Identification of Pediococcus acidilactici and Pediococcus pentosaceus based on 16S rRNA and ldhD gene-targeted multiplex PCR analysis

ABSTRACT Bifidobacteria are one of the most common bacterial types found in the intestines of humans and other animals and may be used as indicators of human fecal pollution. The presence of nine human-related Bifidobacterium species was analyzed in human and animal wastewater samples of different origins by using species-specific primers based on 16S rRNA sequences. Only B. adolescentis and B. dentium were found exclusively in human sewage. A multiplex PCR approach with strain-specific primers was developed. The method showed a sensitivity threshold of 10 cells/ml. This new molecular method could provide useful information for the characterization of fecal pollution sources.

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REP-PCR Analysis to Study Prokaryotic Biodiversity from Lake Meyghan

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.61.69 ◽

2017 ◽

Vol 61 ◽

pp. 69-84 ◽

Cited By ~ 1

Author(s):

Ali Naghoni ◽

Giti Emtiazi ◽

Mohammad Ali Amoozegar ◽

Zahra Etemadifar ◽

Seyed Abolhassan Shahzadeh Fazeli

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Pcr Analysis ◽

Rrna Gene ◽

White Region ◽

Rrna Gene Sequencing

Repetitive extragenic palindromic elements-polymerase chain reaction (rep-PCR) with 16S ribosomal ribonucleic acid (16S rRNA) genes sequences successfully used for the analysis of microbial community. In this study, the prokaryotic community in Lake Meyghan described by using rep-PCR analysis along with 16S rRNA gene sequencing. The water samples were collected from Lake Meyghan in November 2013. All samples were diluted and cultured on three different media. To estimate the number of prokaryotes per milliliter of the lake we used quantitative real‑time PCR (qPCR). Rep-PCR combination with 16S rRNA gene sequencing was performed to investigate prokaryotes biodiversity in the lake. 305 strains were isolated in this work; 113 isolates for green region, 102 isolates for red region, and 90 isolates for white region. The dendrograms generated 10, 7, and 9 clusters for a 70 % similarity cut-off for green, red, and white regions, respectively. Based on rep-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by (77.5 %)Halobacteriacaeand many isolates were related to the generaHalorubrum,Haloarcula,Haloterrigena,Natrinema, andHalovivaxin the white region. In the red region more isolated strains (57.5 %) belonged toBacillaceaeand the remaining 42.5 % of isolates belonged to archaea domain,Halorubrum, andHaloarcula. In the green region members ofGammaproteobacteriawere recoverd, this region was dominant withPseudoalteromonas,Salinivibrio, andAliidiomarina.

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Streptomyces rhizophilus Causes Potato Common Scab Disease

Plant Disease ◽

10.1094/pdis-09-20-1902-re ◽

2021 ◽

Author(s):

Qi Wei ◽

Jie Li ◽

Shuai Yang ◽

Wenzhong Wang ◽

Fanxiang Min ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Common Scab ◽

Bacterial Species ◽

Economic Losses ◽

Pcr Analysis ◽

Rrna Gene ◽

Heilongjiang Province ◽

Epidemic Disease ◽

Genus Streptomyces

Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.

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Clostridium botulinum and Clostridium perfringens Occurrence in Kazakh Honey Samples

Toxins ◽

10.3390/toxins11080472 ◽

2019 ◽

Vol 11 (8) ◽

pp. 472 ◽

Cited By ~ 4

Author(s):

Balgabay Maikanov ◽

Raikhan Mustafina ◽

Laura Auteleyeva ◽

Jan Wiśniewski ◽

Krzysztof Anusz ◽

...

Keyword(s):

Sequence Analysis ◽

Multiplex Pcr ◽

Clostridium Perfringens ◽

Clostridium Botulinum ◽

Anaerobic Bacteria ◽

The Other ◽

Pcr Analysis ◽

Rdna Genes ◽

Toxin Sequence ◽

East Kazakhstan

The aim of this study was to assess occurrence of Clostridium botulinum and Clostridium perfringens in honey samples from Kazakhstan. Analyses were carried out using a set of PCR methods for identification of anaerobic bacteria, and detection of toxin genes of C. botulinum and C. perfringens. Among 197 samples, C. botulinum was noticed in only one (0.5%). The isolated strain of this pathogen showed the presence of the bont/A and ntnh genes. C. perfringens strains were isolated from 18 (9%) samples, and mPCR (multiplex PCR) analysis led to them all being classified as toxin type A with the ability to produce α toxin. Sequence analysis of 16S rDNA genes showed occurrence in 4 samples of other anaerobes related to C. botulinum, which were C. sporogenes and C. beijerinckii strains. C. botulinum prevalence in honey samples from Kazakhstan in comparison to the prevalence in samples collected from the other regions seems to be less. The highest prevalence of Clostridium sp. was noticed in the East Kazakhstan province. Our study is the first survey on BoNT-producing clostridia and C. perfringens prevalence in Kazakh honey.

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Scientific Opinion on the safety and efficacy of Pediococcus acidilactici (CNCM I‐3237, CNCM MA 18/5M‐DSM 11673) and Pediococcus pentosaceus (DSM 23376, NCIMB 12455, NCIMB 30237 and NCIMB 30168) as silage additives for all species

EFSA Journal ◽

10.2903/j.efsa.2012.2733 ◽

2012 ◽

Vol 10 (6) ◽

Cited By ~ 4

Author(s):

Keyword(s):

Pediococcus Acidilactici ◽

Safety And Efficacy ◽

Pediococcus Pentosaceus ◽

Scientific Opinion ◽

Silage Additives

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Plasmid Profile Patterns and Properties of Pediococci Isolated from Caper Fermentations

Journal of Food Protection ◽

10.4315/0362-028x-69.5.1178 ◽

2006 ◽

Vol 69 (5) ◽

pp. 1178-1182 ◽

Cited By ~ 6

Author(s):

RUBÉN PÉREZ PULIDO ◽

HIKMATE ABRIOUEL ◽

NABIL BEN OMAR ◽

ROSARIO LUCAS LÓPEZ ◽

MAGDALENA MARTÍNEZ CAÑAMERO ◽

...

Keyword(s):

Cluster Analysis ◽

Amino Acid ◽

Antimicrobial Resistance ◽

Biogenic Amines ◽

Hemolytic Activity ◽

Plasmid Profile ◽

Pediococcus Acidilactici ◽

Pediococcus Pentosaceus ◽

Large Plasmids ◽

Resistance Tests

A collection comprising 14 isolates of Pediococcus pentosaceus and one Pediococcus acidilactici from the fermentation of caper fruits was studied. All isolates showed very similar fermentation profiles and produced a limited number of exoenzymes. All isolates carried large plasmids of diverse sizes between 20 and 55 kb, while some also contained smaller plasmids between 10 and 16 kb. Cluster analysis of plasmid profiles revealed four main groups with various degrees of similarities. All amino acid decarboxylation tests were negative, suggesting that pediococci are not involved in generation of biogenic amines. None of the isolates showed hemolytic activity. Antimicrobial resistance tests revealed that all isolates were sensitive to 11 different antimicrobials while being resistant to ciprofloxacin (MIC ≥2 mg/liter) and intrinsically resistant to vancomycin (MIC ≥16 mg/liter) and teicoplanin (MIC ≥16 mg/liter).

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Antibiotic Susceptibility, Clonality, and Molecular Characterization of Carbapenem-Resistant Clinical Isolates of Acinetobacter baumannii from Washington DC

International Journal of Microbiology ◽

10.1155/2020/2120159 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Garima Bansal ◽

Rachelle Allen-McFarlane ◽

Broderick Eribo

Keyword(s):

Acinetobacter Baumannii ◽

Multiplex Pcr ◽

Antibiotic Susceptibility ◽

Carbapenem Resistance ◽

The United States ◽

Pcr Analysis ◽

Washington Dc ◽

Antibiotic Resistant ◽

Group 4 ◽

Carbapenem Resistant

The occurrence of carbapenem-resistant (CR) strains of Acinetobacter baumannii is reported to contribute to the severity of several nosocomial infections, especially in critically ill patients in intensive care units. The present study aims to determine the antibiotic susceptibility, clonality, and genetic mechanism of carbapenem resistance in twenty-eight Acinetobacter baumannii isolates from four hospitals in Washington DC. The antibiotic susceptibility of the isolates was determined by VITEK 2 analyses, while PCR was used to examine the presence of antibiotic-resistant genes and mobile genetic elements. Trilocus multiplex-PCR was used along with pulsed-field gel electrophoresis (PFGE) for strain typing and for accessing clonal relationships among the isolates. Antimicrobial susceptibility testing indicated that 46% of the isolates were carbapenem-resistant and possessed MDR and XDR phenotypes. PFGE clustered the 28 isolates into seven clonal (C1–C7) complexes based on >75% similarity cut-off. Thirty-six percent of the isolates belonged to international clone II, while 29% were assigned to Group 4 by trilocus multiplex-PCR. Although the blaOXA-51-like gene was found in all the isolates, only 36% were positive for the blaOXA-23-like gene. PCR analysis also found a metallo-β-lactamase (MBL) gene (blaVIM) in 71% of the isolates. Of the 13 CR isolates, 8 were PCR positive for both blaVIM and blaOXA-23-like genes, while 5 harbored only blaVIM gene. This study revealed the emergence of VIM carbapenemase-producing A. baumannii isolates, which has not been previously reported in the United States.

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