1
|
Chinivasagam HN, Estella W, Finn D, Mayer DG, Rodrigues H, Diallo I. Broiler farming practices using new or re-used bedding, inclusive of free-range, have no impact on Campylobacter levels, species diversity, Campylobacter community profiles and Campylobacter bacteriophages. AIMS Microbiol 2024; 10:12-40. [PMID: 38525040 PMCID: PMC10955168 DOI: 10.3934/microbiol.2024002] [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: 08/03/2023] [Revised: 11/27/2023] [Accepted: 12/25/2023] [Indexed: 03/26/2024] Open
Abstract
A multi-stage option to address food-safety can be produced by a clearer understanding of Campylobacter's persistence through the broiler production chain, its environmental niche and its interaction with bacteriophages. This study addressed Campylobacter levels, species, genotype, bacteriophage composition/ levels in caeca, litter, soil and carcasses across commercial broiler farming practices to inform on-farm management, including interventions. Broilers were sequentially collected as per company slaughter schedules over two-years from 17 farms, which represented four commercially adopted farming practices, prior to the final bird removal (days 39-53). The practices were conventional full clean-out, conventional litter re-use, free-range-full cleanout and free-range-litter re-use. Caeca, litter and soil collected on-farm, and representative carcases collected at the processing plant, were tested for Campylobacter levels, species dominance and Campylobacter bacteriophages. General community profiling via denaturing gradient gel electrophoresis of the flaA gene was used to establish the population relationships between various farming practices on representative Campylobacter isolates. The farming practice choices did not influence the high caeca Campylobacter levels (log 7.5 to log 8.5 CFU/g), the carcass levels (log 2.5 to log 3.2 CFU/carcass), the C. jejuni/C. coli dominance and the on-farm bacteriophage presence/levels. A principal coordinate analysis of the flaA distribution for farm and litter practices showed strong separation but no obvious farming practice related grouping of Campylobacter. Bacteriophages originated from select farms, were not practice-dependent, and were detected in the environment (litter) only if present in the birds (caeca). This multifaceted study showed no influence of farming practices on on-farm Campylobacter dynamics. The significance of this study means that a unified on-farm risk-management could be adopted irrespective of commercial practice choices to collectively address caeca Campylobacter levels, as well as the potential to include Campylobacter bacteriophage biocontrol. The impact of this study means that there are no constraints in re-using bedding or adopting free-range farming, thus contributing to environmentally sustainable (re-use) and emerging (free-range) broiler farming choices.
Collapse
Affiliation(s)
| | - Wiyada Estella
- Department of Agriculture and Fisheries, Eco Sciences Precinct, Dutton Park QLD 4102, Australia
| | - Damien Finn
- Department of Agriculture and Fisheries, Eco Sciences Precinct, Dutton Park QLD 4102, Australia
| | - David G. Mayer
- Department of Agriculture and Fisheries, Eco Sciences Precinct, Dutton Park QLD 4102, Australia
| | - Hugh Rodrigues
- Department of Agriculture and Fisheries, Eco Sciences Precinct, Dutton Park QLD 4102, Australia
| | - Ibrahim Diallo
- Department of Agriculture and Fisheries, Biosecurity Sciences Laboratory, Coopers Plains QLD 4108
| |
Collapse
|
2
|
Torky HA, Saad HM, Khaliel SA, Kassih AT, Sabatier JM, Batiha GES, Hetta HF, Elghazaly EM, De Waard M. Isolation and Molecular Characterization of Corynebacterium pseudotuberculosis: Association with Proinflammatory Cytokines in Caseous Lymphadenitis Pyogranulomas. Animals (Basel) 2023; 13:ani13020296. [PMID: 36670836 PMCID: PMC9854522 DOI: 10.3390/ani13020296] [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: 11/22/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Corynebacterium pseudotuberculosis (C. pseudotuberculosis) is a causative agent of numerous chronic diseases, including caseous lymphadenitis (CLA) in sheep and goats, which has a zoonotic potential in humans in addition to a poor therapeutic response. In this study, out of 120 collected samples, only 12 (10%) were positive for C. pseudotuberculosis by PCR and by intraperitoneal injection of male Guinea pigs and then characterized for antimicrobial susceptibility and its genetic-relatedness by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), which showed 2-4 bands ranging from 100 to 3000 bp that can be clustered into four clusters (C1-C4). Despite the serotype biovar 1 only infecting sheep and goats, ERIC-PCR reveals intra-subtyping variation. Examination of affected LNs and organs revealed marked enlargement with either thick creamy green pus or multiple abscesses of variable sizes with a central caseated core surrounded by dense fibrous capsule. A histopathological examination revealed a central necrotic core surrounded by a peripheral mantle of mononuclear cells and a fibrous capsule. Positive immune expression of nuclear factor kappa B (NF-κB/p65) and interleukin-1β (IL-1β) and negative expression of tumor necrosis factor (TNF) in CLA is the first report to our knowledge. Conclusion: In CLA pyogranulomas, IL1β is a more crucial proinflammatory cytokine than TNF in the regulation of C. pseudotuberculosis infection, which is accompanied by marked NF-κB immunoexpression. Therefore, the NF-κB/p65 signaling pathway is involved in the activation of IL1β, and additional immunohistochemical studies are required to determine the various roles of NF-κB/p65 in the inflammatory response within CLA pyogranulomas to control this pathogen.
Collapse
Affiliation(s)
- Helmy A. Torky
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Abees, Alexandria 21523, Egypt
| | - Hebatallah M. Saad
- Department of Pathology, Faculty of Veterinary Medicine, Matrouh University, Marsa Matruh 51744, Egypt
- Correspondence: (H.M.S.); (M.D.W.)
| | - Samy A. Khaliel
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Abees, Alexandria 21523, Egypt
| | - Asmaa T. Kassih
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Abees, Alexandria 21523, Egypt
| | - Jean-Marc Sabatier
- Institut de Neurophysiopathologie (INP), CNRS UMR 7051, Faculté des Sciences Médicales et Paramédicales, Aix-Marseille Université, 27 Bd Jean Moulin, F-13005 Marseille, France
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Eman M. Elghazaly
- Department of Microbiology, Faculty of Veterinary Medicine, Matrouh University, Marsa Matruh 51744, Egypt
| | - Michel De Waard
- Smartox Biotechnology, 6 Rue des Platanes, F-38120 Saint-Egrève, France
- L’institut Du Thorax, INSERM, CNRS, UNIV NANTES, F-44007 Nantes, France
- LabEx «Ion Channels, Science & Therapeutics», Université de Nice Sophia-Antipolis, F-06560 Valbonne, France
- Correspondence: (H.M.S.); (M.D.W.)
| |
Collapse
|
3
|
Gomes CN, Barker DOR, Duque SDS, Che EV, Jayamanna V, Taboada EN, Falcão JP. Campylobacter coli isolated in Brazil typed by core genome Multilocus Sequence Typing shows high genomic diversity in a global context. INFECTION GENETICS AND EVOLUTION 2021; 95:105018. [PMID: 34332158 DOI: 10.1016/j.meegid.2021.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Campylobacter has been one of the most common causative agent of bacterial food-borne gastroenteritis in humans worldwide. However, in Brazil the campylobacteriosis has been a neglected disease and there is insufficient data to estimate the incidence of this pathogen in the country. AIMS The current study aimed to determine the phylogenetic relationships among Campylobacter coli strains isolated in Brazil and to compare them with international Campylobacter isolates available in some public databases. METHODS AND RESULTS A total of 63C. coli strains isolated in Brazil were studied. The MLST analysis showed 18 different STs including three STs not yet described in the PubMLST database. The cgMLST allocated the Brazilian strains studied into five main clusters and each cluster comprised groups of strains with nearly identical cgMLST profiles and with significant genetic distance observed among the distinct clusters. The comparison of the Brazilian strains with 3401 isolates from different countries showed a wide distribution of these strains isolated in this country. CONCLUSIONS The results showed a high similarity among some strains studied and a wide distribution of the Brazilian strains when compared to isolates from different countries, which is an interesting data set since it showed a high genetic diversity of these strains from Brazil in a global context. This study contributed for a better genomic characterization of C. coli strains isolated in Brazil and provided important information about the diversity of this clinically-relevant pathogen.
Collapse
Affiliation(s)
- Carolina Nogueira Gomes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | - Emily Victoria Che
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Vasena Jayamanna
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
| |
Collapse
|
4
|
Molecular Detection of Drug-Resistance Genes of blaOXA-23-blaOXA-51 and mcr-1 in Clinical Isolates of Pseudomonas aeruginosa. Microorganisms 2021; 9:microorganisms9040786. [PMID: 33918745 PMCID: PMC8069495 DOI: 10.3390/microorganisms9040786] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa has caused high rates of mortality due to the appearance of strains with multidrug resistance (MDR) profiles. This study aimed to characterize the molecular profile of virulence and resistance genes in 99 isolates of P. aeruginosa recovered from different clinical specimens. The isolates were identified by the automated method Vitek2, and the antibiotic susceptibility profile was determined using different classes of antimicrobials. The genomic DNA was extracted and amplified by multiplex polymerase chain reaction (mPCR) to detect different virulence and antimicrobial resistance genes. Molecular typing was performed using the enterobacterial repetitive intergenic consensus (ERIC-PCR) technique to determine the clonal relationship among P. aeruginosa isolates. The drug susceptibility profiles of P. aeruginosa for all strains showed high levels of drug resistance, particularly, 27 (27.3%) isolates that exhibited extensively drug-resistant (XDR) profiles, and the other isolates showed MDR profiles. We detected the polymyxin E (mcr-1) gene in one strain that showed resistance against colistin. The genes that confer resistance to oxacillin (blaOXA-23 and blaOXA-51) were present in three isolates. One of these isolates carried both genes. As far as we know from the literature, this is the first report of the presence of blaOXA-23 and blaOXA-51 genes in P. aeruginosa.
Collapse
|
5
|
Frazão MR, de Souza RA, Medeiros MIC, da Silva Duque S, Cao G, Allard MW, Falcão JP. Molecular typing of Campylobacter jejuni strains: comparison among four different techniques. Braz J Microbiol 2020; 51:519-525. [PMID: 31872391 PMCID: PMC7203312 DOI: 10.1007/s42770-019-00218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/17/2019] [Indexed: 11/29/2022] Open
Abstract
This study compared the ability of pulsed-field gel electrophoresis (PFGE), flaA small variable region (SVR) sequencing, analysis of the clustered regularly interspaced short palindromic repeats locus by high resolution melting analysis (CRISPR-HRMA), and multilocus sequence typing (MLST) for typing 111 Campylobacter jejuni strains isolated from diverse sources during 20 years in Brazil. For this, we used previous results obtained by PFGE and flaA-SVR sequencing from our research group and performed CRISPR-HRMA and MLST typing for the first time. Furthermore, the discrimination index (DI) of each method was accessed. The DI for PFGE, flaA-SVR sequencing, CRISPR-HRMA, and MLST was 0.980, 0.932, 0.868, and 0.931, respectively. By PFGE and flaA-SVR sequencing, some strains from clinical and non-clinical sources and from humans and animals presented ≥ 80% similarity. Similarly, some strains from different origins presented the same ST and CRISPR-HRMA types. In conclusion, despite the different DI values, all assays provided the same epidemiological information suggesting that a potential transmission may have occurred between C. jejuni from clinical and non-clinical sources and from animals and humans in Brazil. Furthermore it was demonstrated the suitability of PFGE that should be used preferably together with MLST and/or flaA-SVR sequencing for typing C. jejuni strains.
Collapse
Affiliation(s)
- Miliane Rodrigues Frazão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, FCFRP-USP, Av. do Café, s/n°- Campus Universitário USP, Ribeirão Preto, SP 14040-903 Brazil
| | - Roberto Antonio de Souza
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, FCFRP-USP, Av. do Café, s/n°- Campus Universitário USP, Ribeirão Preto, SP 14040-903 Brazil
| | | | - Sheila da Silva Duque
- Fundação Oswaldo Cruz (Fiocruz), Instituto Oswaldo Cruz, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ 21040-900 Brazil
| | - Guojie Cao
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740 USA
| | - Marc William Allard
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740 USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, FCFRP-USP, Av. do Café, s/n°- Campus Universitário USP, Ribeirão Preto, SP 14040-903 Brazil
| |
Collapse
|
6
|
Kiatsomphob S, Taniguchi T, Tarigan E, Latt KM, Jeon B, Misawa N. Aerotolerance and multilocus sequence typing among Campylobacter jejuni strains isolated from humans, broiler chickens, and cattle in Miyazaki Prefecture, Japan. J Vet Med Sci 2019; 81:1144-1151. [PMID: 31270309 PMCID: PMC6715926 DOI: 10.1292/jvms.19-0228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is one of the leading causes of human gastroenteritis in Japan. As chickens and cattle are common reservoirs for C. jejuni, this microaerophilic, stress-sensitive bacterium can overcome and survive various stress conditions during zoonotic transmission, particularly foodborne, to humans. How C. jejuni overcomes stress conditions is, however, unclear. In the present study, 70 C. jejuni strains isolated from various sources (26 human, 20 broilers, and 24 cattle isolates) in Miyazaki, Japan, from 2010 to 2012, were subjected to multilocus sequence typing (MLST) and aerotolerance testing (aerobic shaking at 200 rpm). The results demonstrated that C. jejuni strains from Miyazaki belonged to 12 clonal complexes (CCs) and 43 sequence types (STs). CC-21 and CC-460 were mainly detected in human clinical strains. Most tested strains were aerotolerant, and only one (1.4%) was deemed sensitive to aerobic stress. Approximately 40% strains survived the 24-hr vigorous aerobic shaking at 200 rpm, and these hyper-aerotolerant strains were more prevalent in broiler and cattle isolates than in human isolates. Phylogenetic analysis divided the strains into five clusters, each showing a different pattern of host association. Thus, we have demonstrated for the first time that C. jejuni strains with increased tolerance to aerobic stress are highly prevalent in broilers and cattle in Miyazaki, Japan, and that certain clonal populations are frequently implicated in human infection in this area.
Collapse
Affiliation(s)
- Savek Kiatsomphob
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kihara-kiyotakecho, Miyazaki 889-1692, Japan.,Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Takako Taniguchi
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Elpita Tarigan
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Khin Maung Latt
- Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| | - Byeonghwa Jeon
- School of Public Health, University of Alberta, Edmonton, AB, T6G 1C9, Canada
| | - Naoaki Misawa
- Laboratory of Veterinary Public Health, Department of Veterinary Medical Science, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan.,Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki 889-2192, Japan
| |
Collapse
|
7
|
Bisma G, Sabia Q, Amin KZ, Ahmad WS, Nabi MS, Ahmad MF, Isfaqul HM, Aasim H, Ali RM, Shafkat Majeed K, Rafia M, Shafi SM. RFLP analysis of flagellin ( Fla
) gene of Campylobacter jejuni
from ovines of Kashmir, India. J Food Saf 2018. [DOI: 10.1111/jfs.12509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Gull Bisma
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Qureshi Sabia
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Kashoo Zahid Amin
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Wani Shakil Ahmad
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Magray Suhail Nabi
- Disease Investigation Laboratory, Department of Sheep Husbandry; Nowhsera Jammu and Kashmir India
| | - Malik Firdose Ahmad
- Temperate Sericulture Research Institute, SKUAST-K; Mirgund Jammu and Kashmir India
| | - Hussain M. Isfaqul
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Habib Aasim
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Rather Mudasir Ali
- Division of Veterinary Public Health; FVSc &AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Khan Shafkat Majeed
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Maqbool Rafia
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| | - Shah Muneeba Shafi
- Bacteriology Laboratory; FVSc & AH, Shuhama (Aulesteng), SKUAST-K; Srinagar Jammu and Kashmir India
| |
Collapse
|
8
|
Multilocus sequence analysis of Echinococcus granulosus strains isolated from humans and animals in Iran. Exp Parasitol 2017; 183:50-55. [DOI: 10.1016/j.exppara.2017.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/12/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022]
|
9
|
Frazão MR, Medeiros MIC, Duque SDS, Falcão JP. Pathogenic potential and genotypic diversity of Campylobacter jejuni: a neglected food-borne pathogen in Brazil. J Med Microbiol 2017; 66:350-359. [PMID: 28317494 DOI: 10.1099/jmm.0.000424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose and methodology.Campylobacter jejuni is a major zoonotic pathogen that causes food-borne gastroenteritis worldwide. However, there are only a few studies available that have molecularly characterized C. jejuni strains isolated in Brazil. The aim of this study was to genotype 111 C. jejuni strains isolated from sick humans (43), monkey faeces (19), chicken faeces (14), chicken meat (33) and sewage (2) between 1996 and 2016 in Brazil using flaA-SVR (short variable region) sequencing and PFGE. Furthermore, the presence of 16 virulence genes was analysed by PCR. RESULTS Using PFGE and flaA-SVR sequencing, the 111 C. jejuni strains studied were grouped into three and two clusters, respectively, and some strains of different origin presented a similarity of ≥80 %. In total, 35 flaA-SVR alleles were detected. Alleles gt45, gt49 and gt57 were the most prevalent, in contrast with those frequently described in the PubMLST database. All 111 C. jejuni strains contained the genes flaA, flhA, cadF, docA, cdtA, cdtB, cdtC, iamA, ciaB, sodB, dnaJ, pldA, racR and csrA. The wlaN gene was detected in 11 strains (9.9 %), and the virB11 in just one strain (0.9 %). CONCLUSIONS In conclusion, the pathogenic potential of the C. jejuni strains studied was highlighted by the high frequency of the majority of the virulence genes searched. The flaA-SVR sequencing and PFGE results showed that some of the strains studied presented a high genotypic similarity, suggesting potential for transmission between animal sources and humans in this country. Altogether, the results characterize further C. jejuni isolates from Brazil, an important producer and exporter of chicken meat.
Collapse
Affiliation(s)
- Miliane Rodrigues Frazão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
10
|
Clark CG, Berry C, Walker M, Petkau A, Barker DOR, Guan C, Reimer A, Taboada EN. Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population. BMC Genomics 2016; 17:990. [PMID: 27912729 PMCID: PMC5135748 DOI: 10.1186/s12864-016-3340-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates. RESULTS Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain. CONCLUSIONS The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.
Collapse
Affiliation(s)
- Clifford G. Clark
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Chrystal Berry
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Matthew Walker
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Aaron Petkau
- Bioinformatics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2 Canada
| | - Dillon O. R. Barker
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| | - Cai Guan
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Aleisha Reimer
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2 Canada
| | - Eduardo N. Taboada
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB Canada
| |
Collapse
|
11
|
Lucarelli C, Dionisi AM, Trezzi L, Farina C, Passera M, Kärki T, D'Ancona F, Luzzi I. Molecular and Epidemiological Analysis of aCampylobacter jejuniOutbreak in Northern Italy in November 2013. Foodborne Pathog Dis 2016; 13:490-4. [DOI: 10.1089/fpd.2015.2104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Claudia Lucarelli
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- Istituto Superiore di Sanità, Rome, Italy
| | | | - Livia Trezzi
- Azienda Sanitaria Locale di Bergamo, Rome, Italy
| | | | - Marco Passera
- Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Tommi Kärki
- Istituto Superiore di Sanità, Rome, Italy
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Ida Luzzi
- Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
12
|
Prevalence, genetic diversity and antimicrobial susceptibility of Campylobacter jejuni isolated from retail food in China. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.09.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
13
|
Muhamadali H, Weaver D, Subaihi A, AlMasoud N, Trivedi DK, Ellis DI, Linton D, Goodacre R. Chicken, beams, and Campylobacter: rapid differentiation of foodborne bacteria via vibrational spectroscopy and MALDI-mass spectrometry. Analyst 2015; 141:111-22. [PMID: 26523729 DOI: 10.1039/c5an01945a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Campylobacter species are one of the main causes of food poisoning worldwide. Despite the availability of established culturing and molecular techniques, due to the fastidious nature of these microorganisms, simultaneous detection and species differentiation still remains challenging. This study focused on the differentiation of eleven Campylobacter strains from six species, using Fourier transform infrared (FT-IR) and Raman spectroscopies, together with matrix-assisted laser desorption ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), as physicochemical approaches for generating biochemical fingerprints. Cluster analysis of data from each of the three analytical approaches provided clear differentiation of each Campylobacter species, which was generally in agreement with a phylogenetic tree based on 16S rRNA gene sequences. Notably, although C. fetus subspecies fetus and venerealis are phylogenetically very closely related, using FT-IR and MALDI-TOF-MS data these subspecies were readily differentiated based on differences in the lipid (2920 and 2851 cm(-1)) and fingerprint regions (1500-500 cm(-1)) of the FT-IR spectra, and the 500-2000 m/z region of the MALDI-TOF-MS data. A finding that was further investigated with targeted lipidomics using liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that such metabolomics approaches combined with molecular biology techniques may provide critical information and knowledge related to the risk factors, virulence, and understanding of the distribution and transmission routes associated with different strains of foodborne Campylobacter spp.
Collapse
Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Comparative analysis of antimicrobial resistance and genetic diversity of Campylobacter from broilers slaughtered in Poland. Int J Food Microbiol 2015; 210:24-32. [PMID: 26092707 DOI: 10.1016/j.ijfoodmicro.2015.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/12/2015] [Accepted: 06/09/2015] [Indexed: 02/01/2023]
Abstract
In the current study, the relationship of Campylobacter jejuni and Campylobacter coli strains isolated at slaughter was investigated using comparative analysis of antimicrobial resistance (AMR), virulence gene (VG) and PFGE profiling. A total of 254 Campylobacter isolates from poultry caeca and corresponding carcasses, including 139 C. jejuni and 115 C. coli strains were tested. The most prevalent resistance profiles observed in C. jejuni were ciprofloxacin, nalidixic acid and tetracycline (46 out of 139, 33.1% isolates) as well as ciprofloxacin, nalidixic acid, tetracycline and streptomycin among C. coli strains (34 out of 115, 29.6%). Multi-resistance was found more frequently among C. coli than C. jejuni (P<0.05). The presence of 11 virulence genes exhibited 19 different VG profiles in Campylobacter isolates tested. All Campylobacter strains were classified into 154 different PFGE types. Among them, 56 profiles (28 C. jejuni and 28 C. coli) were common for at least two isolates including 9 clusters covering from 4 to 9 strains. Campylobacter composite types generated by a combination of 154 PFGE types, 10 AMR profiles and 19 VG patterns divided 178 distinct types with 95% similarity. The majority of the composite profiles (76 for C. jejuni and 58 for C. coli; 75.3% in total) included only one bacterial isolate. Furthermore, 11 pairs of C. jejuni and 12 pairs of C. coli from caeca and the corresponding carcasses isolated from the same places possessed the identical PFGE, AMR and VG patterns. This study demonstrated that C. jejuni and C. coli isolated from poultry in Poland showed to have a high genetic diversity and a weak clonal population structure. However, the composite analysis revealed a strong evidence for cross-contamination of chicken carcasses during the slaughter process. Additionally, our results confirm that Campylobacter may easily contaminate poultry carcasses at slaughter process and spread around country. More than half of Campylobacter strains tested (50.4%) were resistant to at least two classes of antimicrobials, i.e. quinolones and tetracyclines, which may cause a public health risk.
Collapse
|
15
|
Same-day subtyping of Campylobacter jejuni and C. coli isolates by use of multiplex ligation-dependent probe amplification-binary typing. J Clin Microbiol 2014; 52:3345-50. [PMID: 24989612 DOI: 10.1128/jcm.00815-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Campylobacteriosis is the most commonly reported form of human bacterial gastroenteritis in the world. Sound identification of infectious sources requires subtyping, but the most widely used methods have turnaround times measured in days and require specialist equipment and skills. A multiplex ligation-dependent probe amplification-binary typing (MBiT) assay was developed for subtyping Campylobacter jejuni and Campylobacter coli. It was tested on 245 isolates, including recent isolates from Belgium and New Zealand, and compared to multilocus sequence typing (MLST). When used in an outbreak setting, MBiT identified the predominant genotype and possible additional cases days before pulsed-field gel electrophoresis (PFGE) results were available. MBiT was more discriminatory than MLST and, being a single assay with results produced within 6 h, was more rapid and cost-effective than both MLST and PFGE. In addition, MBiT requires only basic molecular biology equipment and skills.
Collapse
|
16
|
Bronowski C, James CE, Winstanley C. Role of environmental survival in transmission of Campylobacter jejuni. FEMS Microbiol Lett 2014; 356:8-19. [PMID: 24888326 DOI: 10.1111/1574-6968.12488] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 11/29/2022] Open
Abstract
Campylobacter species are the most common cause of bacterial gastroenteritis, with C. jejuni responsible for the majority of these cases. Although it is clear that livestock, and particularly poultry, are the most common source, it is likely that the natural environment (soil and water) plays a key role in transmission, either directly to humans or indirectly via farm animals. It has been shown using multilocus sequence typing that some clonal complexes (such as ST-45) are more frequently isolated from environmental sources such as water, suggesting that strains vary in their ability to survive in the environment. Although C. jejuni are fastidious microaerophiles generally unable to grow in atmospheric levels of oxygen, C. jejuni can adapt to survival in the environment, exhibiting aerotolerance and starvation survival. Biofilm formation, the viable but nonculturable state, and interactions with other microorganisms can all contribute to survival outside the host. By exploiting high-throughput technologies such as genome sequencing and RNA Seq, we are well placed to decipher the mechanisms underlying the variations in survival between strains in environments such as soil and water and to better understand the role of environmental persistence in the transmission of C. jejuni directly or indirectly to humans.
Collapse
Affiliation(s)
- Christina Bronowski
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | | |
Collapse
|
17
|
Ahmed MU, Dunn L, Valcanis M, Hogg G, Ivanova EP. Double-locus sequence typing using porA and peb1A for epidemiological studies of Campylobacter jejuni. Foodborne Pathog Dis 2013; 11:194-9. [PMID: 24404778 DOI: 10.1089/fpd.2013.1634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is the leading cause of foodborne bacterial gastroenteritis worldwide. Bacterial typing schemes play an important role in epidemiological investigations to trace the source and route of transmission of the infectious agent by identifying outbreak and differentiating among sporadic infections. In this study, a double-locus sequence typing (DLST) scheme for C. jejuni based on concatenated partial sequences of porA and peb1A genes is proposed. The DLST scheme was validated using 50 clinical and environmental C. jejuni strains isolated from human (C5, H, H15-H19), chicken (CH1-CH15), water (W2-W17), and ovine samples (OV1-OV6). The scheme was found to be highly discriminatory (discrimination index [DI]=0.964) and epidemiologically concordant based on C. jejuni strains studied. The DLST showed discriminatory power above 0.95 and excellent congruence to multilocus sequence typing and can be recommended as a rapid and low-cost typing scheme for epidemiological investigation of C. jejuni. It is suggested that the DLST scheme is suitable for identification of outbreak strains and differentiation of the sporadic infection strains.
Collapse
Affiliation(s)
- Monir U Ahmed
- 1 Faculty of Life and Social Sciences, Swinburne University of Technology , Victoria, Australia
| | | | | | | | | |
Collapse
|
18
|
Taboada EN, Clark CG, Sproston EL, Carrillo CD. Current methods for molecular typing of Campylobacter species. J Microbiol Methods 2013; 95:24-31. [PMID: 23871858 DOI: 10.1016/j.mimet.2013.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 12/11/2022]
Abstract
Campylobacter remains one of the most common bacterial causes of gastroenteritis worldwide. Tracking sources of this organism is challenging due to the large numbers of human cases, and the prevalence of this organism throughout the environment due to growth in a wide range of animal species. Many molecular subtyping methods have been developed to characterize Campylobacter species, but only a few are commonly used in molecular epidemiology studies. This review examines the applicability of these methods, as well as the role that emerging whole genome sequencing technologies will play in tracking sources of Campylobacter spp. infection.
Collapse
Affiliation(s)
- Eduardo N Taboada
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, PO Box 640, Township Rd. 9-1, Lethbridge, AB T1J 3Z4, Canada.
| | | | | | | |
Collapse
|
19
|
Asakura H, Taguchi M, Ekawa T, Yamamoto S, Igimi S. Continued widespread dissemination and increased poultry host fitness of Campylobacter jejuni
ST-4526 and ST-4253 in Japan. J Appl Microbiol 2013; 114:1529-38. [DOI: 10.1111/jam.12147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/16/2013] [Accepted: 01/17/2013] [Indexed: 12/12/2022]
Affiliation(s)
- H. Asakura
- Division of Biomedical Food Research; National Institute of Health Sciences; Tokyo Japan
| | - M. Taguchi
- Department of Bacteriology; Osaka Prefectural Institute of Public Health; Osaka Japan
| | - T. Ekawa
- Division of Biomedical Food Research; National Institute of Health Sciences; Tokyo Japan
| | - S. Yamamoto
- Division of Biomedical Food Research; National Institute of Health Sciences; Tokyo Japan
| | - S. Igimi
- Division of Biomedical Food Research; National Institute of Health Sciences; Tokyo Japan
| |
Collapse
|
20
|
Asakura H, Brüggemann H, Sheppard SK, Ekawa T, Meyer TF, Yamamoto S, Igimi S. Molecular evidence for the thriving of Campylobacter jejuni ST-4526 in Japan. PLoS One 2012; 7:e48394. [PMID: 23144873 PMCID: PMC3492356 DOI: 10.1371/journal.pone.0048394] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/01/2012] [Indexed: 12/19/2022] Open
Abstract
Campylobacter jejuni is a leading cause of human gastroenteritis worldwide. This study aimed at a better understanding of the genetic diversity of this pathogen disseminated in Japan. We performed multilocus sequence typing (MLST) of Campylobacter jejuni isolated from different sources (100 human, 61 poultry, and 51 cattle isolates) in Japan between 2005 and 2006. This approach identified 62 sequence types (STs) and 19 clonal complexes (CCs), including 11 novel STs. These 62 STs were phylogenetically divided into 6 clusters, partially exhibiting host association. We identified a novel ST (ST-4526) that has never been reported in other countries; a phylogenetic analysis showed that ST-4526 and related STs showed distant lineage from the founder ST, ST-21 within CC-21. Comparative genome analysis was performed to investigate which properties could be responsible for the successful dissemination of ST-4526 in Japan. Results revealed that three representative ST-4526 isolates contained a putative island comprising the region from Cj0737 to Cj0744, which differed between the ST-4526 isolates and the reference strain NCTC11168 (ST-43/CC-21). Amino acid sequence alignment analyses showed that two of three ST-4526 isolates expressed 693aa- filamentous hemagglutination domain protein (FHA), while most of other C. jejuni strains whose genome were sequenced exhibited its truncation. Correspondingly, host cell binding of FHA-positive C. jejuni was greater than that of FHA-truncated strains, and exogenous administration of rFHA protein reduced cell adhesion of FHA-positive bacteria. Biochemical assays showed that this putative protein exhibited a dose-dependent binding affinity to heparan sulfate, indicating its adhesin activity. Moreover, ST-4526 showed increased antibiotic-resistance (nalidixic acid and fluoroquinolones) and a reduced ability for DNA uptake. Taken together, our data suggested that these combined features contributed to the clonal thriving of ST-4526 in Japan.
Collapse
MESH Headings
- Adhesins, Bacterial/chemistry
- Adhesins, Bacterial/metabolism
- Animals
- Bacterial Adhesion
- Base Sequence
- Biological Evolution
- Campylobacter jejuni/classification
- Campylobacter jejuni/genetics
- Campylobacter jejuni/growth & development
- Campylobacter jejuni/isolation & purification
- Cattle
- DNA, Bacterial/metabolism
- Databases, Genetic
- Drug Resistance, Microbial/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genetic Linkage
- Genetic Loci
- Genetic Variation
- Genome, Bacterial/genetics
- Humans
- Japan
- Lipopolysaccharides/metabolism
- Multilocus Sequence Typing/methods
- N-Acetylneuraminic Acid/metabolism
- Phylogeography
- Poultry/microbiology
- Recombination, Genetic/genetics
- Transformation, Genetic
Collapse
Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Tokyo, Japan.
| | | | | | | | | | | | | |
Collapse
|