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.

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 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 High Genetic Diversity ofEnterococcus faeciumandEnterococcus faecalisClinical Isolates by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing from a Hospital in Malaysia

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Poh Leng Weng ◽  
Ramliza Ramli ◽  
Mariana Nor Shamsudin ◽  
Yoke-Kqueen Cheah ◽  
Rukman Awang Hamat
Keyword(s):  
Genetic Diversity ◽  
Gel Electrophoresis ◽  
Multilocus Sequence Typing ◽  
Genetic Relatedness ◽  
Pulsed Field Gel Electrophoresis ◽  
High Genetic Diversity ◽  
Pulsed Field ◽  
Susceptibility Profiles ◽  
Sequence Types ◽  
Multiple Antibiotics

Little is known on the genetic relatedness and potential dissemination of particular enterococcal clones in Malaysia. We studied the antibiotic susceptibility profiles ofEnterococcus faeciumandEnterococcus faecalisand subjected them to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).E. faeciumandE. faecalisdisplayed 27 and 30 pulsotypes, respectively, and 10 representativeE. faeciumandE. faecalisisolates (five each) yielded few different sequence types (STs): ST17 (2 isolates), ST78, ST203, and ST601 forE. faecium, and ST6, ST16, ST28, ST179, and ST399 forE. faecalis. Resistance to tazobactam-piperacillin and ampicillin amongstE. faeciumisolates was highly observed as compared toE. faecalisisolates. All of the isolates were sensitive to vancomycin and teicoplanin. The presence of epidemic and nosocomial strains of selectedE. faeciumSTs: 17, 78, and 203 andE. faecalisST6 as well as high rates of resistance to multiple antibiotics amongstE. faeciumisolates is of a particular concern.

scholarly journals Multilocus Sequence Typing of Non-JP2 Serotype b Aggregatibacter actinomycetemcomitans Strains of Ghanaian and Swedish Origin

2021 ◽  
Vol 11 ◽  
Author(s):  
Rolf Claesson ◽  
Anders Johansson ◽  
Carola Höglund Åberg ◽  
Anders Esberg ◽  
Dorte Haubek ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Diagnostic Procedure ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Negative Bacterium ◽  
Specific Primers ◽  
Mlst Analysis ◽  
Serotype B ◽  
Periodontal Attachment Loss ◽  
Sequence Types

Objective and MethodsThe Gram-negative bacterium, Aggregatibacter actinomycetemcomitans is associated with periodontitis affecting young individuals. The geographic dissemination of the highly leukotoxic JP2 genotype of serotype b of this species was previously studied by multilocus sequence typing (MLST). Here, we have used MLST to genetically characterize non-JP2 genotype strains of serotype b, isolated from individuals living in Ghana (n=41), and in Sweden (n=13), respectively.ResultsThe MLST analysis revealed a total of nine sequence types (ST). Both Ghanaian and Swedish isolates were distributed in ST 1-3. ST 5 and 6 were only identified among the Ghanaian strains, whereas ST 4, 7, 8 and 9 were uniquely represented among the Swedish strains. Previously, we characterized these non-JP2 genotype strains of A. actinomycetemcomitans serotype b by arbitrarily-primed (AP)-PCR, which distributed them into three groups, AP-PCR type 1, 2, and 3, respectively. AP-PCR type 1 strains are generally highly leukotoxic, and are associated with progression of periodontal attachment loss. As AP-PCR type 1 includes both JP2 genotype strains and a proportion of non-JP2 genotype strains of serotype b, a straightforward diagnostic procedure has been sought. This has revealed a gene, cagE, which appears to be conserved only in this AP-PCR type. According to our results, MLST was not a highly discriminatory method to identify AP-PCR type 1, as strains of this AP-PCR type could be found within three different ST: ST 2, ST 3 and ST 8.ConclusionAccording to MLST, a geographic dissemination of non-JP2 genotype A. actinomycetemcomitans serotype b appears to exist. However, aiming to identify carriers of AP-PCR type 1, non-JP2 genotype serotype b, PCR with cagE-specific primers is likely the most efficient diagnostic procedure known today.

Genetic relatedness of antibiotic-resistant pneumococci isolated during case clusters

2004 ◽  
Vol 53 (11) ◽  
pp. 1097-1099 ◽  
Author(s):  
S C Clarke ◽  
D Lawrie ◽  
M A Diggle
Keyword(s):  
Streptococcus Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Genetic Relatedness ◽  
Antibiotic Resistant ◽  
First Time ◽  
Sequence Types

Multilocus sequence typing of Streptococcus pneumoniae associated with two case clusters of disease is reported here for the first time. Isolates from the first cluster were serotype 19F, resistant to penicillin and erythromycin, and were characterized as ST 320. Isolates from the second cluster were serogroup 4, resistant to ciprofloxacin, and were characterized as ST 206. Therefore, the isolates from these clusters were antibiotic-resistant, of serotypes infrequently isolated, and of uncommon sequence types.

scholarly journals Phenotypic and Molecular Analysis of Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates in Poland

2006 ◽  
Vol 51 (1) ◽  
pp. 40-47 ◽  
Author(s):  
Ewa Sadowy ◽  
Radosław Izdebski ◽  
Anna Skoczyńska ◽  
Paweł Grzesiowski ◽  
Marek Gniadkowski ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Molecular Analysis ◽  
Gel Electrophoresis ◽  
Multilocus Sequence Typing ◽  
Susceptibility Testing ◽  
Bacterial Pathogen ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field ◽  
Related Clone ◽  
Sequence Types

ABSTRACT β-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain23F-1, Spain6B-2, Spain9V-3, Taiwan23F-15, Poland23F-16, Poland6B-20, and Sweden15A-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain9V-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

scholarly journals Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Sara Kovanen ◽  
Mirko Rossi ◽  
Mari Pohja-Mykrä ◽  
Timo Nieminen ◽  
Mirja Raunio-Saarnisto ◽  
...  
Keyword(s):  
Host Specificity ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Wild Birds ◽  
Whole Genome ◽  
Mallard Duck ◽  
Content Type ◽  
Game Birds ◽  
Hygienic Measures ◽  
Sequence Types

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

scholarly journals Virulence Gene Profile, Antimicrobial Resistance and Multilocus Sequence Typing of Salmonella enterica Subsp. enterica Serovar Enteritidis from Chickens and Chicken Products

Animals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 97
Author(s):  
Zunita Zakaria ◽  
Latiffah Hassan ◽  
Zawiyah Sharif ◽  
Norazah Ahmad ◽  
Rohaya Mohd Ali ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Multilocus Sequence Typing ◽  
Salmonella Enteritidis ◽  
Molecular Subtypes ◽  
Actin Binding ◽  
Diffusion Method ◽  
Genetic Characteristics ◽  
Meat Samples ◽  
Sequence Types

This study was undertaken to determine the virulence, antimicrobial resistance and molecular subtypes of Salmonella in the Central Region of Peninsular Malaysia. A total of 45 Salmonella Enteritidis were detected from live chicken (cloacal swab), and chicken products (fresh and ready-to-eat meat) samples upon cultural isolation and serotyping. Similarly, an antimicrobial susceptibility test based on the Kirby Bauer disk diffusion method as well as antimicrobial resistance AMR genes, virulence determinants and multilocus sequence typing (MLST) typing were conducted after the Whole Genome Sequencing and analysis of the isolates. The results indicate that sequence types ST1925 (63.7%), and ST11 (26.5%) were the predominant out of the seven sequence types identified (ST292, ST329, ST365, ST423 and ST2132). The phenotypic antimicrobial profile corresponds to the genotypic characterization in that the majority of the isolates that exhibited tetracycline, gentamycin and aminoglycoside resistance; they also possessed the tetC and blaTEM β-Lactam resistance genes. However, isolates from cloacal swabs showed the highest number of resistance genes compared to the chicken products (fresh and ready-to-eat meat) samples. Furthermore, most of the virulence genes were found to cluster in the Salmonella pathogenicity island (SPI). In this study, all the isolates were found to possess SPI-1, which codes for the type III secretion system, which functions as actin-binding proteins (SptP and SopE). The virulence plasmid (VP) genes (spvB, spvC) were present in all genotypes except ST365. The findings of this study, particularly with regard to the molecular subtypes and AMR profiles of the Salmonella Enteritidis serotype shows multidrug-resistance features as well as genetic characteristics indicative of high pathogenicity.

scholarly journals Wide spread of OXA-48-producing Enterobacteriaceae in Algerian hospitals: A four years’ study

2018 ◽  
Vol 12 (11) ◽  
pp. 1039-1044
Author(s):  
Nadjet Aggoune ◽  
Hassiba Tali Maamar ◽  
Farida Assaous ◽  
Badia Guettou ◽  
Rym Laliam ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Genetic Relationships ◽  
Wide Distribution ◽  
Multi Locus Sequence Typing ◽  
Wide Spread ◽  
Multiple Sequence ◽  
Sequence Types ◽  
Susceptibility Patterns ◽  
Urgent Action

Introduction: The aim of this study was to investigate the presence of carbapenemase-producing Enterobacteriaceae (CPE) in Algerian hospitals and to characterize the molecular types of carbapenemases found. Methodology: During a four years study lasting between 2012 and 2015, 81 strains of Enterobacteriaceae with reduced susceptibility to carbapenems were collected from different hospitals. Carbapenemase genes were detected by PCR. Multi locus sequence typing was used to study genetic relationships between carbapenemase- producing Klebsiella pneumoniae isolates. Results: Among 56 confirmed CPE, blaOXA-48 was detected in 98.21% of isolates. Two isolates co-expressed NDM, and a single one was only an NDM producer. The strains displayed various susceptibility patterns to antibiotics with variable levels of resistance to carbapenems. Multilocus sequence typing (MLST) revealed the presence of multiple sequence types in circulation. Conclusions: This report highlights the wide distribution of several clones of OXA-48-producing Enterobacteriaceae in Algeria. Urgent action should be taken to avoid epidemic situations.

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