scholarly journals Simple Method for Assessing Diversity and Dynamics of Microbial Community: Comparison of Dairy Phages from Industrial and Spontaneous Fermentation

2021 ◽  
Author(s):  
Agnieszka Olejnik-Schmidt ◽  
Bernadeta Pietrzak ◽  
Iwona Kawacka ◽  
Klaudia Malak ◽  
Weronika Wawrzyniak ◽  
...  
Keyword(s):  
Phage Type ◽  
Low Complexity ◽  
Universal Primers ◽  
Spontaneous Fermentation ◽  
Simple Method ◽  
Protective Measures ◽  
Production Methods ◽  
Phage Types ◽  
Quality Product ◽  
Sanger Method

Background: The dairy industry heavily relies on fermentation processes driven in high proportion by Lactococcus lactis. The fermentation process can be perturbed or even stopped by bacteriophage activity leading to complete loss of fermentation batch or decreased quality product. Monitoring of the phage diversity and dynamics in the process allows to implement protective measures (e.g. starter rotation) in order to maintain unperturbed production.; Methods: Universal primers were used to amplify sequences of the 936, c2, and P335 Lactococcus phage types. The amplicons were sequences with Sanger method and obtained degenerate sequences were analyzed using simple bioinformatic pipeline in R environment.; Results: The most prevalent phage type is 936, followed by P335, whereas c2 type is less frequent.; Conclusions: Curd cheeses prepared on non-pasteurized milk based on native milk microbiota had higher diversity of phages distinct of these found in dairy plants. Sanger sequencing of heterogenous amplicons generated on metagenome DNA can be used to asses low-complexity microbiota diversity.

scholarly journals A Simple Method for Assessing Diversity and Dynamics of Microbial Community: Comparison of Dairy Phages from Industrial and Spontaneous Fermentation

2021 ◽  
Vol 11 (19) ◽  
pp. 8915
Author(s):  
Agnieszka Olejnik-Schmidt ◽  
Bernadeta Pietrzak ◽  
Iwona Kawacka ◽  
Klaudia Malak ◽  
Weronika Wawrzyniak ◽  
...  
Keyword(s):  
Phage Type ◽  
Low Complexity ◽  
Universal Primers ◽  
Spontaneous Fermentation ◽  
Simple Method ◽  
Protective Measures ◽  
Production Methods ◽  
Phage Types ◽  
Quality Product ◽  
Sanger Method

Background: The dairy industry heavily relies on fermentation processes driven in high proportion by Lactococcus lactis. The fermentation process can be perturbed or even stopped by bacteriophage activity, leading to complete loss of fermentation batch or decreased quality product. The monitoring of the phage diversity and dynamics in the process allows implementing protective measures (e.g., starter rotation) to maintain unperturbed production. Methods: Universal primers were used to amplify sequences of the 936, c2, and P335 Lactococcus phage types. The amplicons were sequenced with the Sanger method and obtained degenerate sequences were analyzed using a simple bioinformatic pipeline in the R environment. Results: The most prevalent phage type is 936, followed by P335, whereas the c2 type is less frequent. Conclusions: Curd cheeses prepared on non-pasteurized milk based on native milk microbiota had a higher diversity of phages distinct from those found in dairy plants. Sanger sequencing of heterogenous amplicons generated on metagenome DNA can be used to assess low-complexity microbiota diversity.

scholarly journals Molecular epidemiology and diversity ofSalmonellaserovar Typhimurium in pigs using phenotypic and genotypic approaches

2005 ◽  
Vol 134 (1) ◽  
pp. 187-198 ◽  
Author(s):  
W. A. GEBREYES ◽  
C. ALTIER ◽  
S. THAKUR
Keyword(s):  
Production Systems ◽  
Phage Type ◽  
Geographical Area ◽  
Multidrug Resistant ◽  
Resistance Pattern ◽  
Public Health Importance ◽  
Pig Production ◽  
Phage Types ◽  
Serovar Typhimurium ◽  
Discriminatory Index

SUMMARYFor epidemiological investigations of the most common and non-host-adaptedSalmonellaserotypes, such as Typhimurium, highly discriminatory approaches are essential. In the present study, we evaluated three genotyping methods; amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE) and repetitive palindromic extragenic–PCR (Rep–PCR) using 40 isolates. AFLP showed the highest discriminatory index (0·939), resolution and throughput. To determine clonality ofSalmonellaTyphimurium isolates and epidemiological relatedness in different commercial pig production units, we employed AFLP in combination with antimicrobial resistance pattern and phage typing.Salmonellaserovar Typhimurium isolates (n=196) obtained from a longitudinal study of 18 pig farms over a 3-year period were studied. Using this approach, 16 distinct clonal types were identified. We found two common multidrug- resistant patterns including AmCmStSuTe and AmKmStSuTe. Two commonly multidrug- resistant phage types that are of known public health importance, DT104 and DT193, were also common. AFLP differentiated distinct clones within DT104, a phage type previously reported to be clonal. Fourteen of the clonal types were unique to one of the two production systems, showing diversity between independent commercial pig production systems located in the same geographical area. Clonal types obtained from nursery farms and corresponding finishing units were, however, similar.

scholarly journals Genotypic Characterization of Salmonella enteritidis Phage Types by Plasmid Analysis, Ribotyping, and Pulsed-Field Gel Electrophoresis

1998 ◽  
Vol 36 (8) ◽  
pp. 2314-2321 ◽  
Author(s):  
A. M. Ridley ◽  
E. J. Threlfall ◽  
B. Rowe
Keyword(s):  
Gel Electrophoresis ◽  
Salmonella Enteritidis ◽  
Profile Analysis ◽  
Phage Type ◽  
Plasmid Profile ◽  
Pulsed Field Gel Electrophoresis ◽  
Single Type ◽  
Pulsed Field ◽  
Phage Types ◽  
Reference Strains

Pulsed-field gel electrophoresis (PFGE) was used to resolveXbaI and SpeI macrorestriction fragments from 60 defined phage type (PT) reference strains of Salmonella enteritidis. The level of discrimination was compared to that afforded by plasmid profile analysis and ribotyping. Twenty-eight distinct XbaI pulsed-field profiles (PFPs) were observed, although a single type, PFP X1, predominated. Absence of the 57-kbspv-associated fragment was observed for three PT reference strains, and the profile was designated PFP X1A. The XbaI macrorestriction profiles of a further four PT reference strains were altered by the presence of plasmid-associated bands. Twenty-sixSpeI-generated PFPs (plus one subtype) were observed for the same strains. No SpeI fragment corresponding to the 38-MDa serovar-specific plasmid was detected. The distribution ofXbaI and SpeI profiles did not always correspond, producing a total of 32 combined PFPs for the 60 PT reference strains. This compared with a total of 18 different plasmid profiles and three PvuII ribotypes generated by the same strains. The results of this study indicate that PFGE may offer an improved level of discrimination over other genotypic typing methods for the epidemiological typing of S. enteritidis.

scholarly journals Salmonella Enteritidis in England and Wales: increases in unusual phage types in 2002

2002 ◽  
Vol 6 (45) ◽  
Author(s):  
S O’Brien ◽  
L Ward
Keyword(s):  
Public Health ◽  
Salmonella Enteritidis ◽  
Phage Type ◽  
Enteric Pathogens ◽  
Public Health Laboratory ◽  
England And Wales ◽  
Laboratory Service ◽  
The Public ◽  
Phage Types

Although Salmonella Enteritidis phage type (PT) 4, responsible for the major epidemic during the late 1980s and early 1990s (1), has continued to decline, there have been increases in a number of the more unusual phage types of S. Enteritidis (2). Isolates of S. Enteritidis PT 3, 6a, 13a and 14b and 21 confirmed by the Public Health Laboratory Service Laboratory of Enteric Pathogens (PHLS LEP) in England have all increased during 2002 (table 1) (3).

scholarly journals Salmonella Typhimurium in livestock in Great Britain – trends observed over a 32-year period

2018 ◽  
Vol 146 (4) ◽  
pp. 409-422 ◽  
Author(s):  
D. Mueller-Doblies ◽  
K. C. R. Speed ◽  
S. Kidd ◽  
R. H. Davies
Keyword(s):  
Retrospective Study ◽  
Great Britain ◽  
Antimicrobial Resistance ◽  
Phage Type ◽  
Livestock Species ◽  
Phage Types ◽  
Specific Phage ◽  
Resistance Patterns ◽  
Over Time

AbstractIn this retrospective study, we describe and analyse Salmonella data from four livestock species in Great Britain between 1983 and 2014, focusing on Salmonella Typhimurium. A total of 96 044 Salmonella isolates were obtained during the study period. S. Typhimurium was the predominant serovar isolated from cattle and pigs and represented 40.7% (18 455/45 336) and 58.3% (4495/7709) of isolates from these species respectively, while it only accounted for 6.7% (2114/31 492) of chicken isolates and 8.1% (926/11 507) of turkey isolates. Over the study period, DT104 was the most common phage type in all four species; however, DT104 peaked in occurrence between 1995 and 1999, but is currently rare.Monophasic strains of S. Typhimurium represented less than 3% of all Salmonella isolates in cattle and chickens in 2014, but accounted for 10.4% of all turkey isolates and 39.0% of all pig isolates in the same year.Salmonella isolates were tested for their in vitro susceptibility to 16 antimicrobials. Antimicrobial resistance of S. Typhimurium isolates is largely influenced by the dominance of specific phage types at a certain time, which are commonly associated with particular resistance patterns. Changes in resistance patterns over time were analysed and compared between species.

Prevalence, Characterization, and Genotypic Analysis of Escherichia coli O157:H7/NM fromSelected Beef Exporting Abattoirs of Argentina

2010 ◽  
Vol 73 (4) ◽  
pp. 649-656 ◽  
Author(s):  
M. O. MASANA ◽  
G. A. LEOTTA ◽  
L. L. DEL CASTILLO ◽  
B. A. D'ASTEK ◽  
P. M. PALLADINO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Phage Type ◽  
Escherichia Coli O157 ◽  
Phage Types ◽  
Clonal Relatedness ◽  
Genotypic Analysis ◽  
Shiga Toxin 2 ◽  
Uremic Syndrome ◽  
Fecal Content

In Argentina, Escherichia coli O157:H7/NM (STEC O157) is the prevalent serotype associated with hemolytic uremic syndrome (HUS), which is endemic in the country with more than 400 cases per year. In order to estimate the prevalence and characteristics of STEC O157 in beef cattle at slaughter, a survey of 1,622 fecal and carcass samples was conducted in nine beef exporting abattoirs from November 2006 to April 2008. A total of 54 samples were found positive for STEC O157, with an average prevalence of 4.1% in fecal content and 2.6% in carcasses. Calves and heifers presented higher percentages of prevalence in feces, 10.5 and 8.5%, respectively. All STEC O157 isolates harbored stx2 (Shiga toxin 2), eae (intimin), ehxA (enterohemolysin), and fliCH7 (H7 flagellin) genes, while stx1 (Shiga toxin 1) was present in 16.7% of the strains. The prevalent (56%) stx genotype identified was stx2 combined with variant stx2c (vh-a), the combination of which is also prevalent (>90%) in STEC O157 post–enteric HUS cases in Argentina. The clonal relatedness of STEC O157 strains was established by phage typing and pulsed-field gel electrophoresis (PFGE). The 54 STEC isolates were categorized into 12 different phage types and in 29 XbaI-PFGE patterns distributed in 27 different lots. STEC O157 strains isolated from 5 of 21 carcasses were identical by PFGE (100% similarity) to strains of the fecal content of the same or a contiguous bovine in the lot. Five phage type–PFGE–stx profiles of 10 strains isolated in this study matched with the profiles of the strains recovered from 18 of 122 HUS cases that occurred in the same period.

scholarly journals Correlation of Phenotype with the Genotype of Egg-Contaminating Salmonella enterica Serovar Enteritidis

2005 ◽  
Vol 71 (8) ◽  
pp. 4388-4399 ◽  
Author(s):  
Cesar A. Morales ◽  
Steffen Porwollik ◽  
Jonathan G. Frye ◽  
Hailu Kinde ◽  
Michael McClelland ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Dna Sequences ◽  
Salmonella Enterica ◽  
Respiratory Activity ◽  
Phage Type ◽  
Field Isolate ◽  
Phenotype Microarray ◽  
Wild Type ◽  
Genomic Changes ◽  
Phage Types

ABSTRACT The genotype of Salmonella enterica serovar Enteritidis was correlated with the phenotype using DNA-DNA microarray hybridization, ribotyping, and Phenotype MicroArray analysis to compare three strains that differed in colony morphology and phage type. No DNA hybridization differences were found between two phage type 13A (PT13A) strains that varied in biofilm formation; however, the ribotype patterns were different. Both PT13A strains had DNA sequences similar to that of bacteriophage Fels2, whereas the PT4 genome to which they were compared, as well as a PT4 field isolate, had a DNA sequence with some similarity to the bacteriophage ST64b sequence. Phenotype MicroArray analysis indicated that the two PT13A strains and the PT4 field isolate had similar respiratory activity profiles at 37°C. However, the wild-type S. enterica serovar Enteritidis PT13A strain grew significantly better in 20% more of the 1,920 conditions tested when it was assayed at 25°C than the biofilm-forming PT13A strain grew. Statistical analysis of the respiratory activity suggested that S. enterica serovar Enteritidis PT4 had a temperature-influenced dimorphic metabolism which at 25°C somewhat resembled the profile of the biofilm-forming PT13A strain and that at 37°C the metabolism was nearly identical to that of the wild-type PT13A strain. Although it is possible that lysogenic bacteriophage alter the balance of phage types on a farm either by lytic competition or by altering the metabolic processes of the host cell in subtle ways, the different physiologies of the S. enterica serovar Enteritidis strains correlated most closely with minor, rather than major, genomic changes. These results strongly suggest that the pandemic of egg-associated human salmonellosis that came into prominence in the 1980s is primarily an example of bacterial adaptive radiation that affects the safety of the food supply.

scholarly journals Application of Fourier Transform Infrared Spectroscopy and Chemometrics for Differentiation of Salmonella enterica Serovar Enteritidis Phage Types

2010 ◽  
Vol 76 (11) ◽  
pp. 3538-3544 ◽  
Author(s):  
Ornella Preisner ◽  
Raquel Guiomar ◽  
Jorge Machado ◽  
Jos� Cardoso Menezes ◽  
Jo�o Almeida Lopes
Keyword(s):  
Fourier Transform ◽  
Ir Spectra ◽  
Salmonella Enterica ◽  
Intact Cell ◽  
Phage Type ◽  
Fourier Transform Infrared ◽  
Intact Cells ◽  
Phage Types ◽  
Ft Ir ◽  
Ir Analysis

ABSTRACT Fourier transform infrared (FT-IR) spectroscopy and chemometric techniques were used to discriminate five closely related Salmonella enterica serotype Enteritidis phage types, phage type 1 (PT1), PT1b, PT4b, PT6, and PT6a. Intact cells and outer membrane protein (OMP) extracts from bacterial cell membranes were subjected to FT-IR analysis in transmittance mode. Spectra were collected over a wavenumber range from 4,000 to 600 cm−1. Partial least-squares discriminant analysis (PLS-DA) was used to develop calibration models based on preprocessed FT-IR spectra. The analysis based on OMP extracts provided greater separation between the Salmonella Enteritidis PT1-PT1b, PT4b, and PT6-PT6a groups than the intact cell analysis. When these three phage type groups were considered, the method based on OMP extract FT-IR spectra was 100% accurate. Moreover, complementary local models that considered only the PT1-PT1b and PT6-PT6a groups were developed, and the level of discrimination increased. PT1 and PT1b isolates were differentiated successfully with the local model using the entire OMP extract spectrum (98.3% correct predictions), whereas the accuracy of discrimination between PT6 and PT6a isolates was 86.0%. Isolates belonging to different phage types (PT19, PT20, and PT21) were used with the model to test its robustness. For the first time it was demonstrated that FT-IR analysis of OMP extracts can be used for construction of robust models that allow fast and accurate discrimination of different Salmonella Enteritidis phage types.

Survey of Salmonella Contamination of Non–United Kingdom-Produced Raw Shell Eggs on Retail Sale in the Northwest of England and London, 2005 to 2006

2007 ◽  
Vol 70 (10) ◽  
pp. 2259-2265 ◽  
Author(s):  
C. L. LITTLE ◽  
S. WALSH ◽  
L. HUCKLESBY ◽  
S. SURMAN-LEE ◽  
K. PATHAK ◽  
...  
Keyword(s):  
United Kingdom ◽  
Salmonella Enteritidis ◽  
Phage Type ◽  
Control Measures ◽  
Retail Sale ◽  
England And Wales ◽  
Shell Eggs ◽  
Phage Types ◽  
Weighted Prevalence

This survey was prompted by a change in the epidemiology of Salmonella Enteritidis infections in England and Wales and elsewhere in Europe and, to our knowledge, is the first survey to provide information on Salmonella contamination of non–United Kingdom eggs on retail sale. Based on 10,464 non–United Kingdom eggs (1,744 pooled samples of six eggs) purchased between March 2005 and July 2006, the total weighted prevalence estimate for all Salmonella detected in non–United Kingdom eggs was 3.3%. Of the eggs sampled, most were produced in Spain (66.3%), France (20.0%), or The Netherlands (7.4%). Salmonella was detected from 4.4 and 0.3% of eggs produced in Spain and France, respectively, with weighted prevalence estimates. Eight different Salmonella serotypes were recovered from non–United Kingdom eggs, of which Salmonella Enteritidis predominated, with an estimated prevalence of 2.6%. Salmonella Enteritidis was obtained only from Spanish eggs. Nine different phage types of Salmonella Enteritidis were identified, with phage type 1 found to be the predominant phage type. Most of the Salmonella Enteritidis isolates obtained from Spanish eggs in the survey were resistant to nalidixic acid with concomitant decreased susceptibility to ciprofloxacin (0.125 to 1.0 mg/liter) or ampicillin (8.0 mg/liter). Salmonella Enteritidis phage type 1 until now had not been detected in eggs examined as part of previous United Kingdom egg surveys but has been detected in eggs of Spanish origin examined during recent national outbreaks of Salmonella Enteritidis non–phage type 4 infections in England and Wales. Eggs are a commonly consumed food that may occasionally be contaminated with Salmonella. The rates of contamination may be linked to the origin of the eggs. Consumers and caterers need to be aware of this continuing hazard, adopt appropriate control measures, and follow advice provided by national food agencies in order to reduce the risk of infection.

A cryptic plasmid of indigenous Rhizobium meliloti possesses reiterated nodC and nifE genes and undergoes DNA rearrangement

1992 ◽  
Vol 38 (6) ◽  
pp. 563-568 ◽  
Author(s):  
V. K. Rastogi ◽  
E. S. P. Bromfield ◽  
S. T. Whitwill ◽  
L. R. Barran
Keyword(s):  
Genomic Dna ◽  
Rhizobium Meliloti ◽  
Phage Type ◽  
Cryptic Plasmid ◽  
Dna Rearrangement ◽  
Homologous Sequences ◽  
Phage Types ◽  
Phage Sensitivity ◽  
Cryptic Plasmids ◽  
Free Strain

Indigenous Rhizobium meliloti were previously characterized on the basis of plasmid profiles and phage sensitivity patterns (phage types). Rhizobium meliloti 1076, which contained two cryptic plasmids, was one of four isolates comprising phage type 23. In this study, the large cryptic plasmid pVS1(size >500 b) was transferred from isolate 1076 into the plasmid-free strain of Agrobacterium tumefaciens UBAPF1. This plasmid contained nucleotide sequences homologous to genes for nodulation (nodB, nodC) and nitrogen fixation (nifH, nifD, nifK, nifE). Cosmid clones possessing the nod and nif homologous sequences, which had been selected from a genomic bank of A. tumefaciens UBAPF1 containing pVS1, complemented R. meliloti nodC and nifE mutants, respectively. These results demonstrate that the nodC and nifE homologous sequences are functionally expressed. Three of four isolates comprising phage type 23 possessed a megaplasmid band in agarose gels characteristic of R. meliloti, as well as two cryptic plasmids. The fourth isolate (No. 323) lacked the large cryptic plasmid corresponding to pVS1, but instead showed a band of lesser mobility than that of the megaplasmids. Nevertheless, its restricted genomic DNA retained the nodC and nifE hybridizing fragments characteristic of pVS1, indicating that the cryptic plasmid has undergone DNA rearrangement. Key words: Rhizobium, plasmid, reiteration, genes, rearrangement.

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