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Lynch C, Peeters C, Walsh N, McCarthy C, Coffey A, Lucey B, Vandamme P. Campylobacter majalis sp. nov. and Campylobacter suis sp. nov., novel Campylobacter species isolated from porcine gastrointestinal mucosa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748456 DOI: 10.1099/ijsem.0.005510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Strains LMG 7974T and LMG 8286T represent single, novel Campylobacter lineages with Campylobacter pinnipediorum and Campylobacter mucosalis as nearest phylogenomic neighbours, respectively. The results of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses of LMG 7974T, LMG 8286T and type strains of species of the genus Campylobacter confirmed that these strains represent novel species of the genus Campylobacter. The 16S rRNA gene sequences of both strains showed highest identity towards C. mucosalis (97.84 and 98.74 %, respectively). Strains LMG 7974T and LMG 8286T shared 72.5 and 73.7% ANI, respectively, with their nearest phylogenomic neighbours and less than 21 % dDDH. The draft genome sizes of LMG 7974T and LMG 8286T are 1 945429 bp and 1 708214 bp in length with percentage DNA G+C contents of 33.8 and 37.2 %, respectively. Anomalous biochemical characteristics and low MALDI-TOF mass spectrometry log scores supported their designation as representing novel species of the genus Campylobacte. We therefore propose to classify strain LMG 7974T (=CCUG 20705T) as the type strain of the novel species Campylobacter majalis sp. nov. and strain LMG 8286T (=CCUG 24193T, NCTC 11879T) as the type strain of the novel species Campylobacter suis sp. nov.
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Affiliation(s)
- Caoimhe Lynch
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Niamh Walsh
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Conor McCarthy
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland.,APC Microbiome Institute, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown Cork T12 P928, Ireland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Phung C, Scott PC, Dekiwadia C, Moore RJ, Van TTH. Campylobacter bilis sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 2022; 72. [PMID: 35442881 DOI: 10.1099/ijsem.0.005314] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species of Campylobacter was isolated from bile samples of chickens with spotty liver disease in Australia, making it the second novel species isolated from chickens with the disease, after Campylobacter hepaticus was isolated and described in 2016. Six independently derived isolates were obtained. They were Gram-stain-negative, microaerobic, catalase-positive, oxidase-positive and urease-negative. Unlike most other species of the genus Campylobacter, more than half of the tested strains of this novel species hydrolysed hippurate and most of them could not reduce nitrate. Distinct from C. hepaticus, many of the isolates were sensitive to 2,3,5-triphenyltetrazolium chloride (0.04%) and metronidazole (4 mg ml-1), and all strains were sensitive to nalidixic acid. Phylogenetic analysis using 16S rRNA and hsp60 gene sequences demonstrated that the strains formed a robust clade that was clearly distinct from recognized Campylobacter species. Whole genome sequence analysis of the strains showed that the average nucleotide identity and the genome blast distance phylogeny values compared to other Campylobacter species were less than 86 and 66%, respectively, which are below the cut-off values generally recognized for isolates of the same species. The genome of the novel species has a DNA G+C content of 30.6 mol%, while that of C. hepaticus is 27.9 mol%. Electron microscopy showed that the cells were spiral-shaped, with bipolar unsheathed flagella. The protein spectra generated from matrix-assisted laser desorption/ionization time of flight analysis demonstrated that they are different from the most closely related Campylobacter species. These data indicate that the isolates belong to a novel Campylobacter species, for which the name Campylobacter bilis sp. nov. is proposed. The type strain is VicNov18T (=ATCC TSD-231T=NCTC 14611T).
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Affiliation(s)
- Canh Phung
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | | | - Chaitali Dekiwadia
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, VIC, Australia
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Lynch CT, Buttimer C, Epping L, O'Connor J, Walsh N, McCarthy C, O'Brien D, Vaughan C, Semmler T, Bolton D, Coffey A, Lucey B. Phenotypic and genetic analyses of two Campylobacter fetus isolates from a patient with relapsed prosthetic valve endocarditis. Pathog Dis 2021; 79:6486444. [PMID: 34962980 DOI: 10.1093/femspd/ftab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/24/2021] [Indexed: 11/12/2022] Open
Abstract
Campylobacter fetus can cause intestinal and systemic disease in humans and are well established veterinary and economic pathogens. We report the complete genomic sequences of two C. fetus subsp. fetus (Cff) isolates recovered in 2017 (CITCf01) and 2018 (CITCf02) from a case of recurrent prosthetic valve endocarditis. Both were capable of growth aerobically. Their genomes were found to be highly conserved and syntenic with 99.97% average nucleotide identity (ANI) while differences in their respective sap loci defined the temporal separation of their genomes. Based on core genome phylogeny and ANI of 83 Cff genomes belonging to the previously described human-associated Cff lineage, CITCf01 and CITCf02 grouped in a clade of eleven sequence type (ST)3 Cff (including the Cff type strain NCTC 10842T). CITCf01 and CITCf02 were marked for their lack of unique genomic features when compared to isolates within the subspecies and the type strain in particular. We identified point mutations in oxidative stress response genes, among others, that may contribute to aerobiosis. We report a case of Cff causing relapsed prosthetic valve endocarditis and we highlight the sap island as a polymorphic site within the genetically stable ST3 lineage, central to pathogenicity.
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Affiliation(s)
- Caoimhe T Lynch
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Colin Buttimer
- APC Microbiome Ireland, University College Cork, College Road, Cork, Ireland
| | - Lennard Epping
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Nordufer 20, Berlin, Germany
| | - James O'Connor
- Department of Microbiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Niamh Walsh
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Conor McCarthy
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
| | - Deirdre O'Brien
- Department of Microbiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Carl Vaughan
- Department of Cardiology, Grenville Place, Mercy University Hospital, Cork, Ireland
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, Nordufer 20, Berlin, Germany
| | - Declan Bolton
- Food Safety Department, Teagasc Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Aidan Coffey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland.,APC Microbiome Ireland, University College Cork, College Road, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Rossa Ave, Bishopstown, Cork, Ireland
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Phylogenomic Characterization of a Novel Corynebacterium Species Associated with Fatal Diphtheritic Stomatitis in Endangered Yellow-Eyed Penguins. mSystems 2021; 6:e0032021. [PMID: 34100641 PMCID: PMC8269222 DOI: 10.1128/msystems.00320-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yellow-eyed penguins, Megadyptes antipodes, are an endangered species that are endemic to New Zealand. Outbreaks of diphtheritic stomatitis have caused significant mortality for this species, especially among young chicks. In this study, we isolated 16 Corynebacterium sp. isolates from the oral cavities of 2- to 14-day-old chicks at a range of infection stages and sequenced the genomes to understand their virulence mechanisms. Phylogenomic and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) characterization indicate that these strains belong to a novel Corynebacterium species. A simple multiplex PCR-based diagnostic assay has been developed to identify these strains rapidly and reliably. Similar to other corynebacteria, genomic islands and prophages introduced significant diversity among these strains that has potentially led to minor functional variations between the two lineages. Despite the presence of multiple corynebacterial virulence genes and a spaDEF-type pilus gene cluster among these strains, the survival rate was much higher in Galleria mellonella larvae than in those inoculated with Corynebacterium ulcerans NZRM 818 and Corynebacterium pseudotuberculosis NZRM 3004. Therefore, these strains are opportunistic pathogens causing high mortality among young penguin chicks due to a less-developed immune system. IMPORTANCE Yellow-eyed penguins, Megadyptes antipodes, are endangered species with a sharp decline in the numbers of breeding pairs over the last 2 decades. Diphtheritic stomatitis, characterized by a thick fibrinopurulent exudate in the oral cavities and symptoms, including inanition and significant weight loss, is responsible for significant mortality among the young chicks. These chicks are treated with antibiotics, amoxicillin-clavulanic acid or enrofloxacin, but do not always recover from the infection. The pathogen causing these infections and the mechanism of pathogenesis are unclear. This study has identified a novel Corynebacterium species to be associated with diphtheritic stomatitis in yellow-eyed penguins with potential virulence genes that are likely involved in pathogenesis. Importantly, a gene encoding an exotoxin, phospholipase D, is present among these strains. The inactivated form of this enzyme could potentially be used as an effective vaccine to protect these penguins from infection.
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Bloomfield S, Wilkinson D, Rogers L, Biggs P, French N, Mohan V, Savoian M, Venter P, Midwinter A. Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand. Int J Syst Evol Microbiol 2020; 70:3775-3784. [PMID: 32501787 PMCID: PMC7395618 DOI: 10.1099/ijsem.0.004231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 05/05/2020] [Indexed: 11/18/2022] Open
Abstract
Six isolates of Campylobacter with similar non-standard colonial morphologies were identified during studies isolating Campylobacter from bird faeces and rivers in New Zealand. Genomic (16S rRNA gene sequencing and whole genome analysis) and phenotypic (MALDI-TOF analysis and conventional biochemical tests) showed that the isolates form a monophyletic clade with genetic relationships to Campylobacter coli/Campylobacter jejuni and Campylobacter peloridis/Campylobacter amoricus. They may be distinguished from other Campylobacter by their MALDI-TOF spectral pattern, their florid α-haemolysis, their ability to grow anaerobically at 37 °C, and on 2 % NaCl nutrient agar, and their lack of hippuricase. This study shows that these isolates represent a novel species within the genus Campylobacter for which the name Campylobacter novaezeelandiae sp. nov. is proposed. The presence of C. novaezeelandiae in water may be a confounder for freshwater microbial risk assessment as they may not be pathogenic for humans. The type strain is B423bT (=NZRM 4741T=ATCC TSD-167T).
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Affiliation(s)
- Samuel Bloomfield
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Present address: Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - David Wilkinson
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Lynn Rogers
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick Biggs
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nigel French
- Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Present address: New Zealand Food Safety and Science Research Centre, Massey University, Palmerston North, New Zealand
| | - Vathsala Mohan
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Present address: Livestock Improvement Corporation, Hamilton, New Zealand
| | - Matthew Savoian
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Pierre Venter
- Fonterra Research and Development Centre, Palmerston North, New Zealand
| | - Anne Midwinter
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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6
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Campylobacter portucalensis sp. nov., a new species of Campylobacter isolated from the preputial mucosa of bulls. PLoS One 2020; 15:e0227500. [PMID: 31923228 PMCID: PMC6953823 DOI: 10.1371/journal.pone.0227500] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/19/2019] [Indexed: 01/31/2023] Open
Abstract
A new species of the Campylobacter genus is described, isolated from the preputial mucosa of bulls (Bos taurus). The five isolates obtained exhibit characteristics of Campylobacter, being Gram-negative non-motile straight rods, oxidase positive, catalase negative and microaerophilic. Phenotypic characteristics and nucleotide sequence analysis of 16S rRNA and hsp60 genes demonstrated that these isolates belong to a novel species within the genus Campylobacter. Based on hsp60 gene phylogenetic analysis, the most related species are C. ureolyticus, C. blaseri and C. corcagiensis. The whole genome sequence analysis of isolate FMV-PI01 revealed that the average nucleotide identity with other Campylobacter species was less than 75%, which is far below the cut-off for isolates of the same species. However, whole genome sequence analysis identified coding sequences highly homologous with other Campylobacter spp. These included several virulence factor coding genes related with host cell adhesion and invasion, transporters involved in resistance to antimicrobials, and a type IV secretion system (T4SS), containing virB2-virB11/virD4 genes, highly homologous to the C. fetus subsp. venerealis. The genomic G+C content of isolate FMV-PI01 was 28.3%, which is one of the lowest values reported for species of the genus Campylobacter. For this species the name Campylobacter portucalensis sp. nov. is proposed, with FMV-PI01 (= LMG 31504, = CCUG 73856) as the type strain.
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Abstract
Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.
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Affiliation(s)
- Daniela Costa
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
- Wellcome Sanger Institute, Hinxton, United Kingdom
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Crawshaw T. A review of the novel thermophilic Campylobacter, Campylobacter hepaticus, a pathogen of poultry. Transbound Emerg Dis 2019; 66:1481-1492. [PMID: 31081981 DOI: 10.1111/tbed.13229] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 11/28/2022]
Abstract
In 2015, a novel thermophilic Campylobacter was isolated from cases of spotty liver disease in laying hens in the UK. In 2016, it was isolated from laying hens in Australia where it was formally named Campylobacter hepaticus and confirmed as the cause of spotty liver disease. It has also been isolated from laying hens in America. It is fastidious, grows slowly on first isolation and does not grow on media used to routinely isolate Campylobacter. Spotty liver disease is an acute, randomly distributed, focal, necrotic hepatitis causing mortality in up to 10% of a flock and a 10%-15% fall in egg production. It occurs mainly in free-range hens or hens reared on the ground at around the time of peak lay. The incidence of the disease has increased in countries where there is an increase in keeping free-range laying hens. It is similar to the condition avian vibrionic hepatitis which was reported in America, Europe and Australasia in the 1950s to 1970s and the agent isolated from cases of avian vibrionic hepatitis and C. hepaticus appear to be very similar. It is not known if C. hepaticus is zoonotic but whole genome sequencing shows that it is most closely related to the known zoonotic campylobacters Campylobacter jejuni and Campylobacter coli. Human exposure to C. hepaticus is likely through similar exposure routes. Analysis of the whole genome showed a reduction in the genes for iron metabolism compared to C. jejuni. A requirement for iron was confirmed as it showed reduced growth in an iron depletion assay and this may explain its tissue tropism. With a move towards free-range egg production in many countries, the incidence of C. hepaticus hepatitis is likely to increase, but the identification of the causal agent will provide opportunities for the development of control methods.
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Affiliation(s)
- Tim Crawshaw
- Charles Sturt University Wagga Wagga, North Wagga Wagga, New South Wales, Australia
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Clayton JB, Danzeisen JL, Johnson TJ, Trent AM, Hayer SS, Murphy T, Wuenschmann A, Elder M, Shen Z, Mannion A, Bryant E, Knights D, Fox JG. Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection. J Med Primatol 2018; 48:114-122. [PMID: 30536921 DOI: 10.1111/jmp.12393] [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: 07/24/2018] [Revised: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND The aim of this study was to longitudinally investigate the prevalence and characterization of Campylobacter spp. from non-human primates primate (NHP) with a history of endemic diarrhea housed at Como Park Zoo. METHODS Fecal samples from 33 symptom-free NHP belonging to eight different species were collected weekly for 9 weeks. Species-level characterization and phylogenetic analysis of isolates included biochemical testing and 16S rRNA sequencing. RESULTS Campylobacter spp. were isolated from the feces of 42% (14/33) of the primates. Three Campylobacter spp. (C upsaliensis, C jejuni, and novel Campylobacter sp.) were identified from three NHP species. A possible positive host Campylobacter species-specificity was observed. However, no statistical association was observed between the isolation of Campylobacter spp. and age and sex of the animal. CONCLUSIONS The study revealed the value of conducting repeated fecal sampling to establish the overall prevalence of Campylobacter in zoo-maintained NHP; it also importantly identifies a novel Campylobacter sp. isolated from white-faced saki monkeys.
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Affiliation(s)
- Jonathan B Clayton
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,GreenViet Biodiversity Conservation Center, Danang, Vietnam.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Jessica L Danzeisen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Primate Microbiome Project, Minneapolis, Minnesota.,Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota
| | - Ava M Trent
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Shivdeep S Hayer
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Tami Murphy
- Como Park Zoo & Conservatory, Saint Paul, Minnesota
| | - Arno Wuenschmann
- Veterinary Diagnostic Laboratory, University of Minnesota, Saint Paul, Minnesota
| | - Megan Elder
- Como Park Zoo & Conservatory, Saint Paul, Minnesota
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Erin Bryant
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Dan Knights
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
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García-Sánchez L, Melero B, Rovira J. Campylobacter in the Food Chain. ADVANCES IN FOOD AND NUTRITION RESEARCH 2018; 86:215-252. [PMID: 30077223 DOI: 10.1016/bs.afnr.2018.04.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Currently Campylobacter is the most commonly reported zoonosis in developed and developing countries. In the European Union, the number of reported confirmed cases of human campylobacteriosis was 246,307 in 2016, which represents 66.3 cases per 100,000 population. The genus Campylobacter includes 31 species with 10 subspecies. Within the genus Campylobacter, C. jejuni subsp. jejuni and C. coli are most frequently associated with human illness. Mainly, the infection is sporadic and self-limiting, although some cases of outbreaks have been also reported and some complications such as Guillain-Barré syndrome might appear sporadically. Although campylobacters are fastidious microaerophilic, unable to multiply outside the host and generally very sensitive, they can adapt and survive in the environment, exhibiting aerotolerance and resistance to starvation. Many mechanisms are involved in this, including pathogenicity, biofilm formation, and antibiotic resistant pathways. This chapter reviews the sources, transmission routes, the mechanisms, and strategies used by Campylobacter to persist in the whole food chain, from farm to fork. Additionally, different strategies are recommended for application along the poultry food chain to avoid the public health risk associated with this pathogen.
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Affiliation(s)
| | - Beatriz Melero
- Biotechnology and Food Science Department, University of Burgos, Burgos, Spain
| | - Jordi Rovira
- Biotechnology and Food Science Department, University of Burgos, Burgos, Spain.
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11
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Gilbert MJ, Zomer AL, Timmerman AJ, Spaninks MP, Rubio-García A, Rossen JW, Duim B, Wagenaar JA. Campylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina). Int J Syst Evol Microbiol 2018; 68:1787-1794. [PMID: 29624164 DOI: 10.1099/ijsem.0.002742] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study to assess the faecal microbiome of common seals (Phoca vitulina) in a Dutch seal rehabilitation centre, 16S rRNA gene sequences of an unknown Campylobacter taxon were identified. Campylobacter isolates, which differed from the established Campylobacter taxa, were cultured and their taxonomic position was determined by a polyphasic study based on ten isolates. The isolates were characterized by 16S rRNA and atpA gene sequence analyses and by conventional phenotypic testing. Based on the whole genome sequences, the average nucleotide identity and core genome phylogeny were determined. The isolates formed a separate phylogenetic clade, divergent from all other Campylobacter taxa and most closely related to Campylobacter corcagiensis, Campylobacter geochelonis and Campylobacter ureolyticus. The isolates can be distinguished phenotypically from all other Campylobacter taxa based on their lack of motility, growth at 25 °C and growth on MacConkey agar. This study shows that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter blaseri sp. nov. is proposed. The type strain for this novel species is 17S00004-5T (=LMG 30333T=CCUG 71276T).
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Affiliation(s)
- Maarten J Gilbert
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), Nijmegen, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Arjen J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mirlin P Spaninks
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ana Rubio-García
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Sealcentre, Pieterburen, The Netherlands.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
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12
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On SLW, Miller WG, Houf K, Fox JG, Vandamme P. Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp. Int J Syst Evol Microbiol 2017; 67:5296-5311. [PMID: 29034857 PMCID: PMC5845751 DOI: 10.1099/ijsem.0.002255] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 01/25/2023] Open
Abstract
Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.
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Affiliation(s)
- Stephen L. W. On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, PO Box 85084, Lincoln, New Zealand
| | - William G. Miller
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, CA, USA
| | - Kurt Houf
- Department of Veterinary Public Health, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - James G. Fox
- Department of Comparative Medicine, Massachusetts Institute of Technology, 77, Massachusetts Avenue, Cambiridge, MA 02139, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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New Identification of Three or More Campylobacter Species on the Basis of a Degenerate PCR-RFLP Method Targeting gyrB Gene. Curr Microbiol 2017; 74:1160-1168. [PMID: 28717848 DOI: 10.1007/s00284-017-1300-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
Abstract
This method was aimed targeting more Campylobacter species than conventional PCR-based identifications. They generally use species-specific primers focusing on clinically common species like C. jejuni, resulting in failure to recognize other species. We made the PCR-based identification more flexible using degenerate primers and DdeI- and MboI-separately used RFLP assay, which were designed on the basis of gyrB nucleotide sequence data of 14 Campylobacter species including C. jejuni, C. coli, and C. fetus. Ninety-four clinical isolates from patients with Campylobacter gastroenteritis and 13 biochemically identified C. fetus were used for its evaluation. In consequence, this method succeeded in identifying C. jejuni, C. coli, and C. fetus with tentative sensitivity (93.4-98.0%) and specificity (89.0-99.0%). According to our data-based analysis, the primers can possibly target other related species including Helicobacter and Arcobacter. This method may be a universal identification for Campylobacter and related organisms and would provide an alternative identification in clinical microbiology.
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Gilbert MJ, Miller WG, Leger JS, Chapman MH, Timmerman AJ, Duim B, Foster G, Wagenaar JA. Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov. Int J Syst Evol Microbiol 2017. [PMID: 28629508 DOI: 10.1099/ijsem.0.001894] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established taxa of the genus Campylobacter, were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobactermucosalis. Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).
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Affiliation(s)
- Maarten J Gilbert
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Judy St Leger
- SeaWorld Parks and Entertainment, San Diego, CA, USA
| | - Mary H Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Arjen J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Birgitta Duim
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, The Netherlands.,WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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15
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Van TTH, Elshagmani E, Gor MC, Scott PC, Moore RJ. Campylobacter hepaticus sp. nov., isolated from chickens with spotty liver disease. Int J Syst Evol Microbiol 2016; 66:4518-4524. [DOI: 10.1099/ijsem.0.001383] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Thi Thu Hao Van
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | | | - Mian Chee Gor
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Peter C. Scott
- Scolexia Pty Ltd, Moonee Ponds, Victoria 3039, Australia
- Poultry Cooperative Research Centre, Armidale, New South Wales 2351, Australia
| | - Robert J. Moore
- Poultry Cooperative Research Centre, Armidale, New South Wales 2351, Australia
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
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16
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Liu F, Lee H, Lan R, Zhang L. Zonula occludens toxins and their prophages in Campylobacter species. Gut Pathog 2016; 8:43. [PMID: 27651834 PMCID: PMC5025632 DOI: 10.1186/s13099-016-0125-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/08/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND We previously showed that zonula occludens toxin (Zot) encoded by Campylobacter concisus zot (808T) gene has the potential to initiate inflammatory bowel disease. This Zot protein caused prolonged intestinal epithelial barrier damage, induced intestinal epithelial and macrophage production of tumor necrosis factor-α and enhanced the responses of macrophages to other microbes. In order to understand the potential virulence of Zot proteins in other Campylobacter species, in this study we examined their presence, similarities, motifs and prophages. METHODS The presence of Zot proteins in Campylobacter species was examined by searching for the Zot family domain in multiple protein databases. Walker A and Walker B motifs in Zot proteins were identified using protein sequence alignment. A phylogenetic tree based on Campylobacter zot genes was constructed using maximum-likelihood method. Campylobacter Zot proteins were compared using protein sequence alignment. The zot-containing prophages in Campylobacter species were identified and compared with known prophage proteins and other viral proteins using protein sequence alignment and protein BLAST. RESULTS Twelve Zot proteins were found in nine Campylobacter species/subspecies. Among these Campylobacter species, three species had two Zot proteins and the remaining six species/subspecies had one Zot protein. Walker A and Walker B motifs and a transmembrane domain were found in all identified Campylobacter Zot proteins. The twelve Campylobacter zot genes from the nine Campylobacter species/subspecies formed two clusters. The ZotCampyType_1 proteins encoded by Cluster 1 Campylobacter zot genes showed high similarities to each other. However, ZotCampyType_2 proteins encoded by Cluster 2 Campylobacter zot genes were more diverse. Furthermore, the zot-containing Campylobacter prophages were identified. CONCLUSION This study reports the identification of two types of Campylobacter Zot proteins. The high similarities of ZotCampyType_1 proteins suggest that they are likely to have similar virulence. ZotCampyType_2 proteins are less similar to each other and their virulent properties, if any, remain to be examined individually.
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Affiliation(s)
- Fang Liu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, 2052 Australia
| | - Hoyul Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, 2052 Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, 2052 Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, 2052 Australia
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17
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Piccirillo A, Niero G, Calleros L, Pérez R, Naya H, Iraola G. Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni). Int J Syst Evol Microbiol 2016; 66:3468-3476. [DOI: 10.1099/ijsem.0.001219] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Giulia Niero
- Department of Comparative Biomedicine and Food Science, University of Padua, Padua, Italy
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur Montevideo, Uruguay
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Gregorio Iraola
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Unidad de Bioinformática, Institut Pasteur Montevideo, Uruguay
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18
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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Abstract
The review centers on the human gastrointestinal tract; focusing first on the bacterial stress responses needed to overcome the physiochemical defenses of the host, specifically how these stress survival strategies can be used as targets for alternative infection control strategies. The concluding section focuses on recent developments in molecular diagnostics; centring on the shifting paradigm from culture to molecular based diagnostics.
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Affiliation(s)
- Roy D Sleator
- a Department of Biological Sciences ; Cork Institute of Technology ; Bishopstown , Cork , Ireland
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