scholarly journals Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

2021 ◽  
Vol 15 (2) ◽  
pp. e0009207
Author(s):  
Veronica Bravo ◽  
Assaf Katz ◽  
Lorena Porte ◽  
Thomas Weitzel ◽  
Carmen Varela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Epidemiological Data ◽  
Diagnostic Methods ◽  
Campylobacter Coli ◽  
South American ◽  
Differential Distribution ◽  
High Genetic Diversity ◽  
A Genome

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

scholarly journals Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

2020 ◽  
Author(s):  
Veronica Bravo ◽  
Assaf Katz ◽  
Lorena Porte ◽  
Thomas Weitzel ◽  
Carmen Varela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
South America ◽  
Campylobacter Jejuni ◽  
Virulence Factors ◽  
Epidemiological Data ◽  
Campylobacter Coli ◽  
Genome Sequences ◽  
High Genetic Diversity ◽  
Clinical Strains

ABSTRACTCampylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.AUTHOR SUMMARYCampylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter. While ~40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.

scholarly journals Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Medelin Ocejo ◽  
Beatriz Oporto ◽  
José Luis Lavín ◽  
Ana Hurtado
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Northern Spain ◽  
Sequence Alignments ◽  
Phenotypic Data ◽  
Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

scholarly journals Prevalence, Population Diversity and Antimicrobial Resistance of Campylobacter coli Isolated in Italian Swine at Slaughterhouse

2020 ◽  
Vol 8 (2) ◽  
pp. 222 ◽  
Author(s):  
Guido Di Donato ◽  
Francesca Marotta ◽  
Roberta Nuvoloni ◽  
Katiuscia Zilli ◽  
Diana Neri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Population Diversity ◽  
Campylobacter Coli ◽  
Gyra Gene ◽  
Genotypic Resistance ◽  
High Genetic Diversity ◽  
Genetic Profiles ◽  
Carcass Contamination ◽  
Sequence Types

Campylobacter spp. are among the microorganisms most commonly associated with foodborne disease. Swine are known to be the main reservoir of Campylobacter coli and a possible source infection of humans as a result of carcass contamination at slaughter. The aim of this study was to evaluate the prevalence of C. coli contamination in swine carcasses, the antimicrobial resistance (AMR) patterns of isolates and the genetic diversity between strains obtained from swine and those isolated from humans. The prevalence of contamination was higher on carcasses (50.4%) than in faeces (32.9%). The 162 C. coli isolated from swine were examined by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The results of PFGE indicated a high genetic diversity among the isolates, with 25 different PFGE types. MLST assigned 51 sequence types (STs) to isolates. The most common genotype was ST-854 (16.04%), ST-9264 (10.49 %) and ST-1016 (6.08 %). Results of AMR showed a high resistance to quinolones and fluoroquinolones together with aminoglycosides and tetracycline. Many strains were multi-resistant with predominant R-type TeSCipNa (57%). Five resistance genes were detected along with mutation in the gyrA gene. A strong correlation between phenotypic and genotypic resistance was found for fluoroquinolone and tetracycline. Genetic profiles obtained in swine isolates were compared to those of 11 human strains. All human strains and 64.19% of animal strains (104/162) were assigned to the ST-828 clonal complex.

scholarly journals Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru

2022 ◽  
Vol 12 ◽  
Author(s):  
Willi Quino ◽  
Junior Caro-Castro ◽  
Verónica Hurtado ◽  
Diana Flores-León ◽  
Narjol Gonzalez-Escalona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Virulence Factors ◽  
In Silico ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Campylobacter Coli ◽  
Global Public Health ◽  
Emerging Pathogens ◽  
High Genetic Diversity

Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (blaoxa–61), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.

scholarly journals Prevalence, antimicrobial resistance and genetic diversity of Campylobacter coli and Campylobacter jejuni in Ecuadorian broilers at slaughter age

2017 ◽  
Vol 96 (7) ◽  
pp. 2366-2374 ◽  
Author(s):  
Christian Vinueza-Burgos ◽  
Magali Wautier ◽  
Delphine Martiny ◽  
Marco Cisneros ◽  
Inge Van Damme ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Campylobacter Coli ◽  
Slaughter Age

Application of a Group II Campylobacter Bacteriophage To Reduce Strains of Campylobacter jejuni and Campylobacter coli Colonizing Broiler Chickens

2009 ◽  
Vol 72 (4) ◽  
pp. 733-740 ◽  
Author(s):  
AYMAN EL-SHIBINY ◽  
ANDREW SCOTT ◽  
ANDREW TIMMS ◽  
YASSER METAWEA ◽  
PHILLIPPA CONNERTON ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Food Chain ◽  
Minor Component ◽  
Poultry Meat ◽  
Campylobacter Coli ◽  
Bacteriophage Therapy ◽  
Human Food ◽  
A Genome ◽  
Human Food Chain ◽  
Group Ii

Members of the genus Campylobacter are frequently responsible for human enteric disease worldwide. Persistent Campylobacter contamination of poultry meat is a common problem that represents a significant food safety risk through the consumption of undercooked poultry meat or through cross-contamination of other foods during the preparation of poultry. Bacteriophage therapy is one possible means by which this colonization of poultry could be controlled, thus limiting the entry of Campylobacter into the human food chain. Previously group III phages with genome sizes of approximately 140 kb had been administered to Campylobacter jejuni–colonized poultry. The application of a group II Campylobacter phage, CP220, with a genome size of 197 kb is described here. Phage CP220 was administered to both C. jejuni– and C. coli–colonized birds. A 2-log CFU/g decline in cecal Campylobacter counts was observed after 48 h in birds colonized with C. jejuni HPC5 and administered with a single 7-log PFU dose of CP220. The incidence of phage resistance developing in Campylobacter-colonized chickens upon exposure to virulent phages was determined to be 2%, and the resistant types remained a minor component of the population. To achieve a similar reduction in Campylobacter numbers in C. coli OR12–colonized birds, a 9-log PFU dose of CP220 was required. Using phage to reduce Campylobacter colonization in poultry offers the prospect of a sustainable intervention measure that may limit the entry of these pathogens into the human food chain.

Prevalence and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolated from Cattle between 2002 and 2006 in France

2010 ◽  
Vol 73 (5) ◽  
pp. 825-831 ◽  
Author(s):  
PIERRE CHÂTRE ◽  
MARISA HAENNI ◽  
DANIÈLE MEUNIER ◽  
MARIE-ANNE BOTREL ◽  
DIDIER CALAVAS ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Fluoroquinolone Resistance ◽  
Campylobacter Coli ◽  
Multiple Resistance ◽  
Upward Trend ◽  
Environmental Reservoir ◽  
Notable Increase ◽  
Clinical Breakpoints

Feces from 2,255 cattle (calves, young beef cattle, and culled cows) were collected at slaughter from nine departments across France. Campylobacter was recovered from 16.5% of the 2,255 samples (C. jejuni from 12.8% and C. coli from 3.7%), predominantly from calves. Antimicrobial resistance to six antibiotics of medical and/or veterinary interest was tested with the E-test. Resistance to tetracycline was found in most isolates (52.8% of C. jejuni isolates and 88.1% of C. coli isolates) in contrast to low but consistent resistance to ampicillin and erythromycin. Only two C. coli isolates were resistant to gentamicin. Multiple resistance was frequently detected in C. jejuni and C. coli isolates, and 0.8% (3 of 372) of the isolates were resistant to five of the six antimicrobials. An upward trend in the resistance to quinolones and fluoroquinolones in C. jejuni from calves was found; resistance to nalidixic acid reached 70.4% in 2006 and fluoroquinolone resistance increased from 29.7 to 70.4% during 2002 through 2006. All data were analyzed in parallel using clinical breakpoints or epidemiological cutoff values, and the results overlapped largely, except those for gentamicin. This 5-year survey (2002 through 2006) gives the first overview of the prevalence and antimicrobial resistance of C. jejuni and C. coli in cattle in France and documents to what extent cattle may contribute to the environmental reservoir of Campylobacter in France in the context of recurrent reports on links between human campylobacterioses and livestock. The results underline a notable increase in the resistance to fluoroquinolones in C. jejuni from cattle that may be of significant importance for public health.

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