The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve l... more The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve laboratory data management and to report human health as well as veterinary public health. LIMS plays an essential role in public health surveillance, outbreak investigations, and pandemic preparedness. The chapter aims is to provide an overview of LIMS use in veterinary fields as well as to report 20 years of experience of a Veterinary Public Institute in working with LIMS, illustrating the features of the LIMS currently in use in the institute and highlighting the different aspects that should be considered when evaluating, choosing, and implementing a LIMS. In depth, the chapter illustrates how LIMS simplifies the accreditation path according to ISO IEC 17025 and the role in the epidemiology and veterinary public health. For this aspect, it is very important to collect clear data, and for this reason, a LIMS has to activate formal checks and controls on business rules. To facilitate this issue, an interconnection between LIMS and other applications (internal or external to laboratory) could be improved to allow automatic data exchange. At the same time, the unique data encoding at national/international level should be used.
Advances in healthcare information systems and administration book series, 2015
The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve l... more The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve laboratory data management and to report human health as well as veterinary public health. LIMS plays an essential role in public health surveillance, outbreak investigations, and pandemic preparedness. The chapter aims is to provide an overview of LIMS use in veterinary fields as well as to report 20 years of experience of a Veterinary Public Institute in working with LIMS, illustrating the features of the LIMS currently in use in the institute and highlighting the different aspects that should be considered when evaluating, choosing, and implementing a LIMS. In depth, the chapter illustrates how LIMS simplifies the accreditation path according to ISO IEC 17025 and the role in the epidemiology and veterinary public health. For this aspect, it is very important to collect clear data, and for this reason, a LIMS has to activate formal checks and controls on business rules. To facilitate this issue, an interconnection between LIMS and other applications (internal or external to laboratory) could be improved to allow automatic data exchange. At the same time, the unique data encoding at national/international level should be used.
Campylobacter is one of the most common foodborne diseases worldwide with increasing rates of ant... more Campylobacter is one of the most common foodborne diseases worldwide with increasing rates of antibiotic resistance. Most cases of campylobacteriosis can be traced back to the consumption of poultry meat. Despite many efforts to reduce contamination in farms and in slaughterhouses, the persistence of this pathogen in poultry products remains a problem. This study aimed to evaluate the genetic diversity and antibiotic resistance of 542 C. jejuni and C. coli in Italian poultry, in the framework of two National Monitoring Programs. Genomes were screened for antibiotic resistance, virulence determinants and contextualized within a global collection of C. jejuni. ST2116, ST2863 and ST 832 were the most prevalent and significantly associated with Italian poultry. A worrying increase in resistance to quinolones, fluoroquinolones and tetracycline was observed in C. jejuni, while an increased occurrence of multidrug resistant (MDR) strains and strains resistant to macrolides was detected in ...
In order to characterize the most commonly detected Salmonella serotypes, we tested 124 isolates ... more In order to characterize the most commonly detected Salmonella serotypes, we tested 124 isolates of S. Typhimurium and 89 isolates of the monophasic variant of S. Typhimurium (S. 1,4, [5],12:i:-) for their antimicrobial susceptibility by means of the Kirby-Bauer disk-diffusion method, and for the detection of 19 genes (four Phage Markers (g13, Sieb, eat, g8), ten prophagerelated virulence genes (gipA, gtgB, nanH, gogB, grvA, sopE, sspH1, sspH2, sodC1, gtgE), and five plasmid-borne virulence genes (spvC, pefA, mig5, rcK, srgA)) by means of PCR-based assays. A total of 213 strains were analyzed from, humans (n = 122), animals (n = 25), food (n = 46), and irrigation water (n = 20). S. Typhimurium isolates showed higher variability, in both their resistance profiles and molecular typing, than S. 1,4, [5],12:i:-. Strains from irrigation water displayed significantly higher susceptibility to antibiotics than those from the other sources. Resistance to ampicillin, streptomycin, sulfonamide, and tetracycline was the most commonly detected resistance profile (R-type), being in serovar S. 1,4, [5],12:i:-, frequently associated to resistance to other antimicrobials. Significant differences in genetic profiles in the two abovementioned Salmonella serotypes were found. None of the plasmid-borne virulence genes investigated were detected in S. 1,4, [5],12:i:-isolates, while those genes, characterized 37.9% of the S. Typhimurium strains. Differences in the prevalence of some molecular targets between the two Salmonella serotypes deserve further study. Importantly, the grvA gene was found exclusively in S.
This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evalu... more This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evaluate the seasonal distribution of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus strains isolated from the Vibrata river (Abruzzo Region, Italy) during a monitoring period of one year. Detection was performed according to ISO/TS 21872-1-2:2007. Species identification and characterisation were achieved using molecular methods. Vibrio spp. were detected in 50% (23) of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 18 (39.1%), 4 (8.7%), and 2 (4.3%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 75% were positive for trh gene. In 30 V. cholerae isolates, the polymerase chain reaction (PCR) assay for detecting virulence and regulatory genes (ctxA, toxR, tcpA, ompU, hlyA, tcpI, zot, and stn/sto) revealed 6 genotypes associated to different levels of pathogenicity. Pulsed-field gel electroph...
Listeria monocytogenes is a significant food-borne human and veterinary pathogen. Contaminated si... more Listeria monocytogenes is a significant food-borne human and veterinary pathogen. Contaminated silage commonly leads to disease in livestock, but the pervasive nature of the bacterium can make it difficult to identify the source of infection. An investigation of bovine listeriosis that occurred on a Pacific Northwest dairy farm (“farm A”) revealed that the clinical strain was closely related to fecal strains from asymptomatic cows, and that farm environment was heavily contaminated with a diversity of L. monocytogenes strains. In addition, the farm A clinical strain was closely related to clinical and environmental strains obtained 1 year prior from a second Northwest dairy farm (“farm B”). To investigate the source(s) of contamination on farm A, environmental samples were collected from farm A at two time points. Pulsed-field gel electrophoresis characterization of 538 isolates obtained from that farm identified 57 different AscI pulsovars. Fecal isolates obtained from individual c...
Pecorino is a typical Italian cheese, mostly produced in central and southern Italy regions using... more Pecorino is a typical Italian cheese, mostly produced in central and southern Italy regions using ewe raw milk and following traditional procedures. The use of raw milk constitutes a risk linked to the potential survival or multiplication of pathogenic microorganisms, as Shiga toxin-producing Escherichia coli (STEC). The aim of this study was to compare different Italian traditional Pecorino production methods to determine if there were any phases that could influence the Escherichia coli O157 survival rate, but also if they could negatively influence lactic acid bacteria survival rate, during the phases of production and ripening. Therefore batches of Pecorino cheese were prepared using different production methods, representing the real and typical cheese production in southern and central Italy regions: 1) heating the milk at 37 °C for about 40 min before curding, 2) heating the milk at 60 °C (thermization) for 13 min, so that the alkaline phosphatase reaction is still positive b...
A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory... more A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory for Brucellosis. This scheme was planned for both qualitative (Rose Bengal Plate Test; RBPT) and quantitative (Complement Fixation Test; CFT) serological tests and involved a total of 42 laboratories. In the preparation of this scheme, reference was made to general protocols and guidelines and to methods reported in the literature, which were applicable to analytical chemistry laboratories. Six field sera from naturally infected animals, one positive serum at a titer below the European Union (EU) positivity threshold, and 5 sera positive at titers between 20 and 851 International Units of Complement Fixation Test (IUCFT)/mL plus one negative serum were used to produce a panel of test sera. To evaluate laboratory performances in the quantitative test for each tested sample examined, z-scores based on robust summary statistics (the median and normalized interquartile range) were used. To ...
This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evalu... more This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evaluate the seasonal distribution of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus strains isolated from the Vibrata river (Abruzzo Region, Italy) during a monitoring period of one year. Detection was performed according to ISO/TS 21872-1-2:2007. Species identification and characterisation were achieved using molecular methods. Vibrio spp. were detected in 50% (23) of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 18 (39.1%), 4 (8.7%), and 2 (4.3%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 75% were positive for trh gene. In 30 V. cholerae isolates, the polymerase chain reaction (PCR) assay for detecting virulence and regulatory genes (ctxA, toxR, tcpA, ompU, hlyA, tcpI, zot, and stn/sto) revealed 6 genotypes associated to different levels of pathogenicity. Pulsed-field gel electroph...
This study estimated the larval biomass of larvae of Trichinella britovi in wild canids in annual... more This study estimated the larval biomass of larvae of Trichinella britovi in wild canids in annual batches of carcasses recovered from the Abruzzi region, Italy, during 2013–2020. The larval biomass decreased from about six million larvae in 2013 to less than three million in 2019–2020. The province of L’Aquila (99 positive specimens out of 109) was the territory most interested by Trichinella infection. As the larval biomass correlates with the larvae per gram, muscle mass and number of positive carcasses, it could be a better indicator to assess Trichinella infection in wildlife than the prevalence alone, which correlates with only positive carcasses and the examined ones.
Widely spread in nature, Yersinia enterocolitica (YE) is a foodborne pathogen of major health and... more Widely spread in nature, Yersinia enterocolitica (YE) is a foodborne pathogen of major health and economic significance in developed countries. The aim of this study is to analyse YE strains isolated from 400 slaughtered pigs from the Abruzzo region, Italy, using biochemical tests and a multiplex polymerase chain reaction PCR detecting 6 chromosomal genes (ystA, irp2, 16s, ail, inv, hemR) and one plasmid-borne virulence gene (yadA). Antimicrobial susceptibility was evaluated and pulsed-field gel electrophoresis (PFGE) was also performed in order to assess phylogenetic diversity. In total, 56 samples of porcine tonsils (14%) were found to be positive for the presence of pathogenic YE. All YE belonged to the pathogenic bioserotype 4/O:3. All YE samples were positive for the chromosomal virulence genes ystA, ail, and inv, whereas results for the presence of yadA and hemR were variable. This study found that YE isolates were resistant to ampicillin (100%), streptomycin (26.79%), sulfiso...
A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory... more A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory for Brucellosis. This scheme was planned for both qualitative (Rose Bengal Plate Test; RBPT) and quantitative (Complement Fixation Test; CFT) serological tests and involved a total of 42 laboratories. In the preparation of this scheme, reference was made to general protocols and guidelines and to methods reported in the literature, which were applicable to analytical chemistry laboratories. Six field sera from naturally infected animals, one positive serum at a titer below the European Union (EU) positivity threshold, and 5 sera positive at titers between 20 and 851 International Units of Complement Fixation Test (IUCFT)/mL plus one negative serum were used to produce a panel of test sera. To evaluate laboratory performances in the quantitative test for each tested sample examined, z-scores based on robust summary statistics (the median and normalized interquartile range) were used. To ...
The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve l... more The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve laboratory data management and to report human health as well as veterinary public health. LIMS plays an essential role in public health surveillance, outbreak investigations, and pandemic preparedness. The chapter aims is to provide an overview of LIMS use in veterinary fields as well as to report 20 years of experience of a Veterinary Public Institute in working with LIMS, illustrating the features of the LIMS currently in use in the institute and highlighting the different aspects that should be considered when evaluating, choosing, and implementing a LIMS. In depth, the chapter illustrates how LIMS simplifies the accreditation path according to ISO IEC 17025 and the role in the epidemiology and veterinary public health. For this aspect, it is very important to collect clear data, and for this reason, a LIMS has to activate formal checks and controls on business rules. To facilitate this issue, an interconnection between LIMS and other applications (internal or external to laboratory) could be improved to allow automatic data exchange. At the same time, the unique data encoding at national/international level should be used.
Advances in healthcare information systems and administration book series, 2015
The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve l... more The Laboratory Information Management System (LIMS) is recognized as a powerful tool to improve laboratory data management and to report human health as well as veterinary public health. LIMS plays an essential role in public health surveillance, outbreak investigations, and pandemic preparedness. The chapter aims is to provide an overview of LIMS use in veterinary fields as well as to report 20 years of experience of a Veterinary Public Institute in working with LIMS, illustrating the features of the LIMS currently in use in the institute and highlighting the different aspects that should be considered when evaluating, choosing, and implementing a LIMS. In depth, the chapter illustrates how LIMS simplifies the accreditation path according to ISO IEC 17025 and the role in the epidemiology and veterinary public health. For this aspect, it is very important to collect clear data, and for this reason, a LIMS has to activate formal checks and controls on business rules. To facilitate this issue, an interconnection between LIMS and other applications (internal or external to laboratory) could be improved to allow automatic data exchange. At the same time, the unique data encoding at national/international level should be used.
Campylobacter is one of the most common foodborne diseases worldwide with increasing rates of ant... more Campylobacter is one of the most common foodborne diseases worldwide with increasing rates of antibiotic resistance. Most cases of campylobacteriosis can be traced back to the consumption of poultry meat. Despite many efforts to reduce contamination in farms and in slaughterhouses, the persistence of this pathogen in poultry products remains a problem. This study aimed to evaluate the genetic diversity and antibiotic resistance of 542 C. jejuni and C. coli in Italian poultry, in the framework of two National Monitoring Programs. Genomes were screened for antibiotic resistance, virulence determinants and contextualized within a global collection of C. jejuni. ST2116, ST2863 and ST 832 were the most prevalent and significantly associated with Italian poultry. A worrying increase in resistance to quinolones, fluoroquinolones and tetracycline was observed in C. jejuni, while an increased occurrence of multidrug resistant (MDR) strains and strains resistant to macrolides was detected in ...
In order to characterize the most commonly detected Salmonella serotypes, we tested 124 isolates ... more In order to characterize the most commonly detected Salmonella serotypes, we tested 124 isolates of S. Typhimurium and 89 isolates of the monophasic variant of S. Typhimurium (S. 1,4, [5],12:i:-) for their antimicrobial susceptibility by means of the Kirby-Bauer disk-diffusion method, and for the detection of 19 genes (four Phage Markers (g13, Sieb, eat, g8), ten prophagerelated virulence genes (gipA, gtgB, nanH, gogB, grvA, sopE, sspH1, sspH2, sodC1, gtgE), and five plasmid-borne virulence genes (spvC, pefA, mig5, rcK, srgA)) by means of PCR-based assays. A total of 213 strains were analyzed from, humans (n = 122), animals (n = 25), food (n = 46), and irrigation water (n = 20). S. Typhimurium isolates showed higher variability, in both their resistance profiles and molecular typing, than S. 1,4, [5],12:i:-. Strains from irrigation water displayed significantly higher susceptibility to antibiotics than those from the other sources. Resistance to ampicillin, streptomycin, sulfonamide, and tetracycline was the most commonly detected resistance profile (R-type), being in serovar S. 1,4, [5],12:i:-, frequently associated to resistance to other antimicrobials. Significant differences in genetic profiles in the two abovementioned Salmonella serotypes were found. None of the plasmid-borne virulence genes investigated were detected in S. 1,4, [5],12:i:-isolates, while those genes, characterized 37.9% of the S. Typhimurium strains. Differences in the prevalence of some molecular targets between the two Salmonella serotypes deserve further study. Importantly, the grvA gene was found exclusively in S.
This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evalu... more This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evaluate the seasonal distribution of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus strains isolated from the Vibrata river (Abruzzo Region, Italy) during a monitoring period of one year. Detection was performed according to ISO/TS 21872-1-2:2007. Species identification and characterisation were achieved using molecular methods. Vibrio spp. were detected in 50% (23) of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 18 (39.1%), 4 (8.7%), and 2 (4.3%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 75% were positive for trh gene. In 30 V. cholerae isolates, the polymerase chain reaction (PCR) assay for detecting virulence and regulatory genes (ctxA, toxR, tcpA, ompU, hlyA, tcpI, zot, and stn/sto) revealed 6 genotypes associated to different levels of pathogenicity. Pulsed-field gel electroph...
Listeria monocytogenes is a significant food-borne human and veterinary pathogen. Contaminated si... more Listeria monocytogenes is a significant food-borne human and veterinary pathogen. Contaminated silage commonly leads to disease in livestock, but the pervasive nature of the bacterium can make it difficult to identify the source of infection. An investigation of bovine listeriosis that occurred on a Pacific Northwest dairy farm (“farm A”) revealed that the clinical strain was closely related to fecal strains from asymptomatic cows, and that farm environment was heavily contaminated with a diversity of L. monocytogenes strains. In addition, the farm A clinical strain was closely related to clinical and environmental strains obtained 1 year prior from a second Northwest dairy farm (“farm B”). To investigate the source(s) of contamination on farm A, environmental samples were collected from farm A at two time points. Pulsed-field gel electrophoresis characterization of 538 isolates obtained from that farm identified 57 different AscI pulsovars. Fecal isolates obtained from individual c...
Pecorino is a typical Italian cheese, mostly produced in central and southern Italy regions using... more Pecorino is a typical Italian cheese, mostly produced in central and southern Italy regions using ewe raw milk and following traditional procedures. The use of raw milk constitutes a risk linked to the potential survival or multiplication of pathogenic microorganisms, as Shiga toxin-producing Escherichia coli (STEC). The aim of this study was to compare different Italian traditional Pecorino production methods to determine if there were any phases that could influence the Escherichia coli O157 survival rate, but also if they could negatively influence lactic acid bacteria survival rate, during the phases of production and ripening. Therefore batches of Pecorino cheese were prepared using different production methods, representing the real and typical cheese production in southern and central Italy regions: 1) heating the milk at 37 °C for about 40 min before curding, 2) heating the milk at 60 °C (thermization) for 13 min, so that the alkaline phosphatase reaction is still positive b...
A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory... more A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory for Brucellosis. This scheme was planned for both qualitative (Rose Bengal Plate Test; RBPT) and quantitative (Complement Fixation Test; CFT) serological tests and involved a total of 42 laboratories. In the preparation of this scheme, reference was made to general protocols and guidelines and to methods reported in the literature, which were applicable to analytical chemistry laboratories. Six field sera from naturally infected animals, one positive serum at a titer below the European Union (EU) positivity threshold, and 5 sera positive at titers between 20 and 851 International Units of Complement Fixation Test (IUCFT)/mL plus one negative serum were used to produce a panel of test sera. To evaluate laboratory performances in the quantitative test for each tested sample examined, z-scores based on robust summary statistics (the median and normalized interquartile range) were used. To ...
This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evalu... more This study aimed to isolate, define the genetic profile, assess potential pathogenicity and evaluate the seasonal distribution of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus strains isolated from the Vibrata river (Abruzzo Region, Italy) during a monitoring period of one year. Detection was performed according to ISO/TS 21872-1-2:2007. Species identification and characterisation were achieved using molecular methods. Vibrio spp. were detected in 50% (23) of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 18 (39.1%), 4 (8.7%), and 2 (4.3%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 75% were positive for trh gene. In 30 V. cholerae isolates, the polymerase chain reaction (PCR) assay for detecting virulence and regulatory genes (ctxA, toxR, tcpA, ompU, hlyA, tcpI, zot, and stn/sto) revealed 6 genotypes associated to different levels of pathogenicity. Pulsed-field gel electroph...
This study estimated the larval biomass of larvae of Trichinella britovi in wild canids in annual... more This study estimated the larval biomass of larvae of Trichinella britovi in wild canids in annual batches of carcasses recovered from the Abruzzi region, Italy, during 2013–2020. The larval biomass decreased from about six million larvae in 2013 to less than three million in 2019–2020. The province of L’Aquila (99 positive specimens out of 109) was the territory most interested by Trichinella infection. As the larval biomass correlates with the larvae per gram, muscle mass and number of positive carcasses, it could be a better indicator to assess Trichinella infection in wildlife than the prevalence alone, which correlates with only positive carcasses and the examined ones.
Widely spread in nature, Yersinia enterocolitica (YE) is a foodborne pathogen of major health and... more Widely spread in nature, Yersinia enterocolitica (YE) is a foodborne pathogen of major health and economic significance in developed countries. The aim of this study is to analyse YE strains isolated from 400 slaughtered pigs from the Abruzzo region, Italy, using biochemical tests and a multiplex polymerase chain reaction PCR detecting 6 chromosomal genes (ystA, irp2, 16s, ail, inv, hemR) and one plasmid-borne virulence gene (yadA). Antimicrobial susceptibility was evaluated and pulsed-field gel electrophoresis (PFGE) was also performed in order to assess phylogenetic diversity. In total, 56 samples of porcine tonsils (14%) were found to be positive for the presence of pathogenic YE. All YE belonged to the pathogenic bioserotype 4/O:3. All YE samples were positive for the chromosomal virulence genes ystA, ail, and inv, whereas results for the presence of yadA and hemR were variable. This study found that YE isolates were resistant to ampicillin (100%), streptomycin (26.79%), sulfiso...
A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory... more A model interlaboratory testing scheme was developed by the Italian National Reference Laboratory for Brucellosis. This scheme was planned for both qualitative (Rose Bengal Plate Test; RBPT) and quantitative (Complement Fixation Test; CFT) serological tests and involved a total of 42 laboratories. In the preparation of this scheme, reference was made to general protocols and guidelines and to methods reported in the literature, which were applicable to analytical chemistry laboratories. Six field sera from naturally infected animals, one positive serum at a titer below the European Union (EU) positivity threshold, and 5 sera positive at titers between 20 and 851 International Units of Complement Fixation Test (IUCFT)/mL plus one negative serum were used to produce a panel of test sera. To evaluate laboratory performances in the quantitative test for each tested sample examined, z-scores based on robust summary statistics (the median and normalized interquartile range) were used. To ...
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