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 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 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 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 Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers

2021 ◽  
Vol 12 ◽  
Author(s):  
Fiona V. Franklin-Alming ◽  
Håkon Kaspersen ◽  
Marit A. K. Hetland ◽  
Ragna-Johanne Bakksjø ◽  
Live L. Nesse ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Monitoring Program ◽  
Genotypic Resistance ◽  
High Genetic Diversity ◽  
Biofilm Production ◽  
Genes Encoding ◽  
Low Levels ◽  
Genomics Tools ◽  
Sequence Types

Klebsiella pneumoniae is a well-studied human pathogen for which antimicrobial resistant and hypervirulent clones have emerged globally. K. pneumoniae is also present in a variety of environmental niches, but currently there is a lack of knowledge on the occurrence and characteristics of K. pneumoniae from non-human sources. Certain environmental niches, e.g., animals, may be associated with high K. pneumoniae abundance, and these can constitute a reservoir for further transmission of strains and genetic elements. The aim of this study was to explore and characterize K. pneumoniae from healthy broilers and turkeys. A total of 511 cecal samples (broiler n = 356, turkey n = 155), included in the Norwegian monitoring program for antimicrobial resistance (AMR) in the veterinary sector (NORM-VET) in 2018, were screened for K. pneumoniae by culturing on SCAI agar. K. pneumoniae was detected in 207 (40.5%) samples. Among the broiler samples, 25.8% were positive for K. pneumoniae, in contrast to turkey with 74.2% positive samples (p < 0.01). Antibiotic susceptibility testing was performed, in addition to investigating biofilm production. Whole genome sequencing was performed on 203 K. pneumoniae isolates, and analysis was performed utilizing comparative genomics tools. The genomes grouped into 66 sequence types (STs), with ST35, ST4710 and ST37 being the most prevalent at 13.8%, 7.4%, and 5.4%, respectively. The overall AMR occurrence was low, with only 11.3% of the isolates showing both pheno- and genotypic resistance. Genes encoding aerobactin, salmochelin or yersiniabactin were detected in 47 (23.2%) genomes. Fifteen hypervirulent genomes belonging to ST4710 and isolated from turkey were identified. These all encoded the siderophore virulence loci iuc5 and iro5 on an IncF plasmid. Isolates from both poultry species displayed good biofilm-forming abilities with an average of OD595 0.69 and 0.64. To conclude, the occurrence of K. pneumoniae in turkey was significantly higher than in broiler, indicating that turkey might be an important zoonotic reservoir for K. pneumoniae compared to broilers. Furthermore, our results show a highly diverse K. pneumoniae population in poultry, low levels of antimicrobial resistance, good biofilm-forming abilities and a novel hypervirulent ST4710 clone circulating in the turkey population.

scholarly journals Antimicrobial Resistance, Virulence Factors, and Genetic Profiles ofVibrio parahaemolyticusfrom Seafood

2018 ◽  
Vol 84 (16) ◽  
Author(s):  
Magdalena Lopatek ◽  
Kinga Wieczorek ◽  
Jacek Osek
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Factors ◽  
Food Poisoning ◽  
High Genetic Diversity ◽  
Content Type ◽  
Genotypic Analysis ◽  
High Level ◽  
Genetic Profiles ◽  
Fish And Shellfish ◽  
Sequence Types

ABSTRACTVibrio parahaemolyticusis a widespread bacterium in the marine environment and is responsible for gastroenteritis in humans. Foodborne infections are mainly associated with the consumption of contaminated raw or undercooked fish and shellfish. The aim of this study was to determine the antimicrobial resistance, virulence factors, and genetic profiles ofV. parahaemolyticusisolates from seafood originating from different countries. A total of 104 (17.5%) isolates were recovered from 595 analyzed samples. The isolates were tested for the presence of thetdhandtrhgenes, involved in the pathogenesis ofV. parahaemolyticusinfections in humans, and these genes were detected in 3 (2.9%) and 11 (10.6%) isolates, respectively. Thetrh-positive isolates also possessed theuregene, which is responsible for urease production. Moreover, the activity of protease A was identified in allV. parahaemolyticusstrains. Antimicrobial resistance revealed that most isolates were resistant to ampicillin (75.0%) and streptomycin (68.3%), whereas all strains were sensitive to chloramphenicol and tetracyclines. Most of the isolates (55.8%) showed resistance against two classes of antimicrobials, mainly to ampicillin and streptomycin (46.2%). Only one isolate displayed a multiresistant pattern. Genotypic analysis ofV. parahaemolyticusrevealed a high degree of diversity among the isolates tested. The pulsed-field gel electrophoresis (PFGE) method distinguished 73 clonal groups, and the most numerous group consisted of 7 strains. Sequencing by the multilocus sequence typing (MLST) method showed 76 sequence types (STs), of which ST481 and ST1361 were most frequently identified. In addition, 51 (67.1%) new sequence types were discovered and added to the PubMLST international database.IMPORTANCEThe presence ofV. parahaemolyticusin seafood may pose a risk for consumers, especially in countries where shellfish are eaten raw. In recent years, a significant increase of food poisoning caused by these bacteria has been also observed in Europe. Our results highlight the high level ofV. parahaemolyticuscontamination of seafood, along with the isolates being potentially pathogenic for humans. However, the first-line antimicrobials, such as tetracyclines and fluoroquinolones, remained highly effective againstV. parahaemolyticus. The monitoring of antimicrobial resistance of isolates is important to ensure the high efficacy in the treatment of human infections. Most ofV. parahaemolyticusstrains possessed new sequence types (STs), which showed the high genetic diversity of the isolates tested.

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 Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jose F. Delgado-Blas ◽  
Cristina M. Ovejero ◽  
Sophia David ◽  
Natalia Montero ◽  
William Calero-Caceres ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Population Genomics ◽  
Population Diversity ◽  
Genomic Diversity ◽  
Resistant Bacteria ◽  
Aquatic Environments ◽  
E Coli ◽  
Water Ecosystems ◽  
Sequence Types

AbstractAquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

scholarly journals Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Moein Khojasteh ◽  
S. Mohsen Taghavi ◽  
Pejman Khodaygan ◽  
Habiballah Hamzehzarghani ◽  
Gongyou Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Global Scale ◽  
Population Diversity ◽  
Bacterial Leaf Streak ◽  
High Genetic Diversity ◽  
Center Of Origin ◽  
Content Type ◽  
Xanthomonas Translucens ◽  
Insight Into

ABSTRACT This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding’s grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding’s grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen. IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads—namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens—have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.

scholarly journals Hyper-Aerotolerant Campylobacter coli from Duck Sources and Its Potential Threat to Public Health: Virulence, Antimicrobial Resistance, and Genetic Relatedness

2019 ◽  
Vol 7 (11) ◽  
pp. 579 ◽  
Author(s):  
Jae-Ho Guk ◽  
Junhyung Kim ◽  
Hyokeun Song ◽  
Jinshil Kim ◽  
Jae-Uk An ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Inhibitory Concentration ◽  
Genetic Relatedness ◽  
Control Strategies ◽  
Campylobacter Coli ◽  
Potential Threat ◽  
High Level ◽  
Sequence Types ◽  
Level Resistance

Campylobacter, a common foodborne human pathogen, is considered sensitive to oxygen. Recently, aerotolerant (AT) Campylobacter jejuni with the ability to survive under aerobic stress has been reported. Here, we investigated the prevalence of hyper-aerotolerant (HAT) Campylobacter coli from duck sources (118 carcasses and meat) and its characteristics to assess potential impacts on public health. Half of 56 C. coli isolates were HAT and most harbored various virulence genes including flaA, cadF, cdtA, ceuB, and wlaN. Moreover, 98.2% of C. coli isolates showed resistance to quinolones, including ciprofloxacin (CIP), and nine (16.1%) showed high-level resistance to ciprofloxacin (Minimum Inhibitory Concentration, MIC ≥ 32 μg/mL) and most of these were HAT. Based on genetic relatedness between C. coli from duck sources and those from human sources (PubMLST and NCBI), HAT isolates sharing the same MLST sequence types were significantly more prevalent than those not sharing the same sequence types as those from human sources. Therefore, HAT C. coli is prevalent in duck sources, and is most likely transmitted to humans through the food chain given its aerotolerance. This being so, it might pose a threat to public health given its virulence and antimicrobial resistance (AMR). This study will assist in improving control strategies to reduce farm-to-table HAT C. coli transmission to humans.

Sign in / Sign up

Export Citation Format

Share Document