scholarly journals First Insights into the Evolution of Streptococcus uberis: a Multilocus Sequence Typing Scheme That Enables Investigation of Its Population Biology

2006 ◽  
Vol 72 (2) ◽  
pp. 1420-1428 ◽  
Author(s):  
Tracey J. Coffey ◽  
Gillian D. Pullinger ◽  
Rachel Urwin ◽  
Keith A. Jolley ◽  
Stephen M. Wilson ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Mastitis ◽  
Housekeeping Gene ◽  
Global Scale ◽  
Streptococcus Uberis ◽  
Capsule Production ◽  
Sequence Types ◽  
Better Than

ABSTRACT Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis throughout the world. Several procedures to differentiate S. uberis isolates have been proposed. However, all are prone to interlaboratory variation, and none is suitable for the description of the population structure. We describe here the development of a multilocus sequence typing (MLST) scheme for S. uberis to help address these issues. The sequences of seven housekeeping gene fragments from each of 160 United Kingdom milk isolates of S. uberis were determined. Between 5 and 17 alleles were obtained per locus, giving the potential to discriminate between 1.3 × 107 sequence types. In this study, 57 sequence types (STs) were identified. Statistical comparisons between the maximum-likelihood trees constructed by using the seven housekeeping gene fragments showed that the congruence was no better than that between each tree and trees of random topology, indicating there had been significant recombination within these loci. The population contained one major lineage (designated the ST-5 complex). This dominated the population, containing 24 STs and representing 112 isolates. The other 33 STs were not assigned to any clonal complex. All of the isolates in the ST-5 lineage carried hasA, a gene that is essential for capsule production. There was no clear association between ST or clonal complex and disease. The S. uberis MLST system offers researchers a valuable tool that allows further investigation of the population biology of this organism and insights into the epidemiology of this disease on a global scale.

scholarly journals Application of Streptococcus uberis Multilocus Sequence Typing: Analysis of the Population Structure Detected among Environmental and Bovine Isolates from New Zealand and the United Kingdom

2006 ◽  
Vol 72 (2) ◽  
pp. 1429-1436 ◽  
Author(s):  
Gillian D. Pullinger ◽  
Mario López-Benavides ◽  
Tracey J. Coffey ◽  
John H. Williamson ◽  
Ray T. Cursons ◽  
...  
Keyword(s):  
United Kingdom ◽  
New Zealand ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Milk ◽  
Capsule Formation ◽  
The United Kingdom ◽  
Streptococcus Uberis ◽  
Sequence Types

ABSTRACT We recently developed a multilocus sequence typing (MLST) scheme to differentiate S. uberis isolates and facilitate an understanding of the population biology of this pathogen. The scheme was initially used to study a collection of 160 bovine milk isolates from the United Kingdom and showed that the majority of isolates were from one clonal complex (designated the ST-5 complex). Here we describe the MLST analysis of a collection of New Zealand isolates. These were obtained from diverse sources, including bovine milk, other bovine anatomical sites, and environmental sources. The complete allelic profiles of 253 isolates were determined. The collection was highly diverse and included 131 different sequence types (STs). The New Zealand and United Kingdom populations were distinct, since none of the 131 STs were represented within the previously studied collection of 160 United Kingdom S. uberis isolates. However, seven of the STs were members of the ST-5 clonal complex, the major complex within the United Kingdom collection. Two new clonal complexes were identified: ST-143 and ST-86. All three major complexes were isolated from milk, other bovine sites, and the environment. Carriage of the hasA gene, which is necessary for capsule formation, correlated with clonal complex and isolation from clinical cases of mastitis.

Nonencapsulated or nontypeableHaemophilus influenzaeare more likely than their encapsulated or serotypeable counterparts to have mutations in their fucose operon

2011 ◽  
Vol 57 (12) ◽  
pp. 982-986 ◽  
Author(s):  
Michelle L. Shuel ◽  
Kathleen E. Karlowsky ◽  
Dennis K.S. Law ◽  
Raymond S.W. Tsang
Keyword(s):  
Nucleotide Sequence ◽  
Haemophilus Influenzae ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Housekeeping Genes ◽  
Sequence Variations ◽  
Sequence Types ◽  
Complete Deletion

Population biology of Haemophilus influenzae can be studied by multilocus sequence typing (MLST), and isolates are assigned sequence types (STs) based on nucleotide sequence variations in seven housekeeping genes, including fucK. However, the ST cannot be assigned if one of the housekeeping genes is absent or cannot be detected by the current protocol. Occasionally, strains of H. influenzae have been reported to lack the fucK gene. In this study, we examined the prevalence of this mutation among our collection of H. influenzae isolates. Of the 704 isolates studied, including 282 encapsulated and 422 nonencapsulated isolates, nine were not typeable by MLST owing to failure to detect the fucK gene. All nine fucK-negative isolates were nonencapsulated and belonged to various biotypes. DNA sequencing of the fucose operon region confirmed complete deletion of genes in the operon in seven of the nine isolates, while in the remaining two isolates, some of the genes were found intact or in parts. The significance of these findings is discussed.

scholarly journals Sequence Types and Antimicrobial Resistance Profiles of Streptococcus uberis Isolated From Bovine Mastitis

2019 ◽  
Vol 6 ◽  
Author(s):  
Nadine Käppeli ◽  
Marina Morach ◽  
Katrin Zurfluh ◽  
Sabrina Corti ◽  
Magdalena Nüesch-Inderbinen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bovine Mastitis ◽  
Streptococcus Uberis ◽  
Sequence Types

scholarly journals Characterization of Streptococcus pneumoniae isolates from India with special reference to their sequence types

2013 ◽  
Vol 7 (02) ◽  
pp. 101-109 ◽  
Author(s):  
Malini Shariff ◽  
Jyoti Choudhary ◽  
Shazia Zahoor ◽  
Monorama Deb
Keyword(s):  
Streptococcus Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
The Elderly ◽  
New Delhi ◽  
Broth Microdilution ◽  
Mortality And Morbidity ◽  
Resistance To Penicillin ◽  
Sequence Types

Introduction: Streptococcus pneumoniae is a major cause of mortality and morbidity in young children and the elderly. In the present study we evaluated antimicrobial susceptibilities, serotypes, and sequence types of pneumococcal isolates recovered in New Delhi, India. Methodology: A total of 126 clinical isolates of Streptococcus pneumoniae were investigated. They were subjected to disk diffusion susceptibility testing, broth microdilution testing, serotyping and multilocus sequence typing. Results: Broth microdilution assay showed that 5%, 20% and 23% of the isolates exhibited resistance to penicillin, erythromycin and ciprofloxacin, respectively. Serotypes19, 1 and 6 were more frequently isolated. Thirty per cent of the strains were comprised of serotypes 1, 3, 5, 19A and 7F, which are not included in the seven-valent vaccine. Fifty-nine isolates were typed using multilocus sequence typing. Thirty new sequence types were encountered in this study. Only one clonal complex with 4 isolates was seen; 11 clonal complexes and 96 sequence types (STs) were observed among 115 Indian isolates. Only 18 of the 96 STs were found globally, of which only 4 STs were found in many countries with larger numbers. Conclusions: This study identifies the non-vaccine serotypes of Streptococcus pneumoniae circulating in India. It is important that an appropriate vaccine which covers all serotypes is used in the region.

Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media

2016 ◽  
Vol 79 (11) ◽  
pp. 1986-1989 ◽  
Author(s):  
M. E. BERRANG ◽  
S. R. LADELY ◽  
R. J. MEINERSMANN ◽  
J. E. LINE ◽  
B. B OAKLEY ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
Sequence Type ◽  
Campylobacter Coli ◽  
Processing Plant ◽  
Full Genome Sequencing ◽  
Multiple Sequence ◽  
Commercial Broiler ◽  
Sequence Types

ABSTRACT The objective of this study was to compare subtypes of Campylobacter jejuni and Campylobacter coli detected on three selective Campylobacter plating media to determine whether each medium selected for different subtypes. Fifty ceca and 50 carcasses (representing 50 flocks) were collected from the evisceration line in a commercial broiler processing plant. Campylobacter was cultured and isolated from cecal contents and carcass rinses on Campy-Cefex, Campy Line, and RF Campylobacter jejuni/coli agars. When a positive result was obtained with all three media, one colony of the most prevalent morphology on each medium was selected for further analysis by full genome sequencing and multilocus sequence typing. Sequence types were assigned according to PubMLST. A total of 49 samples were positive for Campylobacter on all three media. Forty samples contained only C. jejuni, three had only C. coli, and both species were detected in six samples. From 71% of samples, Campylobacter isolates of the same sequence type were recovered on all three media. From 81.6% of samples, isolates were all from the same clonal complex. From significantly fewer samples (26%, P < 0.01), one medium recovered an isolate with a sequence type different from the type recovered on the other two media. When multiple sequence types were detected, six times the medium with the odd sequence type was Campy-Cefex, four times it was Campy-Line, and six times it was RF Campylobacter jejuni/coli. From one sample, three sequence types were detected. In most cases, all three plating media allowed detection of the same type of Campylobacter from complex naturally contaminated chicken samples.

scholarly journals Analysis of Genetic Relatedness of Haemophilus influenzae Isolates by Multilocus Sequence Typing

2007 ◽  
Vol 190 (4) ◽  
pp. 1473-1483 ◽  
Author(s):  
Alice L. Erwin ◽  
Sara A. Sandstedt ◽  
Paul J. Bonthuis ◽  
Jennifer L. Geelhood ◽  
Kevin L. Nelson ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Multilocus Sequence Typing ◽  
Genetic Relatedness ◽  
Geographic Origin ◽  
Maximum Parsimony Analysis ◽  
Negative Bacterium ◽  
Phylogenetic Groups ◽  
Capsule Production ◽  
Metabolic Reactions ◽  
Sequence Types

ABSTRACT The gram-negative bacterium Haemophilus influenzae is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of H. influenzae respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656 H. influenzae strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.

scholarly journals eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data

2004 ◽  
Vol 186 (5) ◽  
pp. 1518-1530 ◽  
Author(s):  
Edward J. Feil ◽  
Bao C. Li ◽  
David M. Aanensen ◽  
William P. Hanage ◽  
Brian G. Spratt
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Large Data ◽  
Realistic Model ◽  
Epidemiological Surveillance ◽  
Bootstrap Support ◽  
Data Sets ◽  
Data Set ◽  
Evolutionary Descent

ABSTRACT The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain23F-1 clonal complex of Streptococcus pneumoniae, “population snapshots” of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

Characterization of Neisseria meningitidis isolates collected from 1974 to 2003 in Japan by multilocus sequence typing

2004 ◽  
Vol 53 (7) ◽  
pp. 657-662 ◽  
Author(s):  
Hideyuki Takahashi ◽  
Toshiro Kuroki ◽  
Yuko Watanabe ◽  
Hiroshi Tanaka ◽  
Hiroo Inouye ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Neisseria Meningitidis ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
The Other ◽  
Mlst Database ◽  
Mlst Analysis ◽  
The Past ◽  
Sequence Types

Analysis of 182 Neisseria meningitidis strains isolated over the past 30 years in Japan by serogroup typing and multilocus sequence typing (MLST) was performed. The serogroups of the 182 Japanese isolates were B (103 isolates), Y (39), W135 (1) and non-groupable (39). By MLST analysis, 65 different sequence types (ST) were identified, 42 of which were not found in the MLST database as of January 2004 and seemed to be unique to Japan. Statistical analysis of the MLST results revealed that, although the Japanese isolates seemed to be genetically divergent, they were classified into six major clonal complexes and other minor complexes. Among these isolates, well-documented ST complexes found worldwide were present, such as ST-23 complex (49 isolates), ST-44 complex (41 isolates) and ST-32 complex (8 isolates). On the other hand, a new clonal complex designated ST-2046 complex (28 isolates), which has not been identified in other countries, was also found, suggesting that this clone was indigenous to Japan. Taken together, it was speculated that meningococcal isolates in Japan comprised heterogeneous clones, which were derived both from clones identified in other countries and clones unique to Japan.

scholarly journals Identification of Streptococcus uberis Multilocus Sequence Types Highly Associated with Mastitis

2007 ◽  
Vol 74 (1) ◽  
pp. 114-124 ◽  
Author(s):  
Takehiro Tomita ◽  
Brian Meehan ◽  
Nalin Wongkattiya ◽  
Jakob Malmo ◽  
Gillian Pullinger ◽  
...  
Keyword(s):  
Clonal Complex ◽  
Subclinical Mastitis ◽  
Sequence Type ◽  
Empirical Estimation ◽  
Somatic Cell Counts ◽  
Streptococcus Uberis ◽  
Cell Counts ◽  
Standardized Index ◽  
First Time ◽  
Sequence Types

ABSTRACT Multilocus sequence typing analysis of Streptococcus uberis has identified a cluster of isolates associated with clinical and subclinical mastitis and a cluster associated with cows with low somatic cell counts in their milk. Specific groups of genotypes (global clonal complex [GCC] sequence type 5s [ST5s] and GCC ST143s) were highly associated (P = 0.006) with clinical and subclinical mastitis and may represent a lineage of virulent isolates, whereas isolates belonging to GCC ST86 were associated with low-cell-count cows. This study has, for the first time, demonstrated the occurrence of identical sequence types (ST60 and ST184) between different continents (Australasia and Europe) and different countries (Australia and New Zealand). The standardized index of association and the empirical estimation of the rate of recombination showed substantial recombination within the S. uberis population in Australia, consistent with previous multilocus sequence type analyses.

Development of a multilocus sequence typing scheme for Streptococcus gallolyticus

Microbiology ◽  
2014 ◽  
Vol 160 (1) ◽  
pp. 113-122 ◽  
Author(s):  
Yusuke Shibata ◽  
Le Hong Thuy Tien ◽  
Ryohei Nomoto ◽  
Ro Osawa
Keyword(s):  
Dna Hybridization ◽  
Multilocus Sequence Typing ◽  
Housekeeping Gene ◽  
Biochemical Tests ◽  
Single Strain ◽  
Discriminatory Ability ◽  
Mlst Scheme ◽  
Streptococcus Gallolyticus ◽  
High Concordance ◽  
Sequence Types

Streptococcus gallolyticus is often found as a member of the normal gut microflora in various animals. However, it has been reported to cause mastitis in cattle, septicaemia in pigeons, and meningitis, septicaemia and endocarditis in humans. However, little is known about the epidemiology and crucial virulence factors of S. gallolyticus. To help address these issues, we developed a multilocus sequence typing (MLST) scheme for S. gallolyticus. Seven housekeeping gene fragments were sequenced from each of 58 S. gallolyticus isolates collected from diverse origins and sources. The MLST scheme had good discriminatory ability. The 63 strains, including the 5 whole genome sequenced strains examined, resolved into 57 sequence types (STs), with 52 STs represented by only a single strain. With respect to the identification of S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus, S. gallolyticus subsp. pasteurianus and S. gallolyticus subsp. macedonicus), the results of biochemical tests and DNA–DNA hybridization were in high concordance with those of the MLST scheme. The MLST scheme developed in this study may be a useful tool capable of replacing the conventional methods used for S. gallolyticus subspecies identification. The results of this study suggest that the biology and virulence of two pathogenic S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus and S. gallolyticus subsp. pasteurianus) are very different. The MLST scheme offers researchers a valuable typing tool that will promote further investigation of the epidemiology of S. gallolyticus.

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