpha), IncFIB (pTU3), Col(B5512), IncQ1, IncL, IncN, IncFIB(pHCM2), and IncFIB (pN55391). Phylogenetic analysis revealed five clusters grouped by sequence type and antimicrobial gene distribution. The study highlights the need for monitoring rare serovars that may become emergent due to multidrug resistance.
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Affiliation(s)
- Anamaria Mota Pereira dos Santos
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Rafaela G. Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Ana Carolina S. de Jesus
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
| | - Alan Clavelland Ochioni
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | | | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
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8
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Katz A, Porte L, Weitzel T, Varela C, Muñoz-Rehbein C, Ugalde JA, Grim C, González-Escalona N, Blondel CJ, Bravo V. Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains. Front Cell Infect Microbiol 2023; 13:1208825. [PMID: 37520433 PMCID: PMC10374022 DOI: 10.3389/fcimb.2023.1208825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/16/2023] [Indexed: 08/01/2023] Open
Abstract
Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at 'Clinica Alemana', Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.
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Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Lorena Porte
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Carmen Varela
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Cristina Muñoz-Rehbein
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Carlos J. Blondel
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Verónica Bravo
- Centro de Investigaciones Biomédicas y Aplicadas (CIBAP), Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
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Distribution of Virulence Genes in Campylobacter spp. Isolated from Agaricus Mushrooms in Iran. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1872655. [PMID: 36760473 PMCID: PMC9904900 DOI: 10.1155/2023/1872655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/03/2022] [Accepted: 11/25/2022] [Indexed: 02/01/2023]
Abstract
The white button mushroom (Agaricus) is a significant nutritional and therapeutic species utilized in the human diet and could transmit various bacterial infections. Campylobacter species are the most common cause of foodborne illness across the world. The present study has been planned to determine the frequency of virulence genes and antibiotic susceptibility test in Campylobacter spp. recovered from Agaricus mushroom. In this study, 740 Agaricus mushroom samples were gathered randomly from various markets from June 2020 to December 2020. Confirmation of Campylobacter spp. using biochemical analyses and 23S rRNA-based PCR was performed. The agar dilution technique was used to determine resistance to antibiotics using gentamicin (GM10μg), ciprofloxacin (CIP5μg), nalidixic acid (NA30μg), tetracycline (TE30μg), ampicillin (AM10μg), amoxicillin+ clavulanic acid (AMC30μg), erythromycine (E15μg), azithromycin (AZM15μg), clindamycin (CC2μg), and chloramphenicol (C30μg). Multiplex PCR was utilized to determine the prevalence of the recR, dnaJ, wlaN, virBll, cdtC, cdtB, cdtA, flaA, cadF, pidA, ciaB, ceuE, and cgtB genes. Campylobacter spp. were detected in 74 out of 740 Agaricus mushroom samples (10%). According to the data, Agaricus mushroom samples included 32 (4.32%) C. jejuni, 11 (1.48%) C. coli, and 31 (4.18%) other Campylobacter spp. Antimicrobial resistance was most common in C. jejuni isolates. C. jejuni isolates also had the lowest resistance rate to gentamycin, ciprofloxacin, and nalidixic acid. C. coli isolates were reported to have the highest antimicrobial resistance to ciprofloxacin, ampicillin, and erythromycine. Resistance to gentamycin and amoxicillin+ clavulanic acid was likewise lowest among C. coli strains. The flaA and ciaB genes were found in 100% of B-lactams-susceptible C. jejuni and C. coli strains. When examining the relationship between antibiotic resistance and the existence of virulence genes, it was observed that there is a statistically significant relationship (p < 0.001) between bacterial resistance and virulence genes. Our findings indicated that changes in resistance patterns in Campylobacter strains have emerged from multiple treatment approaches in Agaricus mushrooms.
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Borovikov S, Tursunov K, Syzdykova A, Begenova A, Zhakhina A. Expression of recombinant Omp18 and MOMP of Campylobacter jejuni and the determination of their suitability as antigens for serological diagnosis of campylobacteriosis in animals. Vet World 2023; 16:222-228. [PMID: 36855354 PMCID: PMC9967712 DOI: 10.14202/vetworld.2023.222-228] [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: 09/30/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
Background and Aim Campylobacteriosis causes gastrointestinal tract lesions in adults and children and may result in severe complications. The primary sources of infection are infected animals and animal products. Immunochemical methods effectively diagnose intestinal infections but require highly specific antigens to detect their antibodies. This study aimed to obtain two recombinant immunogenic antigens of Campylobacter jejuni, an outer membrane protein with a molecular weight of 18 kDa (Omp18) and the major outer membrane protein (MOMP) with a molecular weight of 45 kDa, and evaluate their suitability for the serological diagnosis of campylobacteriosis using immunochromatographic assay (ICA). Materials and Methods The C. jejuni Omp18 and MOMP gene sequences were synthesized de novo (Macrogen, Korea) and cloned into the pET32 expression plasmid. Using these genetic constructs, electrocompetent cells of the Escherichia coli BL21 strain were transformed and cultured under various conditions. Antigens were purified and refolded using metal affinity chromatography. The properties of the purified proteins were studied by western blotting, liquid chromatography with tandem mass spectrometry, and enzyme-linked immunosorbent assay (ELISA). Results We developed two recombinant E. coli BL21 cells producing rOmp18 and Recombinant MOMP (rMOMP) antigens with molecular weights of 36 and 64 kDa, respectively. Amino acid sequence analysis of the obtained antigens showed complete homology with the reference sequences in the PubMed NCBI database. Western blotting using positive-control sera demonstrated the specificity of the recombinant antigens. The results of ELISA with 94 bovine sera showed the interaction of recombinant antigens with specific antibodies. Conclusion The obtained rOmp18 and rMOMP antigens can detect antibodies in the serum of infected or recovered animals and can be used to develop ICA.
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Affiliation(s)
- Sergey Borovikov
- Department of Microbiology and Biotechnology, Faculty of Veterinary and Animal Husbandry Technology, S. Seifullin Kazakh Agro Technical University, 010000, Astana, Kazakhstan,Corresponding author: Sergey Borovikov, e-mail: Co-authors: KT: , AS: , AB: , AZ:
| | - Kanat Tursunov
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, 010000, Astana, Kazakhstan
| | - Alfiya Syzdykova
- Department of Microbiology and Biotechnology, Faculty of Veterinary and Animal Husbandry Technology, S. Seifullin Kazakh Agro Technical University, 010000, Astana, Kazakhstan
| | - Ainagul Begenova
- Department of Microbiology and Biotechnology, Faculty of Veterinary and Animal Husbandry Technology, S. Seifullin Kazakh Agro Technical University, 010000, Astana, Kazakhstan
| | - Alfira Zhakhina
- Department of Microbiology and Biotechnology, Faculty of Veterinary and Animal Husbandry Technology, S. Seifullin Kazakh Agro Technical University, 010000, Astana, Kazakhstan
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11
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Deblais L, Jang H, Kauffman M, Gangiredla J, Sawyer M, Basa S, Poelstra JW, Babu US, Harrison LM, Hiett KL, Balan KV, Rajashekara G. Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio. Front Microbiol 2023; 14:1074548. [PMID: 37025625 PMCID: PMC10071015 DOI: 10.3389/fmicb.2023.1074548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States. Methods The goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020. Results A total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3'-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%). Discussion/Conclusion Our study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.
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Affiliation(s)
- Loic Deblais
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Hyein Jang
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Mike Kauffman
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Marianne Sawyer
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Saritha Basa
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Uma S. Babu
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Lisa M. Harrison
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kelli L. Hiett
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kannan V. Balan
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Gireesh Rajashekara
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
- *Correspondence: Gireesh Rajashekara,
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Prendergast DM, Lynch H, Whyte P, Golden O, Murphy D, Gutierrez M, Cummins J, Johnston D, Bolton D, Coffey A, Lucey B, O'Connor L, Byrne W. Genomic diversity, virulence and source of Campylobacter jejuni contamination in Irish poultry slaughterhouses by whole genome sequencing. J Appl Microbiol 2022; 133:3150-3160. [PMID: 35993276 PMCID: PMC9804324 DOI: 10.1111/jam.15753] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/12/2022] [Accepted: 07/28/2022] [Indexed: 01/05/2023]
Abstract
AIMS The aim was to exploit whole genome sequencing (WGS) to assess genomic diversity, identify virulence genes and deduce the proportion of Campylobacter colonized broilers that directly contaminate their carcasses. METHODS AND RESULTS Campylobacter jejuni isolates (107) from caeca and carcass neck skin samples (50 pairs from the same batch plus 7 individual caeca) sampled at three poultry slaughterhouses over a one-year period were selected for sequencing (MiSeq; Illumina). FastQ files were submitted to BioNumerics for analysis using the wgMLST scheme for allele calling. Campylobacter cgMLST and hierarchical clustering was performed by applying the single linkage algorithm. Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into clonal complexes (CCs) using the Campylobacter PubMLST.org database. Virulence genes were determined by downloading core sequences from the virulence factor database (VFDB) and the National Center for Biotechnology Information (NCBI). A high degree of diversity was observed with 23 different STs identified. ST257 and CC-21 were the most common STs and CCs, respectively. cgMLST analysis suggested that 56% of carcass contamination was a direct result of contamination from caeca from the same batch. Virulence genes known to play a role in human C. jejuni infection were identified such as the wlaN gene and the genes associated with lipooligosaccharide synthesis, which were identified in 30% of isolates. CONCLUSIONS Caecal colonization was the more plausible occurring source of C. jejuni contamination of broiler carcasses, compared with cross-contamination from another batch or the environment. The high rate of genetic diversity observed amongst caecal isolates is consistent with a wide variety of Campylobacter strains circulating in poultry flocks in Ireland. SIGNIFICANCE AND IMPACT OF STUDY The results will further inform broiler processors and regulators about the influence and importance of on-farm colonization versus slaughterhouse cross-contamination and the relationship between C. jejuni in caeca and carcasses during processing.
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Affiliation(s)
| | - Helen Lynch
- Department of Agriculture, Food and the MarineCelbridgeIreland,School of Veterinary Medicine, Veterinary Science CentreUniversity College DublinDublin 4Ireland
| | - Paul Whyte
- School of Veterinary Medicine, Veterinary Science CentreUniversity College DublinDublin 4Ireland
| | - Olwen Golden
- Department of Agriculture, Food and the MarineCelbridgeIreland
| | - Declan Murphy
- Department of Agriculture, Food and the MarineCelbridgeIreland
| | | | - Juliana Cummins
- Department of Agriculture, Food and the MarineCelbridgeIreland
| | - Dayle Johnston
- Department of Agriculture, Food and the MarineCelbridgeIreland
| | | | - Aidan Coffey
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Brigid Lucey
- Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Lisa O'Connor
- Food Safety Authority of Ireland, IFSCDublin 1Ireland
| | - William Byrne
- Department of Agriculture, Food and the MarineCelbridgeIreland
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Gürbüz M, İrem Omurtag Korkmaz B. The anti-campylobacter activity of eugenol and its potential for poultry meat safety: A review. Food Chem 2022; 394:133519. [PMID: 35749879 DOI: 10.1016/j.foodchem.2022.133519] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/04/2022]
Abstract
Poultry is one of the fastest growing industries due to advantages in land use, rapid production and advances in feed technology. The rising trend in the consumption of poultry meat over the last 50 years has also increased concerns about food safety. Campylobacter jejuniis the leading bacterial cause of gastroenteritis, the foremost cause of foodborne deaths. Despite significant progress in food safety methology, the genusCampylobacter remains a common foodborne pathogen in poultry. Increasing consumer demands for natural products require the discovery of new antimicrobials to ensure the safety of poultry meat. Recent studies have revealed that eugenol acts with antimicrobial activity on a wide variety of foodborne microorganisms. Eugenol is generally recognized as safe and is a promising preservative for the food industry. However, specific applications of eugenol need to be identified and validated to clarify the role of the food preservative in poultry meat safety.
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Affiliation(s)
- Murat Gürbüz
- Trakya University, Department of Nutrition and Dietetics, Edirne, Turkey.
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