scholarly journals Multi Locus Sequence Typing and spa Typing of Staphylococcus Aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia

2021 ◽  
Vol 9 (4) ◽  
pp. 725
Author(s):  
Luka Cvetnić ◽  
Marko Samardžija ◽  
Sanja Duvnjak ◽  
Boris Habrun ◽  
Marija Cvetnić ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Housekeeping Genes ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Multi Locus Sequence Typing ◽  
Spa Typing ◽  
Heterogenous Group ◽  
Sequence Types ◽  
Spa Types ◽  
Frequent Allele

Background: The bacterial species S. aureus is the most common causative agent of mastitis in cows in most countries with a dairy industry. The prevalence of infection caused by S. aureus ranges from 2% to more than 50%, and it causes 10–12% of all cases of clinical mastitis. Aim: The objective was to analyze 237 strains of S. aureus isolated from the milk of cows with subclinical mastitis regarding the spa, mecA, mecC and pvl genes and to perform spa and multi-locus sequence typing (MLST). Methods: Sequencing amplified gene sequences was conducted at Macrogen Europe. Ridom StaphType and BioNumerics software was used to analyze obtained sequences of spa and seven housekeeping genes. Results: The spa fragment was present in 204 (86.1%) of strains, while mecA and mecC gene were detected in 10 strains, and the pvl gene was not detected. Spa typing successfully analyzed 153 tested isolates (64.3%), confirming 53 spa types, four of which were new types. The most frequent spa type was t2678 (14%). MLST typed 198 (83.5%) tested strains and defined 32 different allele profiles, of which three were new. The most frequent allele profile was ST133 (20.7%). Six groups (G) and 15 singletons were defined. Conclusion: Taking the number of confirmed spa types and sequence types (STs) into account, it can be concluded that the strains of S. aureus isolated from the milk of cows with subclinical mastitis form a heterogenous group. To check the possible zoonotic potential of isolates it would be necessary to test the persons and other livestock on the farms.

scholarly journals Characterization of Escherichia coli Strains Derived from Cow Milk of Subclinical and Clinical Cases of Mastitis

2021 ◽  
Vol 11 (2) ◽  
pp. 541
Author(s):  
Katarzyna Grudlewska-Buda ◽  
Krzysztof Skowron ◽  
Ewa Wałecka-Zacharska ◽  
Natalia Wiktorczyk-Kapischke ◽  
Jarosław Bystroń ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Economic Problem ◽  
Cow Milk ◽  
P Value ◽  
Dairy Herds ◽  
E Coli ◽  
Bonferroni Test

Mastitis is a major economic problem in dairy herds, as it might decrease fertility, and negatively affect milk quality and milk yield. Out of over 150 bacterial species responsible for the udder inflammation, Escherichia coli is one of the most notable. This study aimed to assess antimicrobial susceptibility, resistance to dipping agents and biofilm formation of 150 E. coli strains isolated from milk of cows with subclinical and clinical mastitis. The strains came from three dairy herds located in Northern and Central Poland. The statistical analyses were performed with post-hoc Bonferroni test and chi-square test (including Yates correction). The data with a p value of <0.05 were considered significant. We found that the tested strains were mostly sensitive to antimicrobials and dipping agents. It was shown that 37.33% and 4.67% of strains were resistant and moderately resistant to at least one antimicrobial agent, respectively. No extended-spectrum beta-lactamases (ESBL)-producing E. coli were detected. The majority of strains did not possess the ability to form biofilm or formed a weak biofilm. The strong biofilm formers were found only among strains derived from cows with subclinical mastitis. The lowest bacteria number was noted for subclinical mastitis cows’ strains, after stabilization with iodine (3.77 log CFU × cm−2) and chlorhexidine (3.96 log CFU × cm−2) treatment. In the present study, no statistically significant differences in susceptibility to antibiotics and the ability to form biofilm were found among the strains isolated from cows with subclinical and clinical mastitis. Despite this, infections in dairy herds should be monitored. Limiting the spread of bacteria and characterizing the most common etiological factors would allow proper treatment.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals The molecular epidemiology of Staphylococcus aureus of bovine mastitis origin

2021 ◽  
Vol 91 (1) ◽  
pp. 1-10
Author(s):  
Tawheed Ahmad Shafi ◽  
◽  
Baljinder K. Bansal ◽  
Shukriti Sharma ◽  
Dhiraj K. Gupta ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Molecular Epidemiology ◽  
Protein A ◽  
Bovine Mastitis ◽  
Subclinical Mastitis ◽  
Staphylococcal Protein A ◽  
Spa Typing ◽  
New Novel ◽  
Spa Types ◽  
High Diversity

The present study was aimed to understand the molecular epidemiology of Staphylococcus aureus (54 isolates), isolated from 422 milk samples obtained from 108 subclinical mastitis affected cows (CMT positive ≥1+ in at least one quarter). The molecular epidemiology of Staphylococcus aureus was studied using coagulase (coa) gene polymorphism, 16S-23S ribosomal spascer (RS-PCR) polymorphism and Staphylococcal protein A (Spa) typing. Staphylococcus aureus produced 7 coagulase genotypes and 8 RS genotypes respectively. Coagulase genotype GTIII (730 bp) was the most prevalent (35 strains) followed by GTV (900 bp, 7 strains) and GTIV (800 bp, 4 strains), whereas RS genotypes GTA accounted for the highest number of strains (31 strains), followed by GTB (11strains), GTH (4 strains) and GTE (3 strains). Coagulase genotype CTIII (730 bp) showed the highest diversity, as isolates within it produced 5 RS genotypes, the majority of them belonging to the RS genotype GTA (29 out of 31 strains). Forty out of 54 Staphylococcus aureus samples isolated in this study were correctly typed by spa typing, and were assigned to 21 known spa types, and one new novel spa type t18462. The study revealed high diversity within Staphylococcus aureus strains, consisting of 7 coagulase genotypes, 8 RS genotypes and 22 spa types.

scholarly journals MLSTar: automatic multilocus sequence typing of bacterial genomes in R

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5098 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Multilocus Sequence Typing ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Bacterial Genomes ◽  
Standard Tool ◽  
Comparable Performance ◽  
R Packages ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals Genotypic Characteristics and Correlation of Epidemiology of Staphylococcus aureus in Healthy Pigs, Diseased Pigs, and Environment

Antibiotics ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 839
Author(s):  
Yuanyuan Zhou ◽  
Xinhui Li ◽  
He Yan
Keyword(s):  
Staphylococcus Aureus ◽  
Large Scale ◽  
Susceptibility Testing ◽  
Multidrug Resistant ◽  
Spa Typing ◽  
Antimicrobial Resistance Gene ◽  
Resistance To Penicillin ◽  
Genotypic Characteristics ◽  
Sequence Types ◽  
Spa Types

China is one of the largest producers of pigs and pork in the world. However, large-scale studies on pig-associated Staphylococcus aureus in relation to healthy pigs, diseased pigs and environment are scarce. The objective of the present study was to characterize and compare S. aureus isolates from healthy pigs, diseased pigs and environment through antimicrobial susceptibility testing, multiple locus sequence typing, spa typing, and antimicrobial resistance gene screening. Results showed all isolates were susceptible to linezolid and vancomycin. However, 66.7% (104/156) isolates were multidrug-resistant by displaying resistance to three or more antibiotics and high rates of resistance to penicillin, tetracycline, clindamycin, and clarithromycin were observed. Of the 20 multilocus sequence types (STs) identified among the isolates, ST9, ST188, and ST7 were most commonly isolated from healthy pigs and environment, while ST1 was most commonly isolated from diseased pigs. In total, 17 spa types were represented among the isolates, while t4792 was most commonly isolated from diseased pigs and t899, t189 were most commonly isolated from healthy pigs and environment. In conclusion, the genotypic and epidemiology characteristics observed among the isolates suggest pigs and pork could be important players in S. aureus dissemination.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals Prevalence and genotypic characteristics of Panton-Valentine Leukocidin-producing Staphylococcus aureus isolates obtained in Jos, North Central Nigeria

2021 ◽  
Vol 11 (2) ◽  
pp. 273-271
Author(s):  
Unyime C. Essien ◽  
Samar S. Boswihi ◽  
Nneka R. Agbakoba ◽  
Edet E. Udo
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Agents ◽  
Opportunistic Pathogen ◽  
Spa Typing ◽  
Tertiary Hospitals ◽  
Genotypic Characteristics ◽  
Sequence Types ◽  
Spa Types ◽  
Panton Valentine Leukocidin ◽  
Valentine Leukocidin

Background: Staphylococcus aureus is an opportunistic pathogen that colonizes and causes infections in humans. Panton Valentine Leukocidin (PVL) is a cytolytic toxin produced by some strains of S. aureus and are mostly associated with skin and soft tissue infections and necrotizing pneumonia. Aim: To investigate the prevalence and genotypic characteristics of PVL-positive S. aureus strains cultured from patients in three tertiary hospitals in Jos, Nigeria. Methods: Two hundred and fourteen clinical S. aureus isolates were obtained from three tertiary hospitals in Jos. Polymerase chain reaction was used to detect lukSF-PV gene that encodes PVL, and sensitivity to antimicrobial agents was performed on PVL-positive S. aureus. Genotypic characteristics of the PVL-positive S. aureus was determined by spa typing and multilocus sequence typing (MLST). Results: The genes for PVL were detected in 67/214 (31.3%) of S. aureus isolates. Majority of the PVL-positive isolates were obtained from wound (n=37; 55.2%), blood (n=11; 16.4%) and urine (n=10; 14.9). Most of PVL-positive isolates (n=58; 34.7%) were methicillin sensitive S. aureus (MSSA) while nine isolates (19.1%) were methicillin resistant S. aureus (MRSA). Spa typing identified 14 different spa types, dominated by t355 (n=33; 49.3%), followed by t174 (n=7; 10.4%), t019 and t159 (n=5; 7.5%). MLST revealed six sequence types (ST) namely, ST152 (n=35), ST121 (n=9), ST1 (n=8), ST30 (n=8), ST772 (n=6) and ST15 (N=1). Conclusion: This study revealed that 31.3% of S. aureus isolated in Jos hospitals carried genes for PVL, belonged to six sequence types and 14 spa types with t355-ST152-MSSA as the dominant genotype.

scholarly journals Multi-locus sequence types of Mycoplasma bovis isolated from Ontario, Canada in the past three decades have a temporal distribution

2017 ◽  
Vol 30 (1) ◽  
pp. 130-135 ◽  
Author(s):  
Patricia Bell-Rogers ◽  
Lois Parker ◽  
Hugh Y. Cai
Keyword(s):  
Sequence Analysis ◽  
Molecular Typing ◽  
Sequence Variation ◽  
Sequence Data ◽  
Temporal Distribution ◽  
Housekeeping Genes ◽  
Multi Locus Sequence Typing ◽  
Mycoplasma Bovis ◽  
The Past ◽  
Sequence Types

A total of 217 Mycoplasma bovis isolates cultured from clinical cases in Ontario, Canada, over the past 30 y were selected to be characterized by a multi-locus sequence typing (MLST) method. Eleven housekeeping genes were evaluated for suitability for MLST; 2 loci that had been used in prior MLST schemes, dnaN and metS, along with hsp70 were chosen for further sequence analysis. The remaining loci— adk, efp, gmk, gyrB, polC, rpoB, tpiA, and uvrC genes—were not used because they had little to no sequence variation. The sequence data from the chosen loci ( dnaN, hsp70, metS) generated 28 sequence types (STs), with the 3 loci having 15, 5, and 7 alleles, respectively. These molecular typing results revealed that the STs had a temporal distribution; over the course of 3 decades, some STs disappeared and new STs appeared. Recent isolates had a greater variety of STs, which may indicate that new strains are emerging more rapidly now than in the past.

scholarly journals Recombination Shapes the Structure of an EnvironmentalVibrio choleraePopulation

2010 ◽  
Vol 77 (2) ◽  
pp. 537-544 ◽  
Author(s):  
Daniel P. Keymer ◽  
Alexandria B. Boehm
Keyword(s):  
Bacterial Species ◽  
Housekeeping Genes ◽  
Small Sample ◽  
Detection Methods ◽  
Significant Linkage Disequilibrium ◽  
Central California ◽  
Intraspecies Diversity ◽  
The Individual ◽  
Significant Linkage ◽  
Sequence Types

ABSTRACTVibrio choleraeconsists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shownV. choleraeto be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmentalV. choleraeisolates and 13 other putativeVibrioisolates from coastal waters and sediments in central California, as well as four clinicalV. choleraeisolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of ourV. choleraeisolates. Despite frequent recombination, significant linkage disequilibrium was still detected among theV. choleraesequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate inV. choleraeof 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination amongV. choleraemay hinder the identification of ecotypes in this bacterioplankton population.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.org/iferres/MLSTar.

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