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Ghssein G, Barakat R, Nehme N, Awada R, Hassan HF. Fecal prevalence of Campylobacter spp. in house dogs in Lebanon: A pilot study. Vet World 2023; 16:2250-2255. [PMID: 38152257 PMCID: PMC10750756 DOI: 10.14202/vetworld.2023.2250-2255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/12/2023] [Indexed: 12/29/2023] Open
Abstract
Background and Aim Campylobacter spp. are Gram-negative bacilli that are widely recognized as a primary cause of bacterial gastroenteritis worldwide. Campylobacteriosis is the disease caused by this pathogen. Recently, greater attention has been given to the prevalence of campylobacteriosis in different animals, including pets. These animals are considered to be significant reservoirs for this zoonosis. In Lebanon, the occurrence of Campylobacter infection is high. Our first-of-its-kind pilot study in Lebanon aimed to estimate the fecal prevalence of Campylobacter species in house dogs. Materials and Methods Thirty-five rectal swabs were collected from male and female house dogs of different ages, both with or without diarrhea. Samples obtained from the dogs were subjected to qualitative microbiological culture testing and molecular diagnosis by polymerase chain reaction assays after bacterial DNA extraction. Results Fecal prevalence of Campylobacter spp. in house dogs in this study was 17%. There was a relatively higher prevalence among young females and a significant difference between healthy dogs and those suffering from diarrhea. Conclusion Campylobacteriosis was found to be prevalent among house dogs in Lebanon, making them potential carriers of Campylobacter species.
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Affiliation(s)
- Ghassan Ghssein
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon
- Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon
| | - Rana Barakat
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon
- Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon
| | - Nada Nehme
- Department of Environmental Sciences and Natural Resources, Faculty of Agricultural Engineering and Veterinary Medicine, Lebanese University, Dekwaneh, Mount Lebanon, Lebanon
| | - Rana Awada
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon
| | - Hussein F. Hassan
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
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Awada R, Ghssein G, El Roz A, Farhat M, Nehme N, Hassan HF. Prevalence of Campylobacter spp. in broilers in North Lebanon. Vet World 2023; 16:322-328. [PMID: 37041998 PMCID: PMC10082710 DOI: 10.14202/vetworld.2023.322-328] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/13/2023] [Indexed: 02/19/2023] Open
Abstract
Background and Aim: Great attention has been given recently to the prevalence of different Campylobacter spp. in poultry since the latter are considered the major contributing reservoir of human campylobacteriosis. In Lebanon, the occurrence of campylobacteriosis in humans is high. The aim of our first-of-its-kind study in the country was to estimate the prevalence of Campylobacter spp. in broilers from a convenient sample of farms in North Lebanon.
Materials and Methods: One hundred twenty-five fecal samples were collected from 25 broiler farms, which were selected, examined, and classified according to their biosecurity level and rearing system. All samples were subjected to qualitative microbiological culture testing and polymerase chain reaction (PCR) assays to detect Campylobacter spp.
Results: Despite the reported use of antibiotics, cell culture and PCR were positive for 44% and 88%, respectively. This implies that this bacterium is resistant to antibiotics used on the farms. Furthermore, Campylobacter infection rate was higher in open (92%) than in closed (85%) system farms. All farms with poor biosecurity measures, and 82% of farms with good biosecurity measures had Campylobacter infections, and the difference was significant (p < 0.05).
Conclusion: Our results show that campylobacteriosis was found prevalent among broilers in North Lebanon, making them potential carriers of Campylobacter spp. Future studies should include antibiotic susceptibility testing to check the susceptibility pattern of isolates.
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Affiliation(s)
- Rana Awada
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon; Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon
| | - Ghassan Ghssein
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon; Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon
| | - Ali El Roz
- Department of Biology, Faculty of Sciences, Lebanese University, Beirut, Lebanon; Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon; Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Mona Farhat
- Department of Laboratory Sciences, Faculty of Public Health, Islamic University of Lebanon, Beirut, Lebanon
| | - Nada Nehme
- Department of Environmental Sciences and Natural Resources, Faculty of Agricultural Engineering and Veterinary Medicine, Lebanese University, Dekwaneh, Mount Lebanon, Lebanon
| | - Hussein F. Hassan
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
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Effect of Probiotic E. coli Nissle 1917 Supplementation on the Growth Performance, Immune Responses, Intestinal Morphology, and Gut Microbes of Campylobacter jejuni Infected Chickens. Infect Immun 2022; 90:e0033722. [PMID: 36135600 PMCID: PMC9584303 DOI: 10.1128/iai.00337-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Campylobacter jejuni is the most common cause of bacterial foodborne gastroenteritis and holds significant public health importance. The continuing increase of antibiotic-resistant Campylobacter necessitates the development of antibiotic-alternative approaches to control infections in poultry and in humans. Here, we assessed the ability of E. coli Nissle 1917 (EcN; free and chitosan-alginate microencapsulated) to reduce C. jejuni colonization in chickens and measured the effect of EcN on the immune responses, intestinal morphology, and gut microbes of chickens. Our results showed that the supplementation of 3-week-old chickens daily with free EcN in drinking water resulted in a 2.0 log reduction of C. jejuni colonization in the cecum, whereas supplementing EcN orally three times a week, either free or microencapsulated, resulted in 2.0 and 2.5 log reductions of C. jejuni colonization, respectively. Gavaged free and microencapsulated EcN did not have an impact on the evenness or the richness of the cecal microbiota, but it did increase the villous height (VH), crypt depth (CD), and VH:CD ratio in the jejunum and ileum of chickens. Further, the supplementation of EcN (all types) increased C. jejuni-specific and total IgA and IgY antibodies in chicken’s serum. Microencapsulated EcN induced the expression of several cytokines and chemokines (1.6 to 4.3-fold), which activate the Th1, Th2, and Th17 pathways. Overall, microencapsulated EcN displayed promising effects as a potential nonantibiotic strategy to control C. jejuni colonization in chickens. Future studies on testing microencapsulated EcN in the feed and water of chickens raised on built-up floor litter would facilitate the development of EcN for industrial applications to control Campylobacter infections in poultry.
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Greening SS, Zhang J, Midwinter AC, Wilkinson DA, Fayaz A, Williamson DA, Anderson MJ, Gates MC, French NP. Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand's commercial poultry network. Epidemics 2021; 37:100521. [PMID: 34775297 DOI: 10.1016/j.epidem.2021.100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/05/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.
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Affiliation(s)
- Sabrina S Greening
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand.
| | - Ji Zhang
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Ahmed Fayaz
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Deborah A Williamson
- Microbiological Diagnostic Unit and Public Health Laboratory, University of Melbourne, Parkville, Victoria, Australia
| | - Marti J Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - M Carolyn Gates
- Epicentre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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5
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Abdelmageed HA, Mandour AS, El Gedawy AA, Fawzy M, Furuya T, Ezzat M. Characterization of Campylobacter jejuni isolated from dogs and humans using flaA-SVR fragment sequencing in Ismailia, Egypt. Comp Immunol Microbiol Infect Dis 2021; 77:101675. [PMID: 34098505 DOI: 10.1016/j.cimid.2021.101675] [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: 03/25/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Dogs are known as asymptomatic carriers forCampylobacter jejuni. The number of pet dogs is increasing in Egypt in the last decade. OBJECTIVE This study aimed to investigate the frequency ofC. jejuni infection in dogs and humans, molecular typing of associated virulence genes, and flaA-SVR gene using sequencing. METHODOLOGY 152 unpaired fecal swabs from dogs (n = 72) and humans (80) were examined for the presence of C. jejuni and Campylobacter 23S rRNA, and the pathogenicity genes including mapA genes, virB11, flaA, wlaN, iam, tetO, and aadA genes. Sequencing of the flaA- amplicon was also performed for the representative isolates. RESULTS The isolation rate ofC. jejuni was 20.8 % and 31.2 %, respectively in dogs and humans, and all isolates were tested positive for 23S rRNA and mapA genes. C. jejuni harbor virB11 and wlaN (20 %, 0%), iam (10 %, 20 %), tetO and aadA1 (40 %, both), and flaA (40 %, 20 %) in human and dog strains, respectively. The flaA-SVR sequences revealed high identity between human and dog isolates (94.8 %), but revealed 18 substitutions in the amino acid sequence, and showed that the dog and human C. jejuni were close to strains isolated from human and poultry sources. CONCLUSION this study demonstrated the comparative sequence analysis ofC. jejuni flaA-SVR fragment in dogs and some Egyptians, which indicated a high identity percentage between them. The results suggest that C. jejuni reservoirs dogs is an alarming public health concern and effective hygienic measures are necessary for house-holding pets to prevent C. jejuni zoonosis in Egypt's community.
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Affiliation(s)
- Hend A Abdelmageed
- Department of Bacteriology, Animal Health Research Institute, Ismailia lab, First District, Ismailia 41522, Egypt; Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Ahmed S Mandour
- Department of Animal Medicine (Internal Medicine), Faculty of Veterinary Medicine, Suez Canal University, Ring road, Ismailia 41522, Egypt; Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.
| | - Attia A El Gedawy
- Department of Bacteriology, Animal Health Research Institute, P.O. Box 264, Giza 12618, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Tetsuya Furuya
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Mahmoud Ezzat
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ring road, Ismailia 41522, Egypt
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Rivas L, Dupont PY, Gilpin B, Withers H. Prevalence and Genotyping of Campylobacter jejuni and Campylobacter coli from Ovine Carcasses in New Zealand. J Food Prot 2021; 84:14-22. [PMID: 32766835 DOI: 10.4315/jfp-20-220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/03/2020] [Indexed: 02/03/2023]
Abstract
ABSTRACT A pilot survey was performed to determine the prevalence of Campylobacter jejuni and Campylobacter coli on three age classes (lamb, hogget, and mutton) of ovine carcass trim postdressing and prechill. Sampling of hogget carcasses was undertaken 6 months before sampling of lamb and mutton carcasses. A total of 120 trim samples were collected from 11 processing plants across New Zealand. All samples were enriched and screened using PCR for the presence of C. jejuni and C. coli, and isolation was attempted for all screen-positive samples. Enumeration of Campylobacter from lamb trim samples showed that Campylobacter bacteria were present in very low numbers (<10 CFU/g). The overall prevalence of Campylobacter for ovine trim based on PCR detection was 33% (39 of 120 samples), with prevalences for hogget, lamb, and mutton carcass trim of 56% (28 of 50), 11% (4 of 35), and 20% (7 of 35), respectively. Whole genome sequencing was performed on a selection of C. jejuni and C. coli isolates, and the data were used to subtype using multilocus sequence typing (MLST) and whole genome MLST. Twenty-five MLST sequence types (STs) were identified among 44 isolates, including ST42, ST50, ST3222, and ST3072, which have been previously reported to be associated with ruminant sources. Four novel STs were also identified. Whole genome MLST analysis further discriminated isolates within a single ST type and demonstrated a genetic diversity among the ovine isolates collected. Genes associated with the oxacillinase class of β-lactamase enzymes were identified in 41 of 44 Campylobacter isolates. This study provides preliminary data that can be incorporated into existing source attribution models to assist in determining the potential contribution of ovine sources to the burden of campylobacteriosis in New Zealand. HIGHLIGHTS
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Affiliation(s)
- Lucia Rivas
- Institute of Environmental Science and Research, P.O. Box 29181, Christchurch, 8053, New Zealand (ORCID: https://orcid.org/0000-0001-9666-495X [L.R.])
| | - Pierre-Yves Dupont
- Institute of Environmental Science and Research, P.O. Box 29181, Christchurch, 8053, New Zealand (ORCID: https://orcid.org/0000-0001-9666-495X [L.R.])
| | - Brent Gilpin
- Institute of Environmental Science and Research, P.O. Box 29181, Christchurch, 8053, New Zealand (ORCID: https://orcid.org/0000-0001-9666-495X [L.R.])
| | - Helen Withers
- New Zealand Food Safety, Ministry for Primary Industries, P.O. Box 2526, Wellington, 6140, New Zealand
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Szott V, Friese A. Emission Sources of Campylobacter from Agricultural Farms, Impact on Environmental Contamination and Intervention Strategies. Curr Top Microbiol Immunol 2021; 431:103-125. [PMID: 33620650 DOI: 10.1007/978-3-030-65481-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Although extensive research has been carried out to describe the transmission pathways of Campylobacter entering livestock farms, the role of livestock farms as source of Campylobacter contamination of the environment is still poorly investigated. It is assumed that Campylobacter-positive livestock farms contribute to an environmental contamination, depending on the animal species on the farm, their Campylobacter status, the housing system, manure management as well as their general farm hygienic and biosecurity management. Different emission sources, like manure, air, water, insects and rodents as well as personnel, including equipment and vehicles, contribute to Campylobacter emission into the environment. Even though Campylobacter are rather fastidious bacteria, they are able to survive in the environment for even a longer period of time, when environmental conditions enable survival in specific niches. We conclude that a significant reduction of Campylobacter emission in the environment can be successfully achieved if various intervention strategies, depending on the farm type, are applied simultaneously, including proper general and personal hygiene, establishing of hygienic barriers, insect controls, manure management and hygienization of stables, barns and exhaust air.
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Affiliation(s)
- Vanessa Szott
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Centre for Infection Medicine, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Anika Friese
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Centre for Infection Medicine, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany.
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Greening SS, Mulqueen K, Rawdon TG, French NP, Gates MC. Estimating the level of disease risk and biosecurity on commercial poultry farms in New Zealand. N Z Vet J 2020; 68:261-271. [PMID: 32212922 DOI: 10.1080/00480169.2020.1746208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Aims: To collect baseline data on the contact risk pathways and biosecurity practices of commercial poultry farms in New Zealand, investigate the relationship between the farm-level disease contact risks and biosecurity practices, and identify important poultry health concerns of producers. Methods: A cross-sectional survey of all registered New Zealand commercial poultry operations was conducted in 2016 collecting information on farm demographics, biosecurity practices, and contact risk pathways. Survey responses were used to generate an unweighted subjective disease risk score based on eight risk criteria and a subjective biosecurity score based on the frequency with which producers reported implementing seven biosecurity measures. Producer opinions towards poultry health issues were also determined. Results: Responses to the survey response were obtained from 120/414 (29.0%) producers, including 57/157 (36.3%) broiler, 33/169 (19.5%) layer, 24/55 (44%) breeder, and 6/32 (19%) other poultry production types. Median disease risk scores differed between production types (p < 0.001) and were lowest for breeder enterprises. The greatest risk for layer and broiler enterprises was from the potential movement of employees between sheds, and for breeder enterprises was the on- and off-farm movement of goods and services. Median biosecurity scores also differed between production types (p < 0.001), and were highest for breeder and broiler enterprises. Across all sectors there was no statistical correlation between biosecurity scores and disease risk scores. Producers showed a high level of concern over effectively managing biosecurity measures. Conclusions: The uptake of biosecurity measures in the commercial poultry farms surveyed was highly variable, with some having very low scores despite significant potential disease contact risks. This may be related to the low prevalence or absence of many important infectious poultry diseases in New Zealand leading farmers to believe there is a limited need to maintain good biosecurity as well as farmer uncertainty around the efficacy of different biosecurity measures. Further research is needed to understand barriers towards biosecurity adoption including evaluating the cost-effectiveness of biosecurity interventions.
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Affiliation(s)
- S S Greening
- Epicentre, Massey University School of Veterinary Science, Palmerston North, New Zealand
| | - K Mulqueen
- Poultry Industry Association of New Zealand (PIANZ), Auckland, New Zealand
| | - T G Rawdon
- Diagnostic and Surveillance Services Directorate, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - N P French
- New Zealand Food Safety Science and Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - M C Gates
- Epicentre, Massey University School of Veterinary Science, Palmerston North, New Zealand
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French NP, Zhang J, Carter GP, Midwinter AC, Biggs PJ, Dyet K, Gilpin BJ, Ingle DJ, Mulqueen K, Rogers LE, Wilkinson DA, Greening SS, Muellner P, Fayaz A, Williamson DA. Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016. Emerg Infect Dis 2020; 25:2226-2234. [PMID: 31742539 PMCID: PMC6874264 DOI: 10.3201/eid2512.190267] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2014, antimicrobial drug–resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. We hypothesize that the tetO gene and a phage were inserted into the chromosome after conjugation, leaving a remnant plasmid that was lost from isolates from company C. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand, coupled with evolutionary change in the accessory genome, demonstrate the need for ongoing Campylobacter surveillance among poultry and humans.
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Hetman BM, Mutschall SK, Carrillo CD, Thomas JE, Gannon VPJ, Inglis GD, Taboada EN. "These Aren't the Strains You're Looking for": Recovery Bias of Common Campylobacter jejuni Subtypes in Mixed Cultures. Front Microbiol 2020; 11:541. [PMID: 32328044 PMCID: PMC7160300 DOI: 10.3389/fmicb.2020.00541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surveillance has led to the identification of strains posing the greatest risk to public health. Past evidence suggests that enrichment methods for Campylobacter jejuni, a leading bacterial foodborne pathogen worldwide, may lead to the differential recovery of subtypes, obscuring our ability to infer the composition of a mixed-strain sample and potentially biasing prevalence estimates in surveillance data. To assess the extent of potential selection bias resulting from enrichment-based isolation methods, we compared enrichment and non-enrichment isolation of mixed subtype cultures of C. jejuni, followed by subtype-specific enumeration using both colony plate-counts and digital droplet PCR. Results differed from the null hypothesis that similar proportions of C. jejuni subtypes are recovered from both methods. Our results also indicated a significant effect of subtype prevalence on isolation frequency post-recovery, with the recovery of more common subtypes being consistently favored. This bias was exacerbated when an enrichment step was included in the isolation procedure. Taken together, our results emphasize the importance of selecting multiple colonies per sample, and where possible, the use of both enrichment and non-enrichment isolation procedures to maximize the likelihood of recovering multiple subtypes present in a sample. Moreover, the effects of subtype-specific recovery bias should be considered in the interpretation of strain prevalence data toward improved risk assessment from microbiological surveillance data.
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Affiliation(s)
- Benjamin M Hetman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada.,National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Steven K Mutschall
- National Centre for Animal Diseases, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Catherine D Carrillo
- Canadian Food Inspection Agency, Ottawa Laboratory (Carling), Ottawa, ON, Canada
| | - James E Thomas
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - G Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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11
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Abraham S, Sahibzada S, Hewson K, Laird T, Abraham R, Pavic A, Truswell A, Lee T, O'Dea M, Jordan D. Emergence of Fluoroquinolone-Resistant Campylobacter jejuni and Campylobacter coli among Australian Chickens in the Absence of Fluoroquinolone Use. Appl Environ Microbiol 2020; 86:e02765-19. [PMID: 32033955 PMCID: PMC7117913 DOI: 10.1128/aem.02765-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/24/2020] [Indexed: 02/07/2023] Open
Abstract
In a structured survey of all major chicken-meat producers in Australia, we investigated the antimicrobial resistance (AMR) and genomic characteristics of Campylobacter jejuni (n = 108) and C. coli (n = 96) from cecal samples of chickens at slaughter (n = 200). The majority of the C. jejuni (63%) and C. coli (86.5%) samples were susceptible to all antimicrobials. Fluoroquinolone resistance was detected among both C. jejuni (14.8%) and C. coli (5.2%), although this only included three sequence types (STs) and one ST, respectively. Multidrug resistance among strains of C. jejuni (0.9%) and C. coli (4.1%) was rare, and fluoroquinolone resistance, when present, was never accompanied by resistance to any other agent. Comparative genome analysis demonstrated that Australian isolates were found dispersed on different branches/clusters within the international collection. The major fluoroquinolone-resistant STs of C. jejuni (ST7323, ST2083, and ST2343) and C. coli (ST860) present in Australian chickens were similar to those of international isolates and have been reported previously in humans and animals overseas. The detection of a subpopulation of Campylobacter isolates exclusively resistant to fluoroquinolone was unexpected since most critically important antimicrobials such as fluoroquinolones are excluded from use in Australian livestock. A number of factors, including the low level of resistance to other antimicrobials, the absence of fluoroquinolone use, the adoption of measures for preventing spread of contagion between flocks, and particularly the genomic identities of isolates, all point to humans, pest species, or wild birds as being the most plausible source of organisms. This study also demonstrates the need for vigilance in the form of surveillance for AMR based on robust sampling to manage AMR risks in the food chain.IMPORTANCECampylobacter is one of the most common causes of gastroenteritis in humans, with infections frequently resulting from exposure to undercooked poultry products. Although human illness is typically self-limiting, a minority of cases do require antimicrobial therapy. Ensuring that Campylobacter originating from meat chickens does not acquire resistance to fluoroquinolones is therefore a valuable outcome for public health. Australia has never legalized the use of fluoroquinolones in commercial chickens and until now fluoroquinolone-resistant Campylobacter has not been detected in the Australian poultry. This structured survey of meat chickens derived from all major Australian producers describes the unexpected emergence of fluoroquinolone resistance in Campylobacter jejuni and C. coli Genetic characterization suggests that these isolates may have evolved outside the Australian poultry sector and were introduced into poultry by humans, pest species, or wild birds. The findings dramatically underline the critical role of biosecurity in the overall fight against antimicrobial resistance.
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Affiliation(s)
- Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Kylie Hewson
- Australian Chicken Meat Federation, North Sydney, NSW, Australia
| | - Tanya Laird
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Rebecca Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Anthony Pavic
- Birling Avian Laboratories, Bringelly, NSW, Australia
| | - Alec Truswell
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Terence Lee
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Mark O'Dea
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - David Jordan
- New South Wales Department of Primary Industries, Wollongbar, NSW, Australia
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12
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Shifts in the Molecular Epidemiology of Campylobacter jejuni Infections in a Sentinel Region of New Zealand following Implementation of Food Safety Interventions by the Poultry Industry. Appl Environ Microbiol 2020; 86:AEM.01753-19. [PMID: 31862724 DOI: 10.1128/aem.01753-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/12/2019] [Indexed: 01/19/2023] Open
Abstract
In 2006, New Zealand had the highest notification rate of campylobacteriosis in the world, and poultry was considered the leading source of campylobacteriosis. Implementation of food safety interventions by the poultry industry led to a decrease in the campylobacteriosis notification rate. The aim is to examine the impact of targeted food safety interventions implemented by the New Zealand poultry industry on the source attribution of Campylobacter jejuni infections in a sentinel region. Campylobacter jejuni isolates collected from the Manawatu region of New Zealand between 2005 and 2007 ("before intervention") and 2008 and 2015 ("after intervention") from human clinical cases, chicken meat, ruminant feces, environmental water, and wild bird sources were subtyped by multilocus sequence typing. Viable counts of Campylobacter spp. from carcasses were analyzed using a zero-inflated Poisson regression model. In the period before intervention, sequence type 474 (ST-474) was the most common sequence type (ST) recovered from human cases, accounting for 28.2% of the isolates. After intervention, the proportion of human cases positive for ST-474 reduced to 9.3%. Modeling indicated that chicken meat, primarily from one supplier, was the main source of C. jejuni infection in the Manawatu region before intervention. However, after intervention poultry collectively had a similar attribution to ruminants, but more human cases were attributed to ruminants than any single chicken supplier. Viable counts on carcasses were lower in all poultry suppliers after intervention. This study provides evidence of changes in the source attribution of campylobacteriosis following targeted food safety interventions in one sector of the food supply chain.IMPORTANCE This study provides a unique insight into the effects of food safety interventions implemented in one sector of the food industry on the transmission routes of a major foodborne agent. Following the implementation of food safety interventions by the poultry industry, shifts in the molecular epidemiology of Campylobacter jejuni infections in a sentinel region of New Zealand were observed. Targeted interventions to reduce disease incidence are effective but require continued surveillance and analysis to indicate where further interventions may be beneficial.
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13
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Wieczorek K, Wołkowicz T, Osek J. MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland. PLoS One 2020; 15:e0226238. [PMID: 31978059 PMCID: PMC6980552 DOI: 10.1371/journal.pone.0226238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C. jejuni from chicken sources (feces, carcasses, and meat) and from humans with diarrhea as well as to subtype the isolates to gain better insight into their population structure present in Poland. C. jejuni were genotyped using multilocus sequence typing (MLST) and sequence types (STs) were assigned in the MLST database. Among 602 isolates tested, a total of 121 different STs, including 70 (57.9%) unique to the isolates' origin, and 32 STs that were not present in the MLST database were identified. The most prevalent STs were ST464 and ST257, with 58 (9.6%) and 52 (8.6%) C. jejuni isolates, respectively. Isolates with some STs (464, 6411, 257, 50) were shown to be common in chickens, whereas others (e.g. ST21 and ST572) were more often identified among human C. jejuni. It was shown that of 47 human sequence types, 26 STs (106 isolates), 23 STs (102 isolates), and 29 STs (100 isolates) were also identified in chicken feces, meat, and carcasses, respectively. These results, together with the high and similar proportional similarity indexes (PSI) calculated for C. jejuni isolated from patients and chickens, may suggest that human campylobacteriosis was associated with contaminated chicken meat or meat products or other kinds of food cross-contaminated with campylobacters of chicken origin. The frequency of various sequence types identified in the present study generally reflects of the prevalence of STs in other countries which may suggest that C. jejuni with some STs have a global distribution, while other genotypes may be more restricted to certain countries.
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Affiliation(s)
- Kinga Wieczorek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Pulawy, Poland
| | - Tomasz Wołkowicz
- Department of Bacteriology and Biocontamination Control, National Institute of Public Health—National Institute of Hygiene, Warsaw, Poland
| | - Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, Pulawy, Poland
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14
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Alvarez J, Lopez G, Muellner P, de Frutos C, Ahlstrom C, Serrano T, Moreno MA, Duran M, Saez JL, Dominguez L, Ugarte‐Ruiz M. Identifying emerging trends in antimicrobial resistance using Salmonella surveillance data in poultry in Spain. Transbound Emerg Dis 2020; 67:250-262. [PMID: 31484211 PMCID: PMC7028142 DOI: 10.1111/tbed.13346] [Citation(s) in RCA: 10] [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: 05/17/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022]
Abstract
Despite of controls and preventive measures implemented along the food chain, infection with non-typhoidal Salmonella (NTS) remains one of the major causes of foodborne disease worldwide. Poultry is considered one of the major sources of NTS. This has led to the implementation of monitoring and control programmes in many countries (including Spain) to ensure that in poultry flocks infection is kept to a minimum and to allow the identification and monitoring of circulating NTS strains and their antimicrobial resistance (AMR) phenotypes. Here, we investigated the information from the monitoring programme for AMR in Salmonella from poultry in Spain in 2011-2017 to assess the diversity in phenotypic resistance and to evaluate the programme's ability to detect multi-resistance patterns and emerging strains in the animal reservoir. Data on serotype and AMR to nine antimicrobials obtained from 3,047 NTS isolates from laying hens (n = 1,060), broiler (n = 765) and turkey (n = 1,222) recovered during controls performed by the official veterinary services and food business operators were analysed using univariate and multivariate methods in order to describe host and serotype-specific profiles. Diversity and prevalence of phenotypic resistance to all but one of the antimicrobials (colistin) were higher in NTS from broiler and turkey compared with laying hen isolates. Certain combinations of serotype and AMR pattern (resistotype) were particularly linked with certain hosts (e.g. susceptible Enteritidis with laying hens, multi-drug resistant (MDR) Derby in turkey, MDR Kentucky in turkey and broiler). The widespread presence of certain serotype-resistotype combinations in certain hosts/years suggested the possible expansion of MDR strains in the animal reservoir. This study demonstrates the usefulness of the analysis of data from monitoring programmes at the isolate level to detect emerging threats and suggests aspects that should be subjected to further research to identify the forces driving the expansion/dominance of certain strains in the food chain.
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Affiliation(s)
- Julio Alvarez
- VISAVET Health Surveillance CenterUniversidad ComplutenseMadridSpain
- Departamento de Sanidad AnimalFacultad de VeterinariaUniversidad ComplutenseMadridSpain
| | - Gema Lopez
- Subdirección General de Sanidad e Higiene Animal y TrazabilidadDirección General de la Producción AgrariaMinisterio de AgriculturaPesca y AlimentaciónMadridSpain
| | - Petra Muellner
- Epi‐InteractiveWellingtonNew Zealand
- Department of Veterinary Population MedicineCollege of Veterinary MedicineUniversity of MinnesotaSt PaulUSA
| | - Cristina de Frutos
- Laboratorio Central de Veterinaria (LCV Algete)Ministerio de Agricultura Pesca y AlimentaciónMadridSpain
| | | | - Tania Serrano
- TRAGSATECTecnologías y Servicios Agrarios S.AMadridSpain
| | - Miguel A. Moreno
- Departamento de Sanidad AnimalFacultad de VeterinariaUniversidad ComplutenseMadridSpain
| | - Manuel Duran
- Laboratorio Central de Veterinaria (LCV Algete)Ministerio de Agricultura Pesca y AlimentaciónMadridSpain
| | - Jose Luis Saez
- Subdirección General de Sanidad e Higiene Animal y TrazabilidadDirección General de la Producción AgrariaMinisterio de AgriculturaPesca y AlimentaciónMadridSpain
| | - Lucas Dominguez
- VISAVET Health Surveillance CenterUniversidad ComplutenseMadridSpain
- Departamento de Sanidad AnimalFacultad de VeterinariaUniversidad ComplutenseMadridSpain
| | - Maria Ugarte‐Ruiz
- VISAVET Health Surveillance CenterUniversidad ComplutenseMadridSpain
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15
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Lopes BS, Strachan NJC, Ramjee M, Thomson A, MacRae M, Shaw S, Forbes KJ. Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom. Emerg Infect Dis 2019; 25:1320-1329. [PMID: 31211671 PMCID: PMC6590748 DOI: 10.3201/eid2507.181572] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined whole-genome–sequenced Campylobacter jejuni and C. coli from 2012–2015 isolated from birds and human stool samples in North East Scotland for the presence of antimicrobial resistance genes. We found that sequence type (ST) 5136 (clonal complex 464) was the most prevalent multidrug-resistant strain of C. jejuni exclusively associated with poultry host reservoirs and recovered from human cases of campylobacteriosis. Tetracycline resistance in ST5136 isolates was due to a tet(O/32/O) mosaic gene, ampicillin resistance was conferred by G → T transversion in the −10 promoter region of blaOXA-193, fluoroquinolone resistance was due to C257T change in gyrA, and aminoglycoside resistance was conferred by aac. Whole-genome analysis showed that the strain ST5136 evolved from ST464. The nationwide emergence of ST5136 was probably due to stepwise acquisition of antimicrobial resistance genes selected by high use of β-lactam, tetracycline, fluoroquinolone, and aminoglycoside classes of drugs in the poultry industry.
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16
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McCarthy Z, Smith B, Fazil A, Ryan SD, Wu J, Munther D. An individual-carcass model for quantifying bacterial cross-contamination in an industrial three-stage poultry scalding tank. J FOOD ENG 2019. [DOI: 10.1016/j.jfoodeng.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Mughini-Gras L, Kooh P, Fravalo P, Augustin JC, Guillier L, David J, Thébault A, Carlin F, Leclercq A, Jourdan-Da-Silva N, Pavio N, Villena I, Sanaa M, Watier L. Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases. Front Microbiol 2019; 10:2578. [PMID: 31798549 PMCID: PMC6861836 DOI: 10.3389/fmicb.2019.02578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022] Open
Abstract
With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top–down, bottom–up, or combined. Top–down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called ‘source-assigned case-control study’ design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom–up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including ‘natural experiments,’ and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon ‘gold’ standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands.,Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Pauline Kooh
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Philippe Fravalo
- Research Chair in Meat-Safety, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | | | - Laurent Guillier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Julie David
- Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | - Anne Thébault
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Frederic Carlin
- UMR 408 SQPOV "Sécurité et Qualité des Produits d'Origine Végétale" INRA, Avignon Université, Avignon, France
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | | | - Nicole Pavio
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Isabelle Villena
- Laboratory of Parasitology-Mycology, EA ESCAPE, University of Reims Champagne-Ardenne, Reims, France
| | - Moez Sanaa
- Department of Risk Assessment, French Agency for Food, Environmental and Occupational Health and Safety, Maisons-Alfort, France
| | - Laurence Watier
- Department of Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Institut National de la Santé et de la Recherche Médicale (INSERM), UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France
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18
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Bojanić K, Midwinter AC, Marshall JC, Biggs PJ, Acke E. Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets. J Vet Diagn Invest 2018; 31:23-32. [PMID: 30574836 DOI: 10.1177/1040638718820082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We applied 7 culture methods to 50 working farm dog fecal samples and 6 methods to 50 frozen home-killed raw meat diet samples to optimize recovery of a wide range of Campylobacter spp. Culture methods combined filtration, enrichment broths, and agars at 37°C and 42°C in conventional and hydrogen-enriched microaerobic atmospheres. Overall, a prevalence of 62% (31 of 50) and 6% (3 of 50) was detected in dog and meat samples, respectively, based on Campylobacter genus PCR. A total of 356 Campylobacter spp. isolates were recovered from dogs, with successful isolation by individual methods ranging from 2 to 25 dogs. The species detected most commonly were C. upsaliensis and C. jejuni, and less commonly C. coli and C. lari. Species isolated that are rarely reported from dogs included C. rectus, C. lari subsp. concheus, C. volucris, and Helicobacter winghamensis. Six isolates from dogs positive by Campylobacter genus PCR were confirmed, using 16S rRNA sequencing, as Arcobacter cryaerophilus (1) and Arcobacter butzleri (5). C. jejuni multi-locus sequence typing results revealed a diversity of sequence types in working dogs, with several uncommonly reported from other C. jejuni sources in New Zealand. Overall, 20 isolates from 3 meat samples were positive by Campylobacter genus PCR; 1 meat sample was positive for C. jejuni, 1 for C. rectus, and 1 isolate was subsequently identified as A. butzleri. The method using Campylobacter enrichment broth in a hydrogen-enriched environment on nonselective agar resulted in significantly reduced recovery of Campylobacter spp. from both sample types.
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Affiliation(s)
- Krunoslav Bojanić
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Anne C Midwinter
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Jonathan C Marshall
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Patrick J Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
| | - Els Acke
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).,IDEXX VetMedLabor, Ludwigsburg, Germany (Acke)
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19
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Nohra A, Grinberg A, Midwinter AC, Marshall JC, Collins-Emerson JM, French NP. Exposure to whole chicken carcasses may present a greater risk of campylobacteriosis compared to exposure to chicken drumsticks. Zoonoses Public Health 2018; 65:822-830. [PMID: 29998484 DOI: 10.1111/zph.12505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/29/2018] [Accepted: 06/20/2018] [Indexed: 11/29/2022]
Abstract
In New Zealand, the major risk factor for campylobacteriosis has been identified as poultry consumption. New Zealanders consume different types of chicken meat which undergo different processing before entering the retail chain. The manipulations and jointing of chicken carcasses into pieces and the subsequent processing and packaging have the potential to cross-contaminate and reshuffle bacterial pathogens among the different products sold. The aim of this study was to analyse: (a) the differences in the viable count and population genetic structure between Campylobacter isolated from chicken drumsticks and whole carcass meat for retail sale over a 1-year period; and (b) the genetic relatedness of human and chicken isolates collected concurrently. Enumeration of Campylobacter was performed using a spiral plater combined with manual spread plating. Campylobacter isolates were identified by polymerase chain reaction and typed by multilocus sequence typing (MLST). C. jejuni was the dominant species among both whole carcasses (63.5%) and drumsticks samples (73.8%), followed by C. coli (27% and 23.1%, respectively). After sample weight adjustment, whole carcasses showed significantly higher Campylobacter counts than drumsticks, with a significant difference in the counts between the commercial suppliers in both types of retail meat. MLST revealed 28 different sequence types among the two types of meat. Using permutational multivariate analysis of variance, statistically significant differences in the population genetic structures were observed between different suppliers but were not observed between the two types of chicken retail meat. In conclusion, we found differences in Campylobacter viable counts, suggesting consumption of whole carcasses may determine an exposure to a higher number of Campylobacter bacteria than consumption of chicken drumsticks. The Campylobacter population genetic structure did not differ between the two types of chicken retail meat. Therefore, source attribution studies based on MLST are unlikely to be biased by the selection of these types of retail meat during sampling.
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Affiliation(s)
- Antoine Nohra
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Alex Grinberg
- Infectious Diseases Group, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Julie M Collins-Emerson
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- Molecular Epidemiology and Veterinary Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand.,New Zealand Food Safety Science and Research Centre, Palmerston North, New Zealand
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20
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Ravel A, Hurst M, Petrica N, David J, Mutschall SK, Pintar K, Taboada EN, Pollari F. Source attribution of human campylobacteriosis at the point of exposure by combining comparative exposure assessment and subtype comparison based on comparative genomic fingerprinting. PLoS One 2017; 12:e0183790. [PMID: 28837643 PMCID: PMC5570367 DOI: 10.1371/journal.pone.0183790] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/12/2017] [Indexed: 12/29/2022] Open
Abstract
Human campylobacteriosis is a common zoonosis with a significant burden in many countries. Its prevention is difficult because humans can be exposed to Campylobacter through various exposures: foodborne, waterborne or by contact with animals. This study aimed at attributing campylobacteriosis to sources at the point of exposure. It combined comparative exposure assessment and microbial subtype comparison with subtypes defined by comparative genomic fingerprinting (CGF). It used isolates from clinical cases and from eight potential exposure sources (chicken, cattle and pig manure, retail chicken, beef, pork and turkey meat, and surface water) collected within a single sentinel site of an integrated surveillance system for enteric pathogens in Canada. Overall, 1518 non-human isolates and 250 isolates from domestically-acquired human cases were subtyped and their subtype profiles analyzed for source attribution using two attribution models modified to include exposure. Exposure values were obtained from a concurrent comparative exposure assessment study undertaken in the same area. Based on CGF profiles, attribution was possible for 198 (79%) human cases. Both models provide comparable figures: chicken meat was the most important source (65-69% of attributable cases) whereas exposure to cattle (manure) ranked second (14-19% of attributable cases), the other sources being minor (including beef meat). In comparison with other attributions conducted at the point of production, the study highlights the fact that Campylobacter transmission from cattle to humans is rarely meat borne, calling for a closer look at local transmission from cattle to prevent campylobacteriosis, in addition to increasing safety along the chicken supply chain.
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Affiliation(s)
- André Ravel
- Groupe de recherche en épidémiologie des zoonoses et santé publique, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
- Département de pathologie et microbiologie, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Matt Hurst
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Nicoleta Petrica
- Groupe de recherche en épidémiologie des zoonoses et santé publique, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Julie David
- Groupe de recherche en épidémiologie des zoonoses et santé publique, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Steven K. Mutschall
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Katarina Pintar
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory at Lethbridge, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | - Frank Pollari
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
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21
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A combined case-control and molecular source attribution study of human Campylobacter infections in Germany, 2011-2014. Sci Rep 2017; 7:5139. [PMID: 28698561 PMCID: PMC5505968 DOI: 10.1038/s41598-017-05227-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/25/2017] [Indexed: 11/28/2022] Open
Abstract
Campylobacter infection is the most commonly notified bacterial enteritis in Germany. We performed a large combined case-control and source attribution study (Nov 2011-Feb 2014) to identify risk factors for sporadic intestinal Campylobacter infections and to determine the relative importance of various animal sources for human infections in Germany. We conducted multivariable logistic regression analysis to identify risk factors. Source attribution analysis was performed using the asymmetric island model based on MLST data of human and animal/food isolates. As animal sources we considered chicken, pig, pet dog or cat, cattle, and poultry other than chicken. Consumption of chicken meat and eating out were the most important risk factors for Campylobacter infections. Additional risk factors were preparation of poultry meat in the household; preparation of uncooked food and raw meat at the same time; contact with poultry animals; and the use of gastric acid inhibitors. The mean probability of human C. jejuni isolates to originate from chickens was highest (74%), whereas pigs were a negligible source for C. jejuni infections. Human C. coli isolates were likely to originate from chickens (56%) or from pigs (32%). Efforts need to be intensified along the food chain to reduce Campylobacter load, especially on chicken meat.
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22
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Miller P, Marshall J, French N, Jewell C. sourceR: Classification and source attribution of infectious agents among heterogeneous populations. PLoS Comput Biol 2017; 13:e1005564. [PMID: 28558033 PMCID: PMC5473572 DOI: 10.1371/journal.pcbi.1005564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/16/2017] [Accepted: 05/10/2017] [Indexed: 11/19/2022] Open
Abstract
Zoonotic diseases are a major cause of morbidity, and productivity losses in both human and animal populations. Identifying the source of food-borne zoonoses (e.g. an animal reservoir or food product) is crucial for the identification and prioritisation of food safety interventions. For many zoonotic diseases it is difficult to attribute human cases to sources of infection because there is little epidemiological information on the cases. However, microbial strain typing allows zoonotic pathogens to be categorised, and the relative frequencies of the strain types among the sources and in human cases allows inference on the likely source of each infection. We introduce sourceR, an R package for quantitative source attribution, aimed at food-borne diseases. It implements a Bayesian model using strain-typed surveillance data from both human cases and source samples, capable of identifying important sources of infection. The model measures the force of infection from each source, allowing for varying survivability, pathogenicity and virulence of pathogen strains, and varying abilities of the sources to act as vehicles of infection. A Bayesian non-parametric (Dirichlet process) approach is used to cluster pathogen strain types by epidemiological behaviour, avoiding model overfitting and allowing detection of strain types associated with potentially high "virulence". sourceR is demonstrated using Campylobacter jejuni isolate data collected in New Zealand between 2005 and 2008. Chicken from a particular poultry supplier was identified as the major source of campylobacteriosis, which is qualitatively similar to results of previous studies using the same dataset. Additionally, the software identifies a cluster of 9 multilocus sequence types with abnormally high 'virulence' in humans. sourceR enables straightforward attribution of cases of zoonotic infection to putative sources of infection. As sourceR develops, we intend it to become an important and flexible resource for food-borne disease attribution studies.
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Affiliation(s)
- Poppy Miller
- CHICAS, Faculty of Health and Medicine, Lancaster University, Lancaster, England, United Kingdom
- * E-mail:
| | - Jonathan Marshall
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- mEpiLab, Massey University, Palmerston North, New Zealand
| | - Nigel French
- mEpiLab, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Palmerston North, New Zealand
- New Zealand Institute for Advanced Studies, Auckland, New Zealand
| | - Chris Jewell
- CHICAS, Faculty of Health and Medicine, Lancaster University, Lancaster, England, United Kingdom
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Mohan V, Stevenson MA, Marshall JC, French NP. Characterisation by multilocus sequence and porA and flaA typing of Campylobacter jejuni isolated from samples of dog faeces collected in one city in New Zealand. N Z Vet J 2017; 65:209-213. [PMID: 28372482 DOI: 10.1080/00480169.2017.1311810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AIMS To investigate the prevalence of Campylobacter spp. and C. jejuni in dog faecal material collected from dog walkways in the city of Palmerston North, New Zealand, and to characterise the C. jejuni isolates by multilocus sequence typing (MLST) and porA and flaA antigen gene typing. METHODS A total of 355 fresh samples of dogs faeces were collected from bins provided for the disposal of dog faeces in 10 walkways in Palmerston North, New Zealand, between August 2008-July 2009. Presumptive Campylobacter colonies, cultured on modified charcoal cefoperazone deoxycholate plates, were screened for genus Campylobacter and C. jejuni by PCR. The C. jejuni isolates were subsequently characterised by MLST and porA and flaA typing, and C. jejuni sequence types (ST) were assigned. RESULTS Of the 355 samples collected, 72 (20 (95% CI=16-25)%) were positive for Campylobacter spp. and 22 (6 (95% CI=4-9)%) were positive for C. jejuni. Of the 22 C. jejuni isolates, 19 were fully typed by MLST. Ten isolates were assigned to the clonal complex ST-45 and three to ST-52. The allelic combinations of ST-45/flaA 21/porA 44 (n=3), ST-45/flaA 22/porA 53 (n=3) and ST-52/ flaA 57/porA 905 (n=3) were most frequent. CONCLUSIONS The successful isolation of C. jejuni from canine faecal samples collected from faecal bins provides evidence that Campylobacter spp. may survive outside the host for at least several hours despite requiring fastidious growth conditions in culture. The results show that dogs carry C. jejuni genotypes (ST-45, ST-50, ST-52 and ST-696) that have been reported in human clinical cases. CLINICAL RELEVANCE Although these results do not provide any evidence either for the direction of infection or for dogs being a potential risk factor for human campylobacteriosis, dog owners are advised to practice good hygiene with respect to their pets to reduce potential exposure to infection.
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Affiliation(s)
- V Mohan
- a mEpiLab, Infectious Disease Research Institute, Institute of Veterinary, Animal and Biomedical Sciences , Massey University , Palmerston North , New Zealand
| | - M A Stevenson
- b Faculty of Veterinary Science , University of Melbourne , Parkville , Victoria , Australia
| | - J C Marshall
- a mEpiLab, Infectious Disease Research Institute, Institute of Veterinary, Animal and Biomedical Sciences , Massey University , Palmerston North , New Zealand
| | - N P French
- a mEpiLab, Infectious Disease Research Institute, Institute of Veterinary, Animal and Biomedical Sciences , Massey University , Palmerston North , New Zealand
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Szczepanska B, Andrzejewska M, Spica D, Klawe JJ. Prevalence and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolated from children and environmental sources in urban and suburban areas. BMC Microbiol 2017; 17:80. [PMID: 28376713 PMCID: PMC5379741 DOI: 10.1186/s12866-017-0991-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacteriosis is a dominant bacterial cause of foodborne infection and is considered the main public health problem in Europe and many other countries worldwide. In the study lasting from 2011 to 2013 we compared the prevalence and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolated from children, domestic animals, poultry meat and surface water in Northern Poland. RESULTS During a 3-years study 1973 samples were analysed. The results proved the presence of Campylobacter spp. in 306 (15.5%) samples. The percentage of Campylobacter-positive samples differed among the sample types, from 0% (freshwater beaches) to 38.6% (poultry meat in 2011). Prevalence of Campylobacter spp. in children isolates was 9.6%. It decreased from 13.2% in 2011 to 8.0% in 2013. It should be highlighted with a particular concern that Campylobacter jejuni was detected in 20.0% of fountains. All children and poultry meat isolates were susceptible to azithromycin. Two C. coli (3.7%) and four C. jejuni (3.3%) isolated from poultry meat were resistant to erythromycin. The highest percentage of C. jejuni isolates with resistance to ciprofloxacin were found in samples from 80% dogs and 85% ponds. Among isolates resistant to two antimicrobials 74.7% C. jejuni and 59.2% C. coli isolates were resistant to ciprofloxacin as well as to tetracycline. Only one cat C. coli isolate was resistant to both azithromycin and erythromycin. One C. jejuni isolate from a fountain was resistant to four antimicrobial agents (erythromycin, azithromycin, tetracycline and ciprofloxacin). CONCLUSIONS The study proved that surface water, poultry meat and pets constituted potential sources of Campylobacter to children. Fountains can be a direct source of children campylobacteriosis but can also pollute other environments with multidrug-resistant Campylobacter. The high resistance to some antimicrobials among the isolates may lead to increasing numbers of difficult-to-treat campylobacteriosis cases among children.
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Affiliation(s)
- Bernadeta Szczepanska
- Department of Hygiene, Epidemiology and Ergonomics, Nicolaus Copernicus University in Torun, Collegium Medicum in Bydgoszcz, 9 Sklodowska-Curie Str, 85-094 Bydgoszcz, PL Poland
| | - Małgorzata Andrzejewska
- Department of Hygiene, Epidemiology and Ergonomics, Nicolaus Copernicus University in Torun, Collegium Medicum in Bydgoszcz, 9 Sklodowska-Curie Str, 85-094 Bydgoszcz, PL Poland
| | - Dorota Spica
- Department of Hygiene, Epidemiology and Ergonomics, Nicolaus Copernicus University in Torun, Collegium Medicum in Bydgoszcz, 9 Sklodowska-Curie Str, 85-094 Bydgoszcz, PL Poland
| | - Jacek J. Klawe
- Department of Hygiene, Epidemiology and Ergonomics, Nicolaus Copernicus University in Torun, Collegium Medicum in Bydgoszcz, 9 Sklodowska-Curie Str, 85-094 Bydgoszcz, PL Poland
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Hong S, Rovira A, Davies P, Ahlstrom C, Muellner P, Rendahl A, Olsen K, Bender JB, Wells S, Perez A, Alvarez J. Serotypes and Antimicrobial Resistance in Salmonella enterica Recovered from Clinical Samples from Cattle and Swine in Minnesota, 2006 to 2015. PLoS One 2016; 11:e0168016. [PMID: 27936204 PMCID: PMC5148076 DOI: 10.1371/journal.pone.0168016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/23/2016] [Indexed: 11/18/2022] Open
Abstract
Salmonellosis remains one of the leading causes of foodborne disease worldwide despite preventive efforts at various stages of the food production chain. The emergence of multi-drug resistant (MDR) non-typhoidal Salmonella enterica represents an additional challenge for public health authorities. Food animals are considered a major reservoir and potential source of foodborne salmonellosis; thus, monitoring of Salmonella strains in livestock may help to detect emergence of new serotypes/MDR phenotypes and to gain a better understanding of Salmonella epidemiology. For this reason, we analyzed trends over a nine-year period in serotypes, and antimicrobial resistance, of Salmonella isolates recovered at the Minnesota Veterinary Diagnostic Laboratory (MVDL) from swine (n = 2,537) and cattle (n = 1,028) samples. Prevalence of predominant serotypes changed over time; in swine, S. Typhimurium and S. Derby decreased and S. Agona and S. 4,5,12:i:- increased throughout the study period. In cattle, S. Dublin, S. Montevideo and S. Cerro increased and S. Muenster became less frequent. Median minimum inhibitory concentration (MIC) values and proportion of antibiotic resistant isolates were higher for those recovered from swine compared with cattle, and were particularly high for certain antibiotic-serotype combinations. The proportion of resistant swine isolates was also higher than observed in the NARMS data, probably due to the different cohort of animals represented in each dataset. Results provide insight into the dynamics of antimicrobial resistant Salmonella in livestock in Minnesota, and can help to monitor emerging trends in antimicrobial resistance.
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Affiliation(s)
- Samuel Hong
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Albert Rovira
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Peter Davies
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | | | | | - Aaron Rendahl
- School of Statistics, University of Minnesota, Minneapolis, United States of America
| | - Karen Olsen
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Jeff B. Bender
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Scott Wells
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN, United States of America
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Reid SA, McKenzie J, Woldeyohannes SM. One Health research and training in Australia and New Zealand. Infect Ecol Epidemiol 2016; 6:33799. [PMID: 27906122 PMCID: PMC5131460 DOI: 10.3402/iee.v6.33799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/01/2022] Open
Abstract
Purpose of the review This review was performed to create a repository of information on One Health research and training in Australia and New Zealand (ANZ). The review sought to determine 1) how many training activities there are in ANZ, 2) how much research on zoonotic diseases is undertaken by multidisciplinary teams, and 3) how collaborative and integrated they are. Recent findings There are few opportunities for training in One Health in ANZ. The majority require enrolment in a postgraduate degree programme, and there is only one postgraduate level course that is also available for continuing professional development (CPD). Of the broad range of One Health research performed in ANZ, the majority is performed by teams with limited disciplinary diversity, although diversity is improving. Summary Progress has been made in building collaboration between human, animal, and environmental health professions. However, the lack of clearly defined competencies and agreed purpose for One Health may be impeding collaboration.
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Affiliation(s)
- Simon A Reid
- School of Public Health, The University of Queensland, Herston, Queensland, Australia;
| | - Joanna McKenzie
- Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North, New Zealand
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Llarena AK, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen ML, Roasto M, Mäesaar M, Taboada E, Barker D, Garofolo G, Cammà C, Di Giannatale E, Corander J, Rossi M. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microb Genom 2016; 2:e000088. [PMID: 28348829 PMCID: PMC5359405 DOI: 10.1099/mgen.0.000088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/12/2016] [Indexed: 01/05/2023] Open
Abstract
The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.
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Affiliation(s)
- Ann-Katrin Llarena
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ji Zhang
- Institute of Veterinary, Animal & Biomedical Sciences, College of Sciences, Massey University, Palmerstone North, New Zealand
| | - Minna Vehkala
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Marjaana Hakkinen
- Food and Feed Microbiology Research Unit, Research and Laboratory Department, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mati Roasto
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Mihkel Mäesaar
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Veterinary and Food Laboratory, VFL, Tartu, Estonia
| | - Eduardo Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Dillon Barker
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Cesare Cammà
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Elisabetta Di Giannatale
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Jukka Corander
- Institute of Basic Medical Sciences, Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Nohra A, Grinberg A, Midwinter AC, Marshall JC, Collins-Emerson JM, French NP. Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014. Appl Environ Microbiol 2016; 82:4363-4370. [PMID: 27208097 PMCID: PMC4959208 DOI: 10.1128/aem.00934-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/04/2016] [Indexed: 01/21/2023] Open
Abstract
UNLABELLED Campylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in New Zealand. Campylobacter jejuni is the predominant species worldwide, accounting for approximately 90% of human cases, followed by Campylobacter coli Most studies in New Zealand have focused on C. jejuni; hence, the impact of C. coli strains on human health is not well understood. The aim of this study was to genotype C. coli isolates collected in the Manawatu region of New Zealand from clinical cases, fresh poultry meat, ruminant feces, and environmental water sources, between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human disease. Campylobacter isolates were identified by PCR and typed by multilocus sequence typing. C. coli accounted for 2.9% (n = 47/1,601) of Campylobacter isolates from human clinical cases, 9.6% (n = 108/1,123) from poultry, 13.4% (n = 49/364) from ruminants, and 6.4% (n = 11/171) from water. Molecular subtyping revealed 27 different sequence types (STs), of which 18 belonged to clonal complex ST-828. ST-1581 was the most prevalent C. coli sequence type isolated from both human cases (n = 12/47) and poultry (n = 44/110). When classified using cladistics, all sequence types belonged to clade 1 except ST-7774, which belonged to clade 2. ST-854, ST-1590, and ST-4009 were isolated only from human cases and fresh poultry, while ST-3232 was isolated only from human cases and ruminant sources. Modeling indicated ruminants and poultry as the main sources of C. coli human infection. IMPORTANCE We performed a molecular epidemiological study of Campylobacter coli infection in New Zealand, one of few such studies globally. This study analyzed the population genetic structure of the bacterium and included a probabilistic source attribution model covering different animal and water sources. The results are discussed in a global context.
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Affiliation(s)
- Antoine Nohra
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
- Infectious Diseases Group, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Alex Grinberg
- Infectious Diseases Group, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
- Infectious Diseases Group, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
| | - Julie M Collins-Emerson
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
- Infectious Diseases Group, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Nigel P French
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, Hopkirk Institute, Massey University, Palmerston North, New Zealand
- Infectious Diseases Group, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method. Appl Environ Microbiol 2016; 82:2347-2355. [PMID: 26873321 PMCID: PMC4959481 DOI: 10.1128/aem.03693-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/30/2016] [Indexed: 01/10/2023] Open
Abstract
The genetic diversity of Campylobacter jejuni and Campylobacter coli isolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645 C. jejuni and 106 C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuni isolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. For C. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms for C. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% for C. coli). These results show the complexity of the population structure of Campylobacter in broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical.
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de Knegt LV, Pires SM, Löfström C, Sørensen G, Pedersen K, Torpdahl M, Nielsen EM, Hald T. Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2016; 36:571-88. [PMID: 27002674 DOI: 10.1111/risa.12483] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Salmonella is an important cause of bacterial foodborne infections in Denmark. To identify the main animal-food sources of human salmonellosis, risk managers have relied on a routine application of a microbial subtyping-based source attribution model since 1995. In 2013, multiple locus variable number tandem repeat analysis (MLVA) substituted phage typing as the subtyping method for surveillance of S. Enteritidis and S. Typhimurium isolated from animals, food, and humans in Denmark. The purpose of this study was to develop a modeling approach applying a combination of serovars, MLVA types, and antibiotic resistance profiles for the Salmonella source attribution, and assess the utility of the results for the food safety decisionmakers. Full and simplified MLVA schemes from surveillance data were tested, and model fit and consistency of results were assessed using statistical measures. We conclude that loci schemes STTR5/STTR10/STTR3 for S. Typhimurium and SE9/SE5/SE2/SE1/SE3 for S. Enteritidis can be used in microbial subtyping-based source attribution models. Based on the results, we discuss that an adjustment of the discriminatory level of the subtyping method applied often will be required to fit the purpose of the study and the available data. The issues discussed are also considered highly relevant when applying, e.g., extended multi-locus sequence typing or next-generation sequencing techniques.
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Affiliation(s)
- Leonardo V de Knegt
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sara M Pires
- Research Group for Risk-Benefit, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Charlotta Löfström
- Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Gitte Sørensen
- Research Group for Diagnostic Engineering, National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Karl Pedersen
- Section for Bacteriology, Pathology and Parasitology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Mia Torpdahl
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Eva M Nielsen
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Tine Hald
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Ozawa M, Hiki M, Kawanishi M, Abo H, Kojima A, Asai T, Hamamoto S. Molecular Typing of Fluoroquinolone-ResistantCampylobacter jejuniIsolated from Broilers in Japan Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis. Foodborne Pathog Dis 2016; 13:1-7. [DOI: 10.1089/fpd.2015.1975] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Manao Ozawa
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry, and Fisheries, Tokyo, Japan
| | - Mototaka Hiki
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry, and Fisheries, Tokyo, Japan
| | - Michiko Kawanishi
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry, and Fisheries, Tokyo, Japan
| | - Hitoshi Abo
- Department of Research and Development, Tempstaff Co., Ltd., Tachikawa Branch Office, Tokyo, Japan
| | - Akemi Kojima
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry, and Fisheries, Tokyo, Japan
| | - Tetsuo Asai
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Science, Gifu University, Gifu, Japan
| | - Shuichi Hamamoto
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry, and Fisheries, Tokyo, Japan
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Silva DTD, Tejada TS, Blum-Menezes D, Dias PA, Timm CD. Campylobacter species isolated from poultry and humans, and their analysis using PFGE in southern Brazil. Int J Food Microbiol 2016; 217:189-94. [DOI: 10.1016/j.ijfoodmicro.2015.10.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 10/20/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
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Sahin O, Kassem II, Shen Z, Lin J, Rajashekara G, Zhang Q. Campylobacter in Poultry: Ecology and Potential Interventions. Avian Dis 2015; 59:185-200. [PMID: 26473668 DOI: 10.1637/11072-032315-review] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Avian hosts constitute a natural reservoir for thermophilic Campylobacter species, primarily Campylobacter jejuni and Campylobacter coli, and poultry flocks are frequently colonized in the intestinal tract with high numbers of the organisms. Prevalence rates in poultry, especially in slaughter-age broiler flocks, could reach as high as 100% on some farms. Despite the extensive colonization, Campylobacter is essentially a commensal in birds, although limited evidence has implicated the organism as a poultry pathogen. Although Campylobacter is insignificant for poultry health, it is a leading cause of food-borne gastroenteritis in humans worldwide, and contaminated poultry meat is recognized as the main source for human exposure. Therefore, considerable research efforts have been devoted to the development of interventions to diminish Campylobacter contamination in poultry, with the intention to reduce the burden of food-borne illnesses. During the past decade, significant advance has been made in understanding Campylobacter in poultry. This review summarizes the current knowledge with an emphasis on ecology, antibiotic resistance, and potential pre- and postharvest interventions.
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Affiliation(s)
- Orhan Sahin
- A Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011
| | - Issmat I Kassem
- B Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691
| | - Zhangqi Shen
- A Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011
| | - Jun Lin
- C Department of Animal Science, The University of Tennessee, Knoxville, TN 37996
| | - Gireesh Rajashekara
- B Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691
| | - Qijing Zhang
- A Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011
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Cody AJ, McCarthy ND, Bray JE, Wimalarathna HML, Colles FM, Jansen van Rensburg MJ, Dingle KE, Waldenström J, Maiden MCJ. Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:782-8. [PMID: 26109474 PMCID: PMC4755149 DOI: 10.1111/1758-2229.12314] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/18/2015] [Indexed: 05/27/2023]
Abstract
The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P = 0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P = 0.003). The highest proportion of wild bird-attributed illness occurred in August (P < 0.001), with a significantly lower proportion in November (P = 0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10,000 annually.
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Affiliation(s)
- Alison J Cody
- Department of Zoology, University of Oxford, Oxford, UK
| | - Noel D McCarthy
- Department of Zoology, University of Oxford, Oxford, UK
- Health Protection Agency, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
- NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | | | - Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Oxford, UK
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Oxford, UK
- NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
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Grange ZL, Gartrell BD, Biggs PJ, Nelson NJ, Marshall JC, Howe L, Balm MGM, French NP. Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1327-1336. [PMID: 25963514 DOI: 10.1111/cobi.12521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 01/21/2015] [Indexed: 06/04/2023]
Abstract
Predicting and preventing outbreaks of infectious disease in endangered wildlife is problematic without an understanding of the biotic and abiotic factors that influence pathogen transmission and the genetic variation of microorganisms within and between these highly modified host communities. We used a common commensal bacterium, Campylobacter spp., in endangered Takahe (Porphyrio hochstetteri) populations to develop a model with which to study pathogen dynamics in isolated wildlife populations connected through ongoing translocations. Takahe are endemic to New Zealand, where their total population is approximately 230 individuals. Takahe were translocated from a single remnant wild population to multiple offshore and mainland reserves. Several fragmented subpopulations are maintained and connected through regular translocations. We tested 118 Takahe from 8 locations for fecal Campylobacter spp. via culture and DNA extraction and used PCR for species assignment. Factors relating to population connectivity and host life history were explored using multivariate analytical methods to determine associations between host variables and bacterial prevalence. The apparent prevalence of Campylobacter spp. in Takahe was 99%, one of the highest reported in avian populations. Variation in prevalence was evident among Campylobacter species identified. C. sp. nova 1 (90%) colonized the majority of Takahe tested. Prevalence of C. jejuni (38%) and C. coli (24%) was different between Takahe subpopulations, and this difference was associated with factors related to population management, captivity, rearing environment, and the presence of agricultural practices in the location in which birds were sampled. Modeling results of Campylobacter spp. in Takahe metapopulations suggest that anthropogenic management of endangered species within altered environments may have unforeseen effects on microbial exposure, carriage, and disease risk. Translocation of wildlife between locations could have unpredictable consequences including the spread of novel microbes between isolated populations.
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Affiliation(s)
- Zoe L Grange
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Brett D Gartrell
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Patrick J Biggs
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Nicola J Nelson
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - Jonathan C Marshall
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Laryssa Howe
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Matthew G M Balm
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Nigel P French
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, 4442, New Zealand
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Seasonality ofCampylobacter jejuniisolates associated with human campylobacteriosis in the Manawatu region, New Zealand. Epidemiol Infect 2015; 144:820-8. [DOI: 10.1017/s0950268815002009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYA 9-year time-series of genotyped human campylobacteriosis cases from the Manawatu region of New Zealand was used to investigate strain-type seasonality. The data were collected from 2005 to 2013 and the samples were multi-locus sequence-typed (MLST). The four most prevalent clonal complexes (CCs), consisting of 1215 isolates, were CC48, CC21, CC45 and CC61. Seasonal decomposition and Poisson regression with autocorrelated errors, were used to display and test for seasonality of the most prevalent CCs. Of the four examined CCs, only CC45 showed a marked seasonal (summer) peak. The association of CC45 with summer peaks has been observed in other temperate countries, but has previously not been identified in New Zealand. This is the first in-depth study over a long time period employing MLST data to examine strain-type-associated seasonal patterns ofC. jejuniinfection in New Zealand.
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Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis. Appl Environ Microbiol 2015; 81:5318-25. [PMID: 26025899 DOI: 10.1128/aem.01151-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni.
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Sheppard SK, Maiden MCJ. The evolution of Campylobacter jejuni and Campylobacter coli. Cold Spring Harb Perspect Biol 2015; 7:a018119. [PMID: 26101080 DOI: 10.1101/cshperspect.a018119] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.
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Affiliation(s)
- Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, Singleton Park, Swansea SA2 8PP, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
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Mohan V. Faeco-prevalence of Campylobacter jejuni in urban wild birds and pets in New Zealand. BMC Res Notes 2015; 8:1. [PMID: 25645429 PMCID: PMC4417317 DOI: 10.1186/1756-0500-8-1] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/11/2014] [Indexed: 11/22/2022] Open
Abstract
Background Greater attention has been given to Campylobacter jejuni (C. jejuni) prevalence in poultry and ruminants as they are regarded as the major contributing reservoirs of human campylobacteriosis. However, relatively little work has been done to assess the prevalence in urban wild birds and pets in New Zealand, a country with the highest campylobacteriosis notification rates. Therefore, the aim of the study was to assess the faeco-prevalence of C. jejuni in urban wild birds and pets and its temporal trend in the Manawatu region of New Zealand. Findings A repeated cross-sectional study was conducted from April 2008 to July 2009, where faecal samples were collected from 906 ducks, 835 starlings, 23 Canadian goose, 2 swans, 2 pied stilts, 498 dogs and 82 cats. The faeco-prevalence of C. jejuni was 20% in ducks, 18% in starlings, 9% in Canadian goose, 5% in dogs and 7% in cats. The faeco-prevalence of C. jejuni was relatively higher during warmer months of the year in ducks, starlings and dogs while starlings showed increased winter prevalence. No such trend could be assessed in Canadian goose, swans, pied stilts and cats as samples could not be collected for the entire study period from these species. Conclusions This study estimated the faeco-prevalence of C. jejuni in different animal species where the prevalence was relatively high during warmer months in general. However, there was relative increase in winter prevalence in starlings. The urban wild bird species and pets may be considered potential risk factors for human campylobacteriosis in New Zealand, particularly in small children.
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Affiliation(s)
- Vathsala Mohan
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand. .,Post-Doctoral Scientist, AgResearch, Grasslands, Palmerston North, New Zealand.
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40
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Evaluation of the representativeness of a sentinel surveillance site for campylobacteriosis. Epidemiol Infect 2014; 143:1990-2002. [PMID: 25428175 DOI: 10.1017/s0950268814003173] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
It is important to assess the suitability of sentinel sites for human disease; however, there have been few publications documenting the process of formal evaluation. We describe an approach to examining the representativeness of a single sentinel site employed for campylobacteriosis surveillance and source attribution, utilizing a selection of data sources and statistical comparisons of demographic, epidemiological and pathogen genotyping data across selected regions of New Zealand. Our findings showed that while this region captured the national variability in many variables, for example by containing sizable urban and rural populations, the relative frequency of these features did vary from other regions of New Zealand. We discuss the value of choosing a sentinel site that represents the national distribution of key variables, compared to a site that captures the broad features of the wider population, but provides greater power for the monitoring of sub-populations.
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Abstract
The search for an association between disease incidence and possible risk factors using surveillance data needs to account for possible spatial and temporal correlations in underlying risk. This can be especially difficult if there are missing values for some important covariates. We present a case study to show how this problem can be overcome in a Bayesian analysis framework by adding to the usual spatio-temporal model a component for modelling the missing data.
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42
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Verdugo C, Pleydell E, Price-Carter M, Prattley D, Collins D, de Lisle G, Vogue H, Wilson P, Heuer C. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms. Prev Vet Med 2014; 117:436-46. [PMID: 25315761 DOI: 10.1016/j.prevetmed.2014.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
Abstract
The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.
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Affiliation(s)
- Cristobal Verdugo
- Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile; EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
| | - Eve Pleydell
- Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Marian Price-Carter
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Deborah Prattley
- Infectious Disease Research Centre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Desmond Collins
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Geoffrey de Lisle
- AgResearch, National Centre for Biosecurity and Infectious Disease, Wallaceville, P.O. Box 40063, Upper Hutt, New Zealand
| | - Hinrich Vogue
- Livestock Improvement Corporation, Private Bag 3016, Hamilton, New Zealand
| | - Peter Wilson
- Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cord Heuer
- EpiCentre, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Kurekci C, Al Jassim R, Hassan E, Bishop-Hurley SL, Padmanabha J, McSweeney CS. Effects of feeding plant-derived agents on the colonization of Campylobacter jejuni in broiler chickens. Poult Sci 2014; 93:2337-46. [DOI: 10.3382/ps.2014-03950] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Using surveillance and monitoring data of different origins in aSalmonellasource attribution model: a European Union example with challenges and proposed solutions. Epidemiol Infect 2014; 143:1148-65. [DOI: 10.1017/s0950268814000429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYMicrobial subtyping approaches are commonly used for source attribution of human salmonellosis. Such methods require data onSalmonellain animals and humans, outbreaks, infection abroad and amounts of food available for consumption. A source attribution model was applied to 24 European countries, requiring special data management to produce a standardized dataset. Salmonellosis data on animals and humans were obtained from datasets provided by the European Food Safety Authority. The amount of food available for consumption was calculated based on production and trade data. Limitations included different types of underreporting, non-participation in prevalence studies, and non-availability of trade data. Cases without travel information were assumed to be domestic; non-subtyped human or animal records were re-identified according to proportions observed in reference datasets; missing trade information was estimated based on previous years. The resulting dataset included data on 24 serovars in humans, broilers, laying hens, pigs and turkeys in 24 countries.
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Tayde RS, Brahmbhatt MN. Biotyping of thermophilic Campylobacter spp. isolated from poultry in and around Anand city, Gujarat, India. Vet World 2014. [DOI: 10.14202/vetworld.2014.321-324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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46
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Wagenaar JA, French NP, Havelaar AH. Preventing Campylobacter at the source: why is it so difficult? Clin Infect Dis 2013; 57:1600-6. [PMID: 24014733 DOI: 10.1093/cid/cit555] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Campylobacteriosis in humans, caused by Campylobacter jejuni and Campylobacter coli, is the most common recognized bacterial zoonosis in the European Union and the United States. The acute phase is characterized by gastrointestinal symptoms. The long-term sequelae (Guillain-Barré syndrome, reactive arthritis, and postinfectious irritable bowel syndrome) contribute considerably to the disease burden. Attribution studies identified poultry as the reservoir responsible for up to 80% of the human Campylobacter infections. In the European Union, an estimated 30% of the human infections are associated with consumption and preparation of poultry meat. Until now, interventions in the poultry meat production chain have not been effectively introduced except for targeted interventions in Iceland and New Zealand. Intervention measures (eg, biosecurity) have limited effect or are hampered by economic aspects or consumer acceptance. In the future, a multilevel approach should be followed, aiming at reducing the level of contamination of consumer products rather than complete absence of Campylobacter.
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Affiliation(s)
- Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University
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47
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Kurekci C, Padmanabha J, Bishop-Hurley SL, Hassan E, Al Jassim RAM, McSweeney CS. Antimicrobial activity of essential oils and five terpenoid compounds against Campylobacter jejuni in pure and mixed culture experiments. Int J Food Microbiol 2013; 166:450-7. [PMID: 24041998 DOI: 10.1016/j.ijfoodmicro.2013.08.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 11/20/2022]
Abstract
The aim of this study was to examine the antimicrobial potential of three essential oils (EOs: tea tree oil, lemon myrtle oil and Leptospermum oil), five terpenoid compounds (α-bisabolol, α-terpinene, cineole, nerolidol and terpinen-4-ol) and polyphenol against two strains of Campylobacter jejuni (ACM 3393 and the poultry isolate C338), Campylobacter coli and other Gram negative and Gram positive bacteria. Different formulations of neem oil (Azadirachta indica) with these compounds were also tested for synergistic interaction against all organisms. Antimicrobial activity was determined by the use of disc diffusion and broth dilution assays. All EOs tested were found to have strong antimicrobial activity against Campylobacter spp. with inhibitory concentrations in the range 0.001-1% (v/v). Among the single compounds, terpinen-4-ol showed the highest activity against Campylobacter spp. and other reference strains. Based on the antimicrobial activity and potential commerciality of these agents, lemon myrtle oil, α-tops (α-terpineol+cineole+terpinen-4-ol) and terpinen-4-ol were also evaluated using an in vitro fermentation technique to test antimicrobial activity towards C. jejuni in the microbiota from the chicken-caecum. EO compounds (terpinen-4-ol and α-tops) were antimicrobial towards C. jejuni at high doses (0.05%) without altering the fermentation profile. EOs and terpenoid compounds can have strong anti-Campylobacter activity without adversely affecting the fermentation potential of the chicken-caeca microbiota. EOs and their active compounds may have the potential to control C. jejuni colonisation and abundance in poultry.
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Affiliation(s)
- Cemil Kurekci
- CSIRO Animal, Food and Health Sciences, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia; School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia
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48
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Mohan V, Stevenson M, Marshall J, Fearnhead P, Holland BR, Hotter G, French NP. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand. Microbiologyopen 2013; 2:659-73. [PMID: 23873654 PMCID: PMC3831628 DOI: 10.1002/mbo3.102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 05/24/2013] [Accepted: 06/03/2013] [Indexed: 11/24/2022] Open
Abstract
A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by FST, and host-genotype association with clonal complexes CC ST-177 and CC ST-682 associated with starlings, and clonal complexes CC ST-1034, CC ST-692, and CC ST-1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host-associated genotypes, such as the starling-associated ST-177 and ST-682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas. We applied molecular epidemiology and population genetics to obtain insights in to the population structure, host-species relationships, gene flow and evolution of Campylobacter jejuni in urban ducks and starlings.
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Affiliation(s)
- Vathsala Mohan
- mEpiLab, Infectious Disease Research Centre, Institute of Veterinary and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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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.
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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.
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Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol 2013; 51:2526-34. [PMID: 23698529 DOI: 10.1128/jcm.00066-13] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sequence-based typing is essential for understanding the epidemiology of Campylobacter infections, a major worldwide cause of bacterial gastroenteritis. We demonstrate the practical and rapid exploitation of whole-genome sequencing to provide routine definitive characterization of Campylobacter jejuni and Campylobacter coli for clinical and public health purposes. Short-read data from 384 Campylobacter clinical isolates collected over 4 months in Oxford, United Kingdom, were assembled de novo. Contigs were deposited at the pubMLST.org/campylobacter website and automatically annotated for 1,667 loci. Typing and phylogenetic information was extracted and comparative analyses were performed for various subsets of loci, up to the level of the whole genome, using the Genome Comparator and Neighbor-net algorithms. The assembled sequences (for 379 isolates) were diverse and resembled collections from previous studies of human campylobacteriosis. Small subsets of very closely related isolates originated mainly from repeated sampling from the same patients and, in one case, likely laboratory contamination. Much of the within-patient variation occurred in phase-variable genes. Clinically and epidemiologically informative data can be extracted from whole-genome sequence data in real time with straightforward, publicly available tools. These analyses are highly scalable, are transparent, do not require closely related genome reference sequences, and provide improved resolution (i) among Campylobacter clonal complexes and (ii) between very closely related isolates. Additionally, these analyses rapidly differentiated unrelated isolates, allowing the detection of single-strain clusters. The approach is widely applicable to analyses of human bacterial pathogens in real time in clinical laboratories, with little specialist training required.
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