scholarly journals Evaluation of the pathogenic potential, antimicrobial susceptibility, and genomic relations of Yersinia enterocolitica strains from food and human origin

2015 ◽  
Vol 61 (11) ◽  
pp. 851-860 ◽  
Author(s):  
Cecilia S.M. Lucero-Estrada ◽  
José Miguel Soria ◽  
Gabriela Isabel Favier ◽  
María Esther Escudero
Keyword(s):  
Yersinia Enterocolitica ◽  
Antimicrobial Susceptibility ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Pathogenic Potential ◽  
Human Samples ◽  
Virulence Markers ◽  
San Luis ◽  
Food Borne ◽  
Genomic Relationships

Yersinia enterocolitica is a food-borne pathogen that causes gastroenteritis with occasional postinfection sequels. This study was aimed to determinate the pathogenic potential, antimicrobial susceptibility, and genomic relationships of Y. enterocolitica strains of different bioserotypes (B/O) isolated from foods and human samples in San Luis, Argentina. Strains obtained by culture were bioserotyped and characterized by phenotypic and genotypic virulence markers, antimicrobial susceptibility, and pulsed-field gel electrophoresis (PFGE). Yersinia enterocolitica was detected in 9.2% of 380 samples, with a distribution of 10.6% (30/284) for food products and 5.2% (5/96) for human samples. Regarding the pathogenic potential, B1A strains of different serotypes were virF– ail–, of which 72.0% (13/18) were ystB+ with virulence-related phenotypic characteristics. Among B2/O:9 isolates, 75.0% (9/12) exhibited the genotype virF+ ail+ ystB– along with phenotypic traits associated with virulence; the same genotype was observed in 80.0% (4/5) of B3/O:3 and B3/O:5 strains. By PFGE, it was possible to separate Y. enterocolitica biotypes into 4 clonal groups (A to D) with 23 genomic types, generating a discriminatory index of 0.96. All isolates were susceptible to antimicrobials used for clinical treatment. This study highlights the presence of pathogenic bioserotypes and the high genomic diversity of the Y. enterocolitica strains isolated in our region.

scholarly journals Genomic Diversity and Virulence Profiles of Historical Escherichia coli O157 Strains Isolated from Clinical and Environmental Sources

2014 ◽  
Vol 81 (2) ◽  
pp. 569-577 ◽  
Author(s):  
Lydia V. Rump ◽  
Narjol Gonzalez-Escalona ◽  
Wenting Ju ◽  
Fei Wang ◽  
Guojie Cao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
The United States ◽  
Genomic Diversity ◽  
Severe Illness ◽  
Pathogenic Potential ◽  
Content Type ◽  
E Coli ◽  
Virulence Markers ◽  
Virulence Potential ◽  
Food Borne

ABSTRACTEscherichia coliO157:H7 is, to date, the majorE. coliserotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n= 400) isolated in the late 1980s to early 1990s in the United States. Strains were predominantly serotype O157:H7 (55%), and various O157:non-H7 (41%) serotypes were not previously reported regarding their pathogenic potential. Although lacking Shiga toxin (stx) andeaegenes, serotypes O157:H1, O157:H2, O157:H11, O157:H42, and O157:H43 carried several virulence factors (iha,terD, andhlyA) also found in virulent serotypeE. coliO157:H7. Pulsed-field gel electrophoresis (PFGE) showed the O157 serogroup was diverse, with strains with the same H type clustering together closely. Among non-H7 isolates, serotype O157:H43 was highly prevalent (65%) and carried important enterohemorrhagicE. coli(EHEC) virulence markers (iha,terD,hlyA, andespP). Isolates from two particular H types, H2 and H11, among the most commonly found non-O157 EHEC serotypes (O26:H11, O111:H11, O103:H2/H11, and O45:H2), unexpectedly clustered more closely with O157:H7 than other H types and carried several virulence genes. This suggests an early divergence of the O157 serogroup to clades with different pathogenic potentials. The appearance of important EHEC virulence markers in closely related H types suggests their virulence potential and suggests further monitoring of those serotypes not implicated in severe illness thus far.

Genotypic and Phenotypic Characteristics of Yersinia enterocolitica Isolated from the Surface of Chicken Eggshells Obtained in Argentina

2005 ◽  
Vol 68 (9) ◽  
pp. 1812-1815 ◽  
Author(s):  
GABRIELA I. FAVIER ◽  
MARÍA E. ESCUDERO ◽  
ANA MARÍA S. de GUZMÁN
Keyword(s):  
Yersinia Enterocolitica ◽  
Genomic Dna ◽  
Diffusion Method ◽  
Phenotypic Characteristics ◽  
Pathogenic Potential ◽  
San Luis ◽  
Production Stages ◽  
Chicken Eggshell ◽  
Enterocolitica Infection ◽  
Dna Profiles

The prevalence of Yersinia enterocolitica on chicken eggshell surfaces in San Luis, Argentina, was investigated. The pathogenic potential of recovered isolates was assessed by means of phenotypic virulence tests and the presence of the 72-kb pYV plasmid. Antimicrobial susceptibility was determined by the agar diffusion method. DNA digested with XbaI was analyzed by pulsed-field gel electrophoresis (PFGE), and relationships between genomic DNA profiles were established. Eight Y. enterocolitica B2 O:9 strains were recovered after enrichment, for a prevalence of 2.27%. All strains harbored the virulence pYV plasmid, bound Congo red, grew in a low-calcium medium, and autoagglutinated at 37°C. They lacked pyrazinamidase activity and did not hydrolyze esculin. These Y. enterocolitica strains were susceptible to amikacin, ciprofloxacin, chloramphenicol, and trimethoprim-sulfamethoxazole and were resistant to rifampin. According to the genomic DNA patterns obtained by PFGE, the isolates clustered into two groups, I and II. The highest similarity coefficient observed between Y. enterocolitica strains was 0.947. Microbiological controls on production stages of eggs and good culinary practices are necessary to reduce the risk of Y. enterocolitica infection for consumers.

scholarly journals Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jaewon Lim ◽  
Hong-Tae Park ◽  
Seyoung Ko ◽  
Hyun-Eui Park ◽  
Gyumin Lee ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Phenotypic Diversity ◽  
Control Strategies ◽  
Genomic Diversity ◽  
Phenotypic Traits ◽  
Whole Genome ◽  
Genomic Features ◽  
Phenotypic Differences ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

scholarly journals Identification and Characterization of Pathogenic Yersinia enterocolitica Isolates by PCR and Pulsed-Field Gel Electrophoresis

2005 ◽  
Vol 71 (7) ◽  
pp. 3674-3681 ◽  
Author(s):  
S. Thisted Lambertz ◽  
M.-L. Danielsson-Tham
Keyword(s):  
Multiplex Pcr ◽  
Yersinia Enterocolitica ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Virulence Plasmid ◽  
Pork Meat ◽  
Pulsed Field ◽  
Pork Products ◽  
Food Borne ◽  
Pork Samples

ABSTRACT Approximately 550 to 600 yersiniosis patients are reported annually in Sweden. Although pigs are thought to be the main reservoir of food-borne pathogenic Yersinia enterocolitica, the role of pork meat as a vehicle for transmission to humans is still unclear. Pork meat collected from refrigerators and local shops frequented by yersiniosis patients (n = 48) were examined for the presence of pathogenic Yersinia spp. A combined culture and PCR method was used for detection, and a multiplex PCR was developed and evaluated as a tool for efficient identification of pathogenic food and patient isolates. The results obtained with the multiplex PCR were compared to phenotypic test results and confirmed by pulsed-field gel electrophoresis (PFGE). In all, 118 pork products (91 raw and 27 ready-to-eat) were collected. Pathogenic Yersinia spp. were detected by PCR in 10% (9 of 91) of the raw pork samples (loin of pork, fillet of pork, pork chop, ham, and minced meat) but in none of the ready-to-eat products. Isolates of Y. enterocolitica bioserotype 4/O:3 were recovered from six of the PCR-positive raw pork samples; all harbored the virulence plasmid. All isolates were recovered from food collected in shops and, thus, none were from the patients' home. When subjected to PFGE, the six isolates displayed four different NotI profiles. The same four NotI profiles were also present among isolates recovered from the yersiniosis patients. The application of a multiplex PCR was shown to be an efficient tool for identification of pathogenic Y. enterocolitica isolates in naturally contaminated raw pork.

scholarly journals Yersinia enterocolitica: In Vitro Antimicrobial Susceptibility

1978 ◽  
Vol 13 (5) ◽  
pp. 888-890 ◽  
Author(s):  
M. Raevuori ◽  
S. M. Harvey ◽  
M. J. Pickett ◽  
W. J. Martin
Keyword(s):  
Yersinia Enterocolitica ◽  
Antimicrobial Susceptibility

Yersinia enterocolitica isolates from humans in California, 1968-1975

1976 ◽  
Vol 4 (2) ◽  
pp. 137-144
Author(s):  
M L Bissett
Keyword(s):  
Yersinia Enterocolitica ◽  
Antimicrobial Susceptibility ◽  
Breast Abscess ◽  
Biochemical Tests ◽  
California Department ◽  
Biochemical Characteristics ◽  
Serotype O ◽  
Department Of Health ◽  
Antimicrobial Susceptibility Tests ◽  
Susceptibility Tests

This paper reports on the serological and biochemical characteristics of 24 human isolates of Yersinia enterocolitica submitted to the California Department of Health from 1968 through 1975. Nine different serotypes were represented. The majority of strains were serotype O:8 (six strains) and serotype O:5 (five strains). Sources of the isolates included feces (12 cases), blood (3), sputum or throat (3), bile or bowel drainage (2), wounds (2), breast abscess (1), and skin abscess (1). Clinical histories indicated a number of different syndromes. Underlying medical conditions existed in 13 cases. Results of selected biochemical tests and antimicrobial susceptibility tests on the strains indicated grouping compatible with the O serotypes of the organisms.

scholarly journals Antimicrobial susceptibility and pathogenicity of Escherichia coli strains of environmental origin

2015 ◽  
Vol 45 (7) ◽  
pp. 1249-1255 ◽  
Author(s):  
Daiane Carvalho ◽  
Fabrine Finkler ◽  
Tiela Trapp Grassotti ◽  
Hiran Castagnino Kunert Filho ◽  
Francisco Esmaile de Sales Lima ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Susceptibility ◽  
Disc Diffusion ◽  
Diffusion Test ◽  
Pathogenic Potential ◽  
Highly Pathogenic ◽  
E Coli ◽  
Intermediate Degree

The study aimed to evaluate the antimicrobial susceptibility of 109 samples of Escherichia coli (E. coli) of environmental origin and to characterize these isolates according to the degree of pathogenicity in vivo, verifying a possible relationship between this variable and susceptibility to the active principles tested. The isolates were subjected to disc diffusion test to 14 antibiotics. From 16.5% to 90% of the samples were sensitive; 1 - 28.5% showed intermediate degree of susceptibility and between 9 to 78% of E. coli analyzed were resistant. The highest resistance percentages were seen in the class of quinolones and tetracyclines (>75%), and for sensitivity in the class of amphenicols (68.8%). By inoculating 1- day - old chicks, the isolates were classified as highly pathogenic (2.7%), intermediate (10.1%), low (42.2%) and apathogenic (45%). It was observed a wide variation in the susceptibility profile of isolates in relation to antimicrobials. It was also found that most of the samples had pathogenic potential (55%), thus being considered as APEC (avian pathogenic E. coli). No relationship between pathogenicity and antimicrobial susceptibility (P≤0.05) was observed.

Seroepidemiology, Antimicrobial Susceptibility and Virulence Characteristics of Clinical Klebsiella pneumoniae Isolates in Mansoura University Hospitals

2021 ◽  
Vol 30 (1) ◽  
pp. 9-18
Author(s):  
Aya H. Elasmer ◽  
Mohammed Y. Ibrahim ◽  
Dina E. Rizk
Keyword(s):  
Genetic Diversity ◽  
Klebsiella Pneumoniae ◽  
Antimicrobial Susceptibility ◽  
Genetic Relatedness ◽  
Diffusion Method ◽  
Serum Resistance ◽  
Beta Lactam ◽  
University Hospitals ◽  
Disk Diffusion Method ◽  
Pathogenic Potential

Background: Klebsiella pneumoniae is one of the crucial causes of nosocomial and community-acquired infections that can result in various infections in human. Objectives: The present study aim to investigate the prevalence of capsular serotypes, antimicrobial susceptibility and virulence characteristics of K. pneumoniae isolated from different Mansoura University Hospitals. Methodology: K. pneumoniae isolates were collected from different clinical sources at Mansoura University Hospitals. The antimicrobial susceptibility to 14 different antibiotics was determined by disk diffusion method. The capsular serotypes were assessed by quelling test. Serum resistance, haemagglutination, biofilm, lipase, protease and lecithinase enzymes production were assessed phenotypically. Moreover, four virulence genes (rmpA, fimH, kfuBC and wabG) were detected by PCR. The genetic relatedness among isolates was investigated using ERIC-PCR molecular typing. Results: Seventy-three isolates were confirmed as K. pneumoniae. The vast majority of isolates demonstrated MDR patterns (72.6%) including a high resistance rate to the beta-lactam antibiotics (ampicillin: 98.6%, amoxicillin-clavulanic acid: 97.26 %, piperacillin: 97.26 %, amoxicillin: 93.15% and cefotaxime: 94.52%). K1 and K2 were the main serotypes found among the isolates, K1 serotype was the predominant (79.45%). It was found that serum resistance was the highest detected virulence factor among isolates (95.9%) and lipase was the lowest detected factor (19.2%). Haemagglutination was detected in 63% of the isolates especially from rectal swab (83.3%) and sputum (72.7%). The biofilm formation was detected mainly among urine and blood isolates. rmpA, fimH, kfuBC and wabG genes were harbored by 20.5%, 92%, 66% and 94.5% of isolates, respectively. ERIC- PCR showed high genetic diversity (100%, typability, Simpson’s index of diversity= 1). Conclusion: The current study revealed the high antibiotic resistance levels, pathogenic potential, and genetic diversity among K. pneumoniae isolated from different clinical sources which is considered a serious health problem that necessitates interventions to control its spread.

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