scholarly journals Selecting rep-PCR markers to source track fecal contamination in Laguna Lake, Philippines

2019 ◽  
Vol 18 (1) ◽  
pp. 19-29 ◽  
Author(s):  
Kevin L. Labrador ◽  
Mae Ashley G. Nacario ◽  
Gicelle T. Malajacan ◽  
Joseth Jermaine M. Abello ◽  
Luiza H. Galarion ◽  
...  
Keyword(s):  
Average Rate ◽  
Fecal Contamination ◽  
Total Coliform ◽  
Source Tracking ◽  
Library Size ◽  
Significant Difference ◽  
Host Origin ◽  
Polymerase Chain ◽  
Element Sequence ◽  
Laguna Lake

Abstract Fecal contamination is one of the factors causing deterioration of Laguna Lake. Although total coliform levels are constantly monitored, no protocol is in place to identify their origin. This can be addressed using the library-dependent microbial source tracking (MST) method, repetitive element sequence-based polymerase chain reaction (rep-PCR) fingerprinting. Serving as a prerequisite in developing the host-origin library, we assessed the discriminatory power of three fingerprinting primers, namely BOX-A1R, (GTG)5, and REP1R-1/2-1. Fingerprint profiles were obtained from 290 thermotolerant Escherichia coli isolated from sewage waters and fecal samples of cows, chickens, and pigs from regions surrounding the lake. Band patterns were converted into binary profiles and were classified using the discriminant analysis of principal components. Results show that: (1) REP1R-1/2-1 has a low genotyping success rate and information content; (2) increasing the library size led to more precise estimates of library accuracy; and (3) combining fingerprint profiles from BOX-A1R and (GTG)5 revealed the best discrimination (average rate of correct classification (ARCC) = 0.82 ± 0.06) in a two-way categorical split; while (4) no significant difference was found between the combined profiles (0.74 ± 0.15) and using solely BOX-A1R (0.76 ± 0.09) in a four-way split. Testing the library by identifying known isolates from a separate dataset has shown that a two-way classification performed better (ARCC = 0.66) than a four-way split (ARCC = 0.29). The library can be developed further by adding more representative isolates per host source. Nevertheless, our results have shown that combining profiles from BOX-A1R and (GTG)5 is recommended in developing the MST library for Laguna Lake.

Optimization and validation of rep-PCR genotypic libraries for microbial source tracking of environmental Escherichia coli isolates

2010 ◽  
Vol 56 (1) ◽  
pp. 8-17 ◽  
Author(s):  
Emilie Lyautey ◽  
Zexun Lu ◽  
David R. Lapen ◽  
Tanya E. Berkers ◽  
Thomas A. Edge ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Average Rate ◽  
Agricultural Landscapes ◽  
Source Tracking ◽  
Nearest Neighbour ◽  
Environmental Isolates ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Polymerase Chain Reaction Primers ◽  
Maximum Similarity

Escherichia coli can be used to help identify sources of fecal contamination in the environment. Escherichia coli genotypic fecal libraries and pattern-matching algorithms were assessed for their effectiveness in correctly identifying sources. Fecal samples (n = 172) were collected from various sources from three agricultural landscapes in Canada. Escherichia coli isolates were fingerprinted using BOX- and enterobacterial repetitive intergenic consensus (ERIC) - polymerase chain reaction primers, revealing 769 and 1 057 distinct genotypes, respectively, for the 9 047 isolates collected in 2004 in Ontario. The average rate of correct classification (ARCC) was comparable for BOX- (48%) and ERIC-based (62%) libraries and between libraries with clones removed per sample (55%) and clones removed per unit (54%). ARCC increased with fewer classification units (from 44% to 65%). ARCC for k-nearest neighbour (64%) and maximum similarity (60%) algorithms were comparable, but maximum similarity had better sensitivity and specificity than k-nearest neighbour. Geographical and temporal shifts in community composition resulted in loss of accuracy. Several ERIC genotypes (n = 112) were common between sources and were removed from the library, improving ARCC (77%). The latter library proved to be more accurate, but its accuracy with respect to sourcing environmental isolates remains to be tested.

Choice of indicator organism and library size considerations for phenotypic microbial source tracking by FAME profiling

2009 ◽  
Vol 60 (10) ◽  
pp. 2659-2668 ◽  
Author(s):  
Metin Duran ◽  
Deniz Yurtsever ◽  
Timur Dunaev
Keyword(s):  
Average Rate ◽  
Acid Methyl Ester ◽  
Primary Objective ◽  
Source Tracking ◽  
Indicator Organism ◽  
Indicator Organisms ◽  
Library Size ◽  
Level Indicator ◽  
E Coli

The primary objective of this study was to investigate the effects of choice of the indicator organisms on the accuracy of classifying the fatty acid methyl ester (FAME) profiles of the known-source library isolates. First, a known-source library containing the FAME profiles of Enterococcus isolates cultured from six different possible sources of microbial pollution was developed. A total of 511 Enterococcus isolates were profiled: 120 isolates from sewage samples representing humans; 69 from dairy and cattle cow; 74 from chicken; 76 from swine; 94 from deer; and 78 from waterfowl. Classification of known-source Enterococcus isolates into their respective host categories resulted with a 66% average rate of correct classification (ARCC) in a six-way discriminant analysis (DA). The ARCC increased to 75% when the individual hosts were pooled into larger categories of human, livestock, and wildlife. The accuracy was 80% when isolates of human origin were discriminated against those of non-human origins. Recently, several studies reported the ARCCs for various classification schemes associated with total coliform (TC), fecal coliform (FC), and Escherichia coli of the known-source isolates. When the accuracy of classification of Enterococcus isolates was compared to those reported for TC, FC, and E. coli isolates, the lowest ARCCs were associated with classification of E. coli isolates, the only species level indicator organism among the four compared. It was found that the degree of discrimination increases as the indicator becomes more inclusive of bacteria from different genus. In addition, random cluster formation analysis indicates that known-source libraries with isolate numbers between 300 and 500 might be sufficient for MST by FAME.

scholarly journals Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

2021 ◽  
Author(s):  
Laurice Beatrice Raphaelle O. dela Peña ◽  
Kevin L. Labrador ◽  
Mae Ashley G. Nacario ◽  
Nicole R. Bolo ◽  
Windell L. Rivera
Keyword(s):  
Surface Waters ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
The Philippines ◽  
Source Tracking ◽  
Source Attribution ◽  
Monitoring Methods ◽  
K Nearest Neighbors ◽  
Fecal Indicator ◽  
Laguna Lake

Abstract Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed.

scholarly journals Molecular surveillance of Cryptosporidium spp. for microbial source tracking of fecal contamination in Laguna Lake, Philippines

2021 ◽  
Author(s):  
Laurice Beatrice Raphaelle O. dela Peña ◽  
Mark Raymond A. Vejano ◽  
Windell L. Rivera
Keyword(s):  
Water Samples ◽  
Fecal Contamination ◽  
Small Subunit ◽  
Source Tracking ◽  
Rrna Gene ◽  
Molecular Surveillance ◽  
Cryptosporidium Spp ◽  
To Come ◽  
Water Quality Deterioration ◽  
Laguna Lake

Abstract Water quality deterioration in source waters poses increased health, environmental, and economic risks. Here, we genotyped Cryptosporidium spp. obtained from water samples of Laguna Lake, Philippines, and its tributaries for the purpose of source-tracking fecal contamination. A total of 104 surface water samples were collected over a 1-year period (March 2018 to April 2019). Detection of Cryptosporidium was carried out using genus-specific primers targeting a fragment of the small subunit (SSU) rRNA gene. The study revealed 8 (14%) tributary samples and 1 (2.77%) lake sample positive for contamination. The species were determined to be C. parvum (n = 4), C. muris (n = 2), C. hominis (n = 1), C. galli (n = 1), C. baileyi (n = 1), C. suis (n = 1), as well as rat genotype IV (n = 1). Two species were detected in duck (C. baileyi) and cattle (C. parvum) fecal samples. The data presented suggest that Cryptosporidium contamination is likely to come from sewage or human feces as well as various agricultural sources (i.e. cattle, swine, and poultry). This information reveals the importance of mitigating fecal pollution in the lake system and minimizing health risks due to exposure to zoonotic Cryptosporidium species.

scholarly journals Library-independent source tracking of fecal contamination in selected stations and tributaries of Laguna Lake, Philippines

2021 ◽  
Author(s):  
Joseth Jermaine M. Abello ◽  
Gicelle T. Malajacan ◽  
Kevin L. Labrador ◽  
Mae Ashley G. Nacario ◽  
Luiza H. Galarion ◽  
...  
Keyword(s):  
Water Quality ◽  
Management Practices ◽  
Fecal Contamination ◽  
The Philippines ◽  
Source Tracking ◽  
Lake Ecology ◽  
Heat Stable ◽  
Industrial Complexes ◽  
Laguna Lake

Abstract Laguna Lake is the largest inland freshwater body in the Philippines. Although it is classified to be usable for agricultural and recreational purposes by the country's Department of Environment and Natural Resources (DENR), studies looking at lake ecology revealed severe fecal contamination which contributes to the deterioration of water quality. Determining the sources of fecal contamination is necessary for lake protection and management. This study utilized a library-independent method of microbial source tracking (LIM-MST) to identify sources of fecal contamination in selected Laguna Lake stations and tributaries. Genetic markers of the host-associated Escherichia coli, heat-labile toxin (LTIIA) and heat-stable II (STII), were used to identify cattle and swine fecal contaminations, respectively. Meanwhile, human mitochondrial DNA (mtDNA) was used to identify human fecal contamination. Results identified the presence of agricultural and human fecal contamination in Laguna Lake Stations 1 and 5, Mangangate River, and Alabang River. The selected sites are known to be surrounded by residential and industrial complexes, and most of their discharges find their way into the lake. The identification of the specific sources of fecal contamination will guide management practices that aim to regulate the discharges in order to improve the water quality of Laguna Lake.

Investigation of microbial contamination of Powdered Infant Formula during different storage periods after opening

2019 ◽  
Vol 10 (03) ◽  
Author(s):  
Mohammed Khalid Al-atrash
Keyword(s):  
Infant Formula ◽  
Environmental Protection Agency ◽  
Microbial Contamination ◽  
Total Coliform ◽  
Viable Count ◽  
Risk Level ◽  
Powdered Infant Formula ◽  
Total Viable Count ◽  
Coliform Count ◽  
Significant Difference

The present study was carried out to knowing effect different storage periods of the microbial quality for the Powdered Infant Formula (PIF) after opening the tin, and ensuring from the safety note (after opening, use within 3 weeks). Thirty (30) samples of (PIF) from category (1 – 6 months) in five different types are collected from pharmacies and local markets in Baquba city / Iraq, which are used as substitutes for breast milk during the first day of opening the tin powders such as Total viable count, Total coliform count, Salmonella count and Yeast and Molds count. These experiments repeated at each week of same samples within (5) weeks. Results were obtained at opening the tin, Total viable count (less than 0.05 1.0 x 103 ±1.5x10 CFU/g) were significantly higher than Total Coliform count (less than 0.05 ± 0.3 x 10 CFU/g) and Total Salmonella count (less than 0.05 0 x 10 CFU/g) and Yeasts and Molds (less than 0.05 ± 0.3 x 10 CFU/g). while results obtained at fifth week were (less than 0.05 8.8 x 103 ±5.5x102 CFU/g), (less than 0.05 0.9 x 102 ± 0.4x101 CFU/g), (less than 0.05 0 x 10 CFU/g), (less than 0.05 9.5 x 10 ± 1.2x101 CFU /g) respectively. All samples of (PIF) having non-significant difference. These results compared to Iraqi Quality Standards (IQS), all the results from the opening samples to fifth week were within the range of IQS and USA Environmental Protection Agency (USEPA) and as indicates the hygienic condition of (PIF) without risk level for human health. also observed increase in microbial contamination in each week because increase the moisture content for powdered milk. Can be used more than 3 weeks after opening if stored in good conditions with good hygienic practices during milk preparation.

Pandora’s box in the dental clinic

2021 ◽  
pp. 1-5
Author(s):  
Debby Ben-David ◽  
Azza Vaturi ◽  
Ester Solter ◽  
Bina Rubinovitch ◽  
Jonathan Lellouche ◽  
...  
Keyword(s):  
Healthcare Workers ◽  
Healthcare Professionals ◽  
Dental Procedure ◽  
Dental Clinics ◽  
Intravenous Drugs ◽  
Environmental Surfaces ◽  
Outpatient Procedures ◽  
Polymerase Chain ◽  
And Control ◽  
Element Sequence

Abstract Background: In June 2018, the Ministry of Health received notification from 2 hospitals about 2 patients who presented with overwhelming Enterobacter kobei sepsis that developed within 24 hours after a dental procedure. We describe the investigation of this outbreak. Methods: The epidemiologic investigation included site visits in 2 dental clinics and interviews with all involved healthcare workers. Chart reviews were conducted for case and control subjects. Samples were taken from medications and antiseptics, environmental surfaces, dental water systems, and from the involved healthcare professionals. Isolate similarity was assessed using repetitive element sequence-based polymerase chain reaction (REP-PCR). Results: The 2 procedures were conducted in different dental clinics by different surgeons and dental technicians. A single anesthesiologist administered the systemic anesthetic in both cases. Cultures from medications, fluids and healthcare workers’ hands were negative, but E. kobei was detected from the anesthesiologist’s portable medication cart. The 2 human isolates and the environmental isolate shared the same REP-PCR fingerprinting profile. None of the 21 patients treated by the anesthesiologist in a general hospital during the same period, using the hospital’s medications, developed infection following surgery. Conclusions: An outbreak of post–dental-procedure sepsis was linked to a contaminated medication cart, emphasizing the importance of medication storage standards and strict aseptic technique when preparing intravenous drugs during anesthesia. Immediate reporting of sepsis following these outpatient procedures enabled early identification and termination of the outbreak.

Evaluating the Role of Anesthesia on Intraoperative Blood Loss and Visibility during Endoscopic Sinus Surgery: A Meta-analysis

2021 ◽  
pp. 194589242198915
Author(s):  
David C. Moffatt ◽  
Robert A. McQuitty ◽  
Alex E. Wright ◽  
Tawanda S. Kamucheka ◽  
Ali L. Haider ◽  
...  
Keyword(s):  
Heart Rate ◽  
Blood Loss ◽  
Endoscopic Sinus Surgery ◽  
Average Rate ◽  
Meta Analysis ◽  
Sinus Surgery ◽  
Total Blood Loss ◽  
Total Blood ◽  
Intraoperative Bleeding ◽  
Significant Difference

Background Previous studies and meta analyses have led to incongruent and incomplete results respectively when total intravenous anesthesia (TIVA) and inhalational anesthesia (IA) are compared in endoscopic sinus surgeries in regards to intraoperative bleeding and visibility. Objective To perform a more comprehensive meta-analysis on randomized controlled trial (RCTs) comparing TIVA with IA in endoscopic sinus surgery to evaluate their effects on intraoperative bleeding and visibility. Methods A systematic review and meta-analysis of studies comparing TIVA and IA in endoscopic sinus surgery for chronic rhinosinusitis was completed in May 2020. Utilizing databases, articles were systematically screened for analysis and 19 studies met our inclusion criteria. The primary outcome included intraoperative visibility scores combining Boezaart, Wormald and Visual Analogue Scale (VAS). Secondary outcomes included rate of blood loss (mL/kg/min), estimated total blood loss (mL), Boezaart, Wormald scores, VAS, heart rate, and mean arterial pressure (MAP). Results 19 RCTs with 1,010 patients were analyzed. TIVA had a significantly lower intraoperative bleeding score indicating better endoscopic visibility (Boezaart, VAS, and Wormald) than IA (−0.514, p = 0.020). IA had a significantly higher average rate of blood loss than TIVA by 0.563 mL/kg/min (p = 0.016). Estimated total blood loss was significantly lower in TIVA than IA (−0.853 mL, p = 0.002). There were no significant differences between TIVA and IA in the mean heart rate (−0.225, p = 0.63) and MAP values (−0.126, p = 0.634). The subgroup analyses revealed no significant difference between TIVA and IA when remifentanil was not utilized and whenever desflurane was the IA agent. Conclusion TIVA seemed to have superior intraoperative visibility scores and blood loss during endoscopic sinus surgery when compared to IA. However, the results are not consistent when stratifying the results based on the use of remifentanil and different inhaled anesthetics. Therefore, the conclusion cannot be made that one approach is superior to the other.

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