Z. Kubicová, M. Filipová, J. Jurovčíková and L Cabanová
., 2013: ECDC starts pilot phase for collection of moleculartyping data. Euro Surveill. , 18, pii: 20357.
11. Véghová, A., Koreňová, J., Minarovičová, J., Drahovská, H., Siekel, P., Kaclíková, E., 2015: Isolation and characterization of Listeria monocytogenes from the environment of three ewes’ milk processing factories in Slovakia. Journal of Food and Nutrition Research , 54, 252—259.
Ioannis Sakaridis, Theofilos Papadopoulos, Evridiki Boukouvala, Loukia Ekateriniadou, Georgios Samouris and Antonios Zdragas
Campylobacter species are one of the leading causes of foodborne disease. Poultry is a major reservoir and source of its transmission to humans. The aim of this study was to estimate the prevalence and antimicrobial resistance of Campylobacter spp. isolated from chicken carcasses, the environment, and processing equipment of a poultry slaughterhouse in Greece, to identify the dominant Campylobacter species and to determine if there are clonal relationships among the isolates. Fifty poultry samples and 25 environmental samples were examined using microbial cultures and PCR. Forty-nine of 50 poultry samples (98%) were found to be positive for Campylobacter spp. The environment of the slaughterhouse was also found to be significantly contaminated with Campylobacter spp. Thirty-seven isolates were found to be susceptible to all antimicrobials tested (56.1%) and 29 isolates showed resistance to at least two of the antimicrobials tested (43.9%). We observed 24 different PFGE-types among the 53 isolates with 14 of them isolated only once, while five PFGE-types were represented by two isolates. The remaining 29 isolates were represented by five PFGE-types each consisting of three to 12 isolates. Regarding the relationship of the PFGE types and corresponding resistance profiles, all strains of each PFGE-type shared the same antimicrobial resistance profile. This study reports evidence for Campylobacter spp. cross-contamination among broiler carcasses in a Greek slaughterhouse.
Nourkhoda Sadeghifard, Reza Ranjbar, Javad Zaeimi, Mohammad Yousef Alikhani, Sobhan Ghafouryan, Mohammad Raftari, Ahmed Sahib Abdulamir, Ali Delpisheh, Reza Mohebi and Fatimah Abu Bakar
Background: Multiple-drug resistant Acinetobacter have widely spread in the last decades imposing a serious nosocomial source of infection. Nevertheless, little knowledge was gaimed on tracing the development of antibiotic resistance in Acinetobacter species. Objectives: Explore Acinetobacter spp. via antimicrobial susceptibility, plasmid profiles, and random amplified polymorphism DNA polymerase chain reaction (RAPD-PCR) typing. Methods: One hundred twelve Acinetobacter isolates (including 66 A. baumannii and 46 non-Acinetobacter baumannii strains) were obtained from three university hospitals. The source of infection of these isolates included blood, urine, wound, and respiratory tract. Their susceptibilities to 17 antibiotics were tested and then all Acinetobacter isolates were typed by plasmid analysis and RAPD-PCR method. Results: A. baumannii isolates revealed nine different patterns of antibiotic resistance. Of those, non- A. baumannii, were associated with plasmid and RAPD-PCR typings (p <0.05). A. baumannii was more resistant to multiple antibiotics than non-A. baumannii (p <0.05). Seven different plasmid profiles were observed among 112 Acinetobacter isolates. Plasmids were found in 107 (95.5%) of the 112 isolates. Unlike in RAPD-PCR typing, there was no difference between the type of Acinetobacter, A. or non-A. baumannii strains and plasmid profiles (p >0.05). By RAPD-PCR, six profiles were found for each A. and non-A. baumannii strains. The pattern 6 was the most common pattern among the isolates. Both plasmid and RAPD-PCR typing showed no association between plasmid profiling and site of infection (p >0.05). Conclusion: There is a wide spread of multi-drug resistant Acinetobacter spp., particularly A. baumannii, in the Middle East region that can be traced efficiently by plasmid and genotyping typing of Acinetobacter. More care should be taken for tracing the development of antimicrobial resistance of Acinetobacter using precise molecular typing techniques.
polymorphism.Vet Rec. 1993; 132:325-6.
11. Natarajaseenivasan K, Prabhu N, Selvanayaki K, Raja SS, Ratnam S. Human leptospirosis in Erode, South India: serology, isolation, and characterization of the isolates by randomly amplified polymorphic DNA (RAPD) fingerprinting. Jpn J Infect Dis. 2004; 7: 193-7.
12. Perolat P, Grimont F, Regnault B, Grimont PA, Fournie E, Thevenet H, et al. rRNA gene restriction patterns of Leptospira: a moleculartyping system. Res Microbiol. 1990; 141:159-71.
13. Kositanont U, Chotinantakul K
infectious diseases are a leading cause of morbidity worldwide ( Rowell et al., 2012 ; Palm et al., 2014).
The aim of this outline is to review the value of strain typing in public health and in the food industry. Selected examples are used to give an overview on current moleculartyping tools, discussing the potential as well as the shortcomings of diverse techniques in reference to our own work and to present an outlook on upcoming technologies based on WGS.
Identification of microorganisms
Identification denotes the assignment of a microorganism into a
Gorica Popova, Dean Jankuloski, Benjamin Felix, Katerina Boskovska, Biljana Stojanovska-Dimzovska, Velibor Tasic and Katerina Blagoevska
20. Caprioli, A., Maugliani, A., Michelacci, V., Morabito, S. (2014). Moleculartyping of Verocytotoxin -producing E. coli (VTEC) strains isolated from food, feed and animals : state of play and standard operating procedures for pulsed field gel electrophoresis (PFGE) typing, profiles interpretation and curation. EFSA journal EN704, 55.
21. Barrett, T.J., Gerner-Smidt, P., Swaminathan, B. (2006). Interpretation of pulsed-field gel electrophoresis patterns in foodborne disease investigations and surveillance. Foodborne Pathog Dis. 3(1): 20
spa type MRSA strains evolving in a Romanian newborns unit in 2010. Rom Rev Lab Med. 2011 Jun;Suppl.19 (2/4):S81-2.
64. Franco A, Hasman H, Iurescia M, Lorenzetti R, Stegger M, Pantosti A, et al. Molecular characterization of spa type t127, sequence type 1 methicillin-resistant Staphylococcus aureus from pigs. J Antimicrob Chemother. 2011 Jun;66(6):1231-5. DOI: 10.1093/jac/dkr115
65. Monecke S, Muller E, Dorneanu OS, Vremeră T, Ehricht R. MolecularTyping of MRSA and of Clinical Staphylococcus aureus Isolates from Iasi, Romania. PLoS ONE. 2014 May;9(5):e
Ferenc Kiskároly, Ivana Morić, Lidija Đokić, Branka Vasiljević, Lidija Šenerović and Dušan Mišić
The aim of the study was to evaluate and adapt the PCR-based protocol that utilizes the developed serotype-specific primers to identify Salmonella enterica species and its serotypes that are most frequently isolated from poultry samples in Vojvodina. Using the slide agglutination test, 64 and 33 out of 107 Salmonella isolates were identified as S. Infantis and S. Enteritidis, respectively, while ten isolates were identified as eight different Salmonella serovars. Using the same isolates, presence of 993-bp (bcfC gene), 636-bp (steB gene) and 293-bp (sdf locus) amplicons in multiplex PCR unambiguously identified 31 isolates as S. Enteritidis. Two isolates identified as Enteritidis in slide agglutination test were not identified as such in PCR-based approach since they both were missing 293-bp long PCR product. Thirty-nine isolates produced a 727-bp amplicon in the specific simplex PCR, and thus were identified as S. Infantis. The greatest discrepancy in comparison to the results of conventional serotyping has been observed in the case of S. Infantis, since 25 more isolates were noted as S. Infantis by conventional serotyping. Seven isolates, with unexpected PCR profiles stayed unidentified by molecular typing, although they were serotyped as S. Typhimurium (1) and S. Infantis (6). S. Gallinarum serovar has to be additionally confirmed, since it shares the same PCR profile with S. Livingstone. Clearly, PCR-based identification has to be thoroughly checked, verified and adapted if it is to be applied as the routine identification protocol.
Enterobiasis is a human intestinal parasitic disease caused by human pinworm, Enterobius vermicularis. Despite being the most prevalent nematode infection in Europe and North America, predominantly among in school aged children, the data concerning infection rate and knowledge of genetic variability of pinworms are incomplete. The aim of the study was the estimation of prevalence and molecular typing of Enterobius vermicularis among healthy children in north-eastern Poland. In 2013 – 2015, 296 individuals (aged 2 – 18 years) from 12 kindergartens, schools and orphanages were examined by the adhesive cellophane tape method. Data on socio-demographic status were collected using a questionnaire. Molecular analysis was performed using the DNA of adult female pinworms and primers targeting the region of cytochrome oxidase I gene. The overall prevalence of enterobiasis was 10.1 %. Enterobius vermicularis infection rates were 3.9 % in children living in families and 32.8 % among the orphans (OR=0.08; 95 % CI: 0.04 – 0.19; p<0.001). There were no associations between distribution of enterobiasis and gender, pets possession and the season of examination. In 43.3 % of the infected children enterobiasis was asymptomatic. Based on a molecular marker three different haplotypes of pinworm were identified. All sequences clustered within type B, together with human E. vermicularis isolates from Denmark, Germany, Greece, and Japan. This paper provides complementary data on the occurrence and intraspecific variability of E. vermicularis in human population in Europe.
Genomics is a comprehensive study of the whole genome, genetic products, and their interactions. Human genome project has identified around 25,000-30,000 genes, and prevailing presence in tumor pathogenesis, high number of mutations, epigenetic changes, and other gene disorders have been identified. Microarrays technology is used for the analysis of these changes. Postgenome age has begun, and the initial results ensure the improvement of molecular tumor diagnostics and the making of a new taxonomic tumor classification, as well as the improvement, optimization and individualization of anti-tumor therapy. First genomic classifications have been made of leukemias, non-Hodgkin lymphoma, and many solid tumors. For example, 4 molecular types of breast carcinoma, three types of diffuse B cell lymphoma, two types of chromophobic renal carcinoma have been identified. Also, gene structures for favorable and unfavorable outcome in leukemia, breast cancer, prostate, bronchi, and other tumors have been identified. It is absolutely possible to diagnose the primary outcome of tumors with which standard tumor position may not be proved using standard diagnostic tools. Pharmacogenomic profiles have ensured better definition of interindividual differences during therapy using antineoplastic drugs and the decrease of their toxicity, as well as individual treatment approach and patient selection with which favorable clinical outcome is expected. Pharmacogenomics has impacted the accelerated development of target drugs, which have showed to be useful in practice. New genomic markers mtDNA, meDNA, and miRNA have been identified, which, with great certainty, help the detection and diagnostics of carcinoma. In the future, functional genomics in clinical oncology provides to gain knowledge about tumor pathogenesis; it will improve diagnostics and prognosis, and open up new therapeutic options.