Publications by authors named "Saïd Oulghazi"

10 Publications

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Occurrence, antimicrobial resistance, serotyping and virulence genes of isolated from foods.

Heliyon 2021 Feb 2;7(2):e06169. Epub 2021 Feb 2.

Cellular Genomics and Molecular Techniques of Investigations, Moulay Ismail University Faculty of Sciences, BP 11201 Zitoune Meknes, Morocco.

is a pathogen contaminated food, it is the cause of listeriosis worldwide. The aims of this study were to investigate the occurrence, antimicrobial resistance, serotyping and virulence genes of isolated from foods in Meknes city of Morocco. From June 2017 to May 2018, 520 food samples were randomly collected from a traditional market and two overcrowded popular neighborhoods (Lahdim and Hamria) and subjected to the detection of . Then, the antimicrobial susceptibility of the isolated strains were evaluated using the standard disk diffusion method and the determination of serotypes and virulence genes was performed by PCR. The results showed the detection of in fifteen (2.9%) of 520 samples, including three (5.7%) isolates in traditional whey, raw minced meat and raw sausage, two (3.8%) in raw milk and one (1.9%) in smen (traditional butter), raw bovine meat, raw poultry meat and raw fish, while salads and rayeb (traditional coagulated milk) were not contaminated. Among the fifteen isolated , nine (60%) belonged to the serogroup (1/2a, 1/2c, 3a and 3c), two (13.3%) belonged to the serogroup (1/2b, 3b, 4b and 4d) and four (26.6%) do not belong to any studied serogroup. Furthermore, fifteen (100%) isolates showed the presence of gene, fourteen (93.3%) harbored , and genes, thirteen (86.7%) carried and genes and twelve (80%) showed gene. The antimicrobial susceptibility analysis showed that the isolated strains were more resistant to amoxicillin/clavulanic acid (67.0%), erythromycin (60.0%), sulphamethoxazole (40.0%), ampicillin and sulphamethoxazole/trimethoprim (33.0%) and tetracycline (20.0%). Furthermore, 66.7% (10/15) were multidrug-resistant. From this study, we can conclude that foods marketed in Meknes city were contaminated by multidrug-resistant strains of harboring virulence genes, which may cause a serious risk to public health.
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http://dx.doi.org/10.1016/j.heliyon.2021.e06169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889945PMC
February 2021

: Genomics, Host Range and Disease Management.

Microorganisms 2021 Jan 5;9(1). Epub 2021 Jan 5.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France.

(Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
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http://dx.doi.org/10.3390/microorganisms9010106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824751PMC
January 2021

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Microbiol Resour Announc 2020 Aug 6;9(32). Epub 2020 Aug 6.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, Gif-sur-Yvette, France

is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of SS95, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.
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http://dx.doi.org/10.1128/MRA.00420-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409842PMC
August 2020

Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.

Microorganisms 2020 Jun 13;8(6). Epub 2020 Jun 13.

Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.

Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.
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http://dx.doi.org/10.3390/microorganisms8060895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356628PMC
June 2020

Species Diversity of and Causing Potato Blackleg Disease in Pakistan.

Plant Dis 2020 May 8;104(5):1492-1499. Epub 2020 Mar 8.

Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.

Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (), SS28 (), SS70 (), SS90 (), SS95 (), and SS96 () were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (, , , , , , , , , , , , and ). Phylogenetic analysis revealed considerable genetic diversity in the genus . DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference and strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: , , , , , and .
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http://dx.doi.org/10.1094/PDIS-08-19-1743-REDOI Listing
May 2020

Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Isolated from Sausages.

Eur J Microbiol Immunol (Bp) 2019 Jun 9;9(2):56-61. Epub 2019 Apr 9.

Cellular Genomics and Molecular Techniques of Investigations, Moulay Ismail University Faculty of Sciences, BP. 11201 Zitoune Meknes, Morocco.

is a major cause of morbidity and mortality in humans worldwide, and the infection with multidrug-resistant strains can cause severe diseases. This study was designed to evaluate the antimicrobial resistance, to detect the virulence genes, and to study the genetic diversity of isolated strains using 16S rRNA sequences. For this, 34 strains isolated from sausages were identified using biochemical and serological methods. Molecular tools were used to evaluate the presence of virulence genes , and using simplex and multiplex polymerase chain reaction (PCR) and to sequence 16S rRNA genes for phylogenetic analysis. The susceptibility to 24 selected antibiotics was also studied. The results of this study showed that all isolated were positive for targeted virulence genes and were resistant to at least one antibiotic. However, the multidrug resistance was observed in 44% of isolated strains. The phylogenetic analysis of 16S rRNA sequences highlighted that isolates were divided into 3 clusters and 3 sub-clusters, with a ≥98% similarity to species. From this study, we conclude that sausages are considered as a potential source of , which could be a major risk to public health.
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http://dx.doi.org/10.1556/1886.2018.00035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563686PMC
June 2019

Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.

Int J Syst Evol Microbiol 2019 Aug 5;69(8):2440-2444. Epub 2019 Jun 5.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91 190 Gif-sur-Yvette, France.

Strains 2B12, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947 (=CFBP 8607) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12 (=CFBP 8650=LMG 30903) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.003497DOI Listing
August 2019

Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium.

Int J Syst Evol Microbiol 2019 Feb 2;69(2):470-475. Epub 2019 Jan 2.

1​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium carotovorum M022 has been isolated from a waterfall source in Selangor district (Malaysia). Using genomic and phenotypic tests, we re-examined the taxonomical position of this strain. Based on 14 concatenated housekeeping genes (fusA, rpoD, rpoS, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB), multi-locus sequence analysis revealed that strain M022 falls into a novel clade separated from the other Pectobacterium species. The in silico DNA-DNA hybridization and average nucleotide identity values were lower than the 70 and 95 % threshold values, respectively. In addition, by combining genomic and phenotypic tests, strain M022 may be distinguished from the other Pectobacterium isolates by its incapacity to grow on d(+)-xylose, l-rhamnose, cellobiose and lactose. Strain M022 (=CFBP 8629=LMG 30744) is proposed as the type strain of the Pectobacteriumfontis sp. nov.
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http://dx.doi.org/10.1099/ijsem.0.003180DOI Listing
February 2019

Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.

Int J Syst Evol Microbiol 2018 Nov 21;68(11):3551-3556. Epub 2018 Sep 21.

2​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium isolates SS95, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95, from its closest relatives, i.e. P. parmentieri RNS 08-42-1A and P. wasabiae CFBP3304, as well as from all the other known Pectobacteriumspecies. In silico DNA-DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95 compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95 (=CFBP 8604=LMG 30622).
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http://dx.doi.org/10.1099/ijsem.0.003029DOI Listing
November 2018

Occurrence, molecular and antimicrobial resistance of spp. isolated from raw cow's milk trade by street trading in Meknes city, Morocco.

Germs 2018 06 4;8(2):77-84. Epub 2018 Jun 4.

PhD, Bioactive Molecules, Structures and Functions, Sidi Mohamed Ben Abdallah University Faculty of Sciences and Technologies Fes, Morocco.

Background: spp. belongs to a group of pathogens which are responsible for serious infections. This study aims at highlighting the raw milk microbiological contamination and at providing data for prevalence and antimicrobial resistance of spp. isolated from raw cow's milk marketed (without any pasteurization) by street traders.

Methods: During the period of May 2015 through April 2016, 150 cow's raw milk samples were collected from street traders in Meknes city. They were examined for the identification of spp. using biochemical tests and 16S rRNA gene sequencing. The antimicrobial susceptibility of the isolates was determined.

Results: The results showed that 11.3% (17/150) of samples were positive for the presence of spp., of which 64.7% were identified as , 17.6% as , 11.8% as and 5.9% as . The antimicrobial susceptibility showed that all spp. were resistant to ampicillin. The species , , and were resistant to streptomycin, with percentages of 52.9% (9/17), 11.8% (2/17), 11.8% (2/17), and 5.9% (1/17) respectively. All isolated strains of and were resistant to tetracycline. The multiple antibiotic resistance index was elevated in the majority of spp., reaching values higher than 0.5, indicating a risk for public health.

Conclusion: This study shows that the raw milk consumed by the population is contaminated with strains of resistant to antibiotics used in breeding for prophylactic purposes. This requires raising the awareness of those involved in the production and marketing of milk, so as to take measures to apply good hygienic practices and rationalize the use of zootechnical antibiotics.
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http://dx.doi.org/10.18683/germs.2018.1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019956PMC
June 2018