scholarly journals Multilocus Variable Number of Tandem Repeat Analysis for molecular typing of uropathogenic Escherichia coli

2020 ◽  
Author(s):  
Reza Ranjbar ◽  
Farhad Safarpoor Dehkordi ◽  
Morteza Mashhouri ◽  
Omid Farahani
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Variable Number Tandem Repeat ◽  
Pcr Amplification ◽  
Variable Number ◽  
E Coli ◽  
Repeat Analysis

Abstract Background: The aim of this study was genotyping of Uropathogenic Escherichia coli (UPEC) based on Variable Number of Tandem Repeats (VNTRs) sequences. Methods: E. coli strains isolated from urine samples were included in this study. Seven VNTR loci were subjected to Multilocus variable-number tandem repeat analysis (MLVA) based on PCR amplification. Then data was analyzed via online mlvaplus software and the information was displayed in the form of MST analysis. Results: A total of 100 E. coli strains were isolated and subjected to the study. MLVA was able to differentiate 56 different genotypes. Also, the technique could classify E. coli isolates in 5 clonal complexes. Based on UPGMA dendrograms, E. coli isolates were classified into 4 clusters (clusters A to D). The strains associated with Complex No. 1 appeared to be dominant pathogens of UPEC in Tehran's patients. The present study provides valuable insights into the genetic relationships of E. coli isolates recovered from clinical cases in a major hospital in Iran. Conclusions: The analysis of MLVA profiles using the MST algorithm showed the usefulness of the MLVA method in the classification of uropathogenic E. coli collected in different periods. We evaluated MLVA in a laboratory equipped with simple molecular equipment. Based on these results, it has been assumed that the E. coli strains were derived from a limited number of clones that have undergo a small genetic change during this period.

Microbiological Effects of a Routine Treatment for Decontaminating Hide-On Carcasses at a Large Beef Packing Plant

2015 ◽  
Vol 78 (2) ◽  
pp. 256-263 ◽  
Author(s):  
XIANQIN YANG ◽  
MADHU BADONI ◽  
FRANCES TRAN ◽  
COLIN O. GILL
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Routine Treatment ◽  
Multiple Locus ◽  
E Coli ◽  
Repeat Analysis ◽  
Before And After

To investigate the microbiological effects of a hide-on carcass decontaminating treatment recently implemented at a beef packing plant, carcasses undergoing routine processing at the plant were sampled during successive periods in January/February, April/May, and September/October. During each period, samples were collected from carcasses before and after the decontamination of hide-on carcasses, after skinning, before decontamination of the skinned carcasses, and at the end of the carcass dressing process. At each stage of processing during each period, samples were obtained by swabbing an area of 1,000 cm2 on each of 25 carcasses. Aerobes, coliforms, and Escherichia coli were enumerated. In most samples, coliforms were predominantly E. coli. In all three periods, the log mean numbers of aerobes and E. coli recovered from hides before decontamination were between 6.6 and 6.8 and between 5.3 and 5.9 log CFU/1,000 cm2, respectively. The log mean numbers of aerobes recovered from decontaminated hides were 6.6 log CFU/1,000 cm2 in January/February and April/May but 5.4 log CFU/1,000 cm2 in September/October. The log total numbers of E. coli recovered from decontaminated hides in January/February and April/May were 2.4 and 3.8 log CFU/25,000 cm2, respectively, but no E. coli was recovered from such carcasses in September/October. Log total numbers of aerobes and E. coli recovered from skinned or dressed carcasses were mostly >4 and between 1 and 2 log CFU/25,000 cm2, respectively. Typing of 480 E. coli isolates by multiple-locus variable-number tandem repeat analysis (MLVA) identified 218 MLVA types. Most isolates recovered from carcasses in different periods or at different stages of processing were of different MLVA types. However, small numbers of MLVA types were recovered in more than one period or from both hides before and after decontamination and skinned or dressed carcasses. The findings show that the hide-decontaminating treatment disrupted the usual transfer of E. coli from hides to meat surfaces during carcass skinning.

Escherichia coli O157:H7 Outbreak Associated with Restaurant Beef Grinding

2015 ◽  
Vol 78 (7) ◽  
pp. 1272-1279 ◽  
Author(s):  
LAUREN M. TORSO ◽  
RONALD E. VOORHEES ◽  
STEPHEN A. FOREST ◽  
ANDREW Z. GORDON ◽  
SHARON A. SILVESTRI ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Gel Electrophoresis ◽  
Variable Number Tandem Repeat ◽  
Ground Beef ◽  
Variable Number ◽  
Pulsed Field Gel Electrophoresis ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Repeat Analysis

Escherichia coli O157:H7 is a common cause of foodborne illness in the United States. Beef ground at establishments regulated by the U.S. Department of Agriculture, Food Safety and Inspection Service is routinely tested for E. coli O157:H7. Prior to December 2013, boxed beef product (wholesale cuts of beef, such as beef loin, packaged into bags and boxed for shipping) was not always tested for this pathogen. Downstream processors or retailers may grind the product; and, if the ground beef is not cooked to the recommended temperature, pathogens on the exterior of the beef introduced to the interior through grinding may survive. On 18 October 2013, the Allegheny County Health Department identified two E. coli O157:H7 cases, both of whom were food handlers at restaurant A, a restaurant that ground locally produced boxed beef for hamburgers on site. Case finding was conducted through public messaging, employee surveys, and disease surveillance. All potential cases were interviewed using a standard questionnaire. A confirmed case was defined as laboratory-confirmed E. coli O157:H7 with exposure to restaurant A. A probable case was defined as a patient with compatible symptoms and exposure to restaurant A but without laboratory confirmation. All human and food isolates were characterized by pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis. The analysis identified 14 confirmed and 10 probable cases of E. coli; 18 nonintact ground beef samples tested positive for E. coli O157:H7. Nine confirmed cases were restaurant A employees. All confirmed cases recalled eating a restaurant A hamburger in the 10 days before illness onset; most cases reported consuming medium to rare hamburgers. Multiple pulsed-field gel electrophoresis and multilocus variable-number tandem repeat analysis patterns were identified among both the human and ground beef isolates, and the patient isolates matched those found in ground beef samples. Restaurant A voluntarily closed for 1.5 days, changed beef suppliers, ceased grinding beef in-house, and has had no new cases since reopening.

scholarly journals Multilocus Variable-Number Tandem-Repeat Analysis for Genotyping of Escherichia coli Strains Isolated from Hospital Wastewater, Tehran, Iran

2020 ◽  
Author(s):  
Omid FARAHANI ◽  
Reza RANJBAR ◽  
Sahar HONARMAND JAHROMY ◽  
Bahareh ARABZADEH
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Bacterial Infections ◽  
Minimum Spanning Tree ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Hospital Wastewater ◽  
E Coli ◽  
Repeat Analysis ◽  
Hospital Wastewaters

Background: Escherichia coli is one of the most frequent causes of many common bacterial infections. As a potential reservoir, hospital wastewater is considered for the dissemination of bacterial pathogens such as E. coli. Therefore, research on hospital waste’s bacteria by low-cost, rapid and easy molecular typing methods such as multilocus variable-number tandem-repeat analysis (MLVA) can be helpful for the study of epidemics. Methods: E. coli strains were isolated from hospital wastewater sources in Tehran, Iran, over a 24-month sampling period (Jun 2014- Jun 2016) and identified by standard bacteriological methods. The diversity of repeated sequences of seven variable-number tandem-repeat (VNTR) loci was studied by MLVA method base on polymerase chain reaction (PCR). Results: Overall, 80 E. coli isolates were discriminated into 51 different genotypes. Analysis of the MLVA profiles using a minimum spanning tree (MST) algorithm showed two clonal complexes with 71 isolates and only nine isolates were stayed out of clonal complexes in the form of a singleton. High genotypic diversity was seen among E. coli strains isolated from hospital wastewaters; however, a large number of isolates showed a close genetic relationship. Conclusion: MLVA showed to be a rapid, inexpensive and useful tool for the analysis of the phylogenetic relationships between E. coli strains under the study

Determination of Sources of Escherichia coli on Beef by Multiple-Locus Variable-Number Tandem Repeat Analysis

2015 ◽  
Vol 78 (7) ◽  
pp. 1296-1302 ◽  
Author(s):  
XIANQIN YANG ◽  
FRANCES TRAN ◽  
MOHAMED K. YOUSSEF ◽  
COLIN O. GILL
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Conveyor Belt ◽  
Variable Number ◽  
Surface Type ◽  
Multiple Locus ◽  
E Coli ◽  
Repeat Analysis

The possible origin of Escherichia coli found on cuts and trimmings in the breaking facility of a beef packing plant was examined using multiple-locus variable-number tandem repeat analysis. Coliforms and E. coli were enumerated in samples obtained from 160 carcasses that would enter the breaking facility when work commenced and after each of the three production breaks throughout the day, from the conveyor belt before work and after each break, and from cuts and trimmings when work commenced and after each break. Most samples yielded no E. coli, irrespective of the surface types. E. coli was recovered from 7 (<5%) carcasses, at numbers mostly ≤1.0 log CFU/160,000 cm2. The log total numbers of E. coli recovered from the conveyor belt, cuts, and trimmings were mostly between 1 and 2 log CFU/80,000 cm2. A total of 554 E. coli isolates were recovered. Multiple-locus variable-number tandem repeat analysis of 327 selected isolates identified 80 distinct genotypes, with 37 (46%) each containing one isolate. However, 28% of the isolates were of genotypes that were recovered from more than one sampling day. Of the 80 genotypes, 65 and 2% were found in one or all four sampling periods throughout the day. However, they represented 23 and 14% of the isolates, respectively. Of the genotypes identified for each surface type, at least one contained ≥9 isolates. No unique genotypes were associated with carcasses, but 10, 17, and 19 were uniquely associated with cuts, trimmings, and the belt, respectively. Of the isolates recovered from cuts, 49, 3, and 19% were of genotypes that were found among isolates recovered from the belt, carcasses, or both the belt and carcasses, respectively. A similar composition was found for isolates recovered from trimmings. These findings show that the E. coli found on cuts and trimmings at this beef packing plant mainly originated from the conveyor belt and that small number of E. coli strains survived the daily cleaning and sanitation process, thus persisting in the plant.

scholarly journals Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli

2016 ◽  
Vol 125 ◽  
pp. 70-80 ◽  
Author(s):  
Chris Timmons ◽  
Eija Trees ◽  
Efrain M. Ribot ◽  
Peter Gerner-Smidt ◽  
Patti LaFon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Shiga Toxin ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis

Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producing Escherichia coli O157 to facilitate data sharing

2014 ◽  
Vol 143 (1) ◽  
pp. 104-107 ◽  
Author(s):  
A. HOLMES ◽  
N. PERRY ◽  
G. WILLSHAW ◽  
M. HANSON ◽  
L. ALLISON
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Escherichia Coli O157 ◽  
Consensus Guidelines ◽  
International Consensus ◽  
Repeat Analysis ◽  
Repeat Units ◽  
International Consensus Guidelines

SUMMARYMulti-locus variable number tandem repeat analysis (MLVA) is used in clinical and reference laboratories for subtyping verocytotoxin-producing Escherichia coli O157 (VTEC O157). However, as yet there is no common allelic or profile nomenclature to enable laboratories to easily compare data. In this study, we carried out an inter-laboratory comparison of an eight-loci MLVA scheme using a set of 67 isolates of VTEC O157. We found all but two isolates were identical in profile in the two laboratories, and repeat units were homogeneous in size but some were incomplete. A subset of the isolates (n = 17) were sequenced to determine the actual copy number of representative alleles, thereby enabling alleles to be named according to international consensus guidelines. This work has enabled us to realize the potential of MLVA as a portable, highly discriminatory and convenient subtyping method.

scholarly journals Effects of Environmental Stress on Stability of Tandem Repeats in Escherichia coli O157:H7

2010 ◽  
Vol 76 (10) ◽  
pp. 3398-3400 ◽  
Author(s):  
Michael B. Cooley ◽  
Diana Carychao ◽  
Kimberly Nguyen ◽  
Linda Whitehand ◽  
Robert Mandrell
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Diversity ◽  
Tandem Repeats ◽  
Elevated Temperatures ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Source Tracking ◽  
Escherichia Coli O157 ◽  
Repeat Analysis ◽  
Starvation Conditions

ABSTRACT Multilocus variable-number tandem-repeat analysis (MLVA) is used for source tracking Escherichia coli O157:H7 in agricultural environments. Tandem repeats were stable after limited replication but changed after exposure to irradiation, elevated temperatures, and starvation conditions. The pO157 plasmid was frequently lost under these stress conditions. Environmental stresses may increase phylogenetic diversity as measured by MLVA.

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