scholarly journals Multilocus Sequence Typing Scheme for the Characterization of 936-Like Phages Infecting Lactococcus lactis

2012 ◽  
Vol 78 (13) ◽  
pp. 4646-4653 ◽  
Author(s):  
Maxim Moisan ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
Multilocus Sequence Typing ◽  
Phylogenetic Analyses ◽  
Clonal Evolution ◽  
Phage Group ◽  
Content Type ◽  
Mlst Scheme ◽  
Routine Identification ◽  
Set Up

ABSTRACTLactococcus lactisphage infections are costly for the dairy industry because they can slow down the fermentation process and adversely impact product safety and quality. Although many strategies have been developed to better control phage populations, new virulent phages continue to emerge. Thus, it is beneficial to develop an efficient method for the routine identification of new phages within a dairy plant to rapidly adapt antiphage tactics. Here, we present a multilocus sequence typing (MLST) scheme for the characterization of the 936-like phages, the most prevalent phage group infectingL. lactisstrains worldwide. The proposed MLST system targets the internal portion of five highly conserved genomic sequences belonging to the packaging, morphogenesis, and lysis modules. Our MLST scheme was used to analyze 100 phages with different restriction fragment length polymorphism (RFLP) patterns isolated from 11 different countries between 1971 and 2010. PCR products were obtained for all the phages analyzed, and sequence analysis highlighted the high discriminatory power of the MLST system, detecting 93 different sequence types. A conserved locus within thelysgene (coding for endolysin) was the most discriminative, with 65 distinct alleles. The locus within themcpgene (major capsid protein) was the most conserved (54 distinct alleles). Phylogenetic analyses of the concatenated sequences exhibited a strong concordance of the clusters with the phage host range, indicating the clonal evolution of these phages. A public database has been set up for the proposed MLST system, and it can be accessed athttp://pubmlst.org/bacteriophages/.

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

scholarly journals Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

Role of river stage in characterization of phreatic line

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Vikram Kumar ◽  
Srivastava Granthi
Keyword(s):  
Irrigation Planning ◽  
Content Type ◽  
Measured Distance ◽  
Model Set ◽  
Downstream Section ◽  
Large Water ◽  
Set Up ◽  
Observation Wells

Purpose The purpose of this study is to understand the basics of interactions of groundwater and surface water, which is needed for effective management of water resources. Design/methodology/approach The experimental setup was framed using curved flume and the straight flume, which simulates the model of river and groundwater storage, respectively. The model set up further consists, downstream, central and upstream sections where 14 observation wells, which are arranged at a measured distance from the canal side. Findings Exit gradient is higher at downstream when the average head differences between canal and river are 31.9 cm and 35.7 cm. Free seepage height is more in the downstream wells than upstream and central wells. At the downstream section, there is a greater chance of instability of the riverbank. Research limitations/implications Results will be used for better planning of hydraulic structural design. Practical implications Results will help in storing the large water and better irrigation planning for the water acute states and locations. Originality/value The originality is own developed physical model and its own first type to understand the basic of interaction and effects.

scholarly journals Multilocus Sequence Typing for Characterization of Methicillin-Resistant and Methicillin-Susceptible Clones ofStaphylococcus aureus

2000 ◽  
Vol 38 (3) ◽  
pp. 1008-1015 ◽  
Author(s):  
Mark C. Enright ◽  
Nicholas P. J. Day ◽  
Catrin E. Davies ◽  
Sharon J. Peacock ◽  
Brian G. Spratt
Keyword(s):  
Multilocus Sequence Typing ◽  
Reference Strain ◽  
Housekeeping Genes ◽  
Invasive Disease ◽  
Healthy Individuals ◽  
Allelic Profile ◽  
Methicillin Resistant ◽  
Mlst Scheme ◽  
Hospital Acquired

A multilocus sequence typing (MLST) scheme has been developed forStaphylococcus aureus. The sequences of internal fragments of seven housekeeping genes were obtained for 155 S. aureusisolates from patients with community-acquired and hospital-acquired invasive disease in the Oxford, United Kingdom, area. Fifty-three different allelic profiles were identified, and 17 of these were represented by at least two isolates. The MLST scheme was highly discriminatory and was validated by showing that pairs of isolates with the same allelic profile produced very similar SmaI restriction fragment patterns by pulsed-field gel electrophoresis. All 22 isolates with the most prevalent allelic profile were methicillin-resistant S. aureus (MRSA) isolates and had allelic profiles identical to that of a reference strain of the epidemic MRSA clone 16 (EMRSA-16). Four MRSA isolates that were identical in allelic profile to the other major epidemic MRSA clone prevalent in British hospitals (clone EMRSA-15) were also identified. The majority of isolates (81%) were methicillin-susceptible S. aureus (MSSA) isolates, and seven MSSA clones included five or more isolates. Three of the MSSA clones included at least five isolates from patients with community-acquired invasive disease and may represent virulent clones with an increased ability to cause disease in otherwise healthy individuals. The most prevalent MSSA clone (17 isolates) was very closely related to EMRSA-16, and the success of the latter clone at causing disease in hospitals may be due to its emergence from a virulent MSSA clone that was already a major cause of invasive disease in both the community and hospital settings. MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet.

scholarly journals Global Multilocus Sequence Typing Analysis of Mycoplasma bovis Isolates Reveals Two Main Population Clusters

2014 ◽  
Vol 53 (3) ◽  
pp. 789-794 ◽  
Author(s):  
R. S. Rosales ◽  
C. P. Churchward ◽  
C. Schnee ◽  
K. Sachse ◽  
I. Lysnyansky ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Housekeeping Genes ◽  
Population Based ◽  
Economic Losses ◽  
Mycoplasma Bovis ◽  
Content Type ◽  
Clinical Presentations ◽  
High Discriminatory Power ◽  
Clonal Nature

Mycoplasma bovisis a major bovine pathogen associated with bovine respiratory disease complex and is responsible for substantial economic losses worldwide.M. bovisis also associated with other clinical presentations in cattle, including mastitis, otitis, arthritis, and reproductive disorders. To gain a better understanding of the genetic diversity of this pathogen, a multilocus sequence typing (MLST) scheme was developed and applied to the characterization of 137M. bovisisolates from diverse geographical origins, obtained from healthy or clinically infected cattle. Afterin silicoanalysis, a final set of 7 housekeeping genes was selected (dnaA,metS,recA,tufA,atpA,rpoD, andtkt). MLST analysis demonstrated the presence of 35 different sequence types (STs) distributed in two main clonal complexes (CCs), defined at the double-locus variant level, namely, CC1, which included most of the British and German isolates, and CC2, which was a more heterogeneous and geographically distant group of isolates, including European, Asian, and Australian samples. Index of association analysis confirmed the clonal nature of the investigatedM. bovispopulation, based on MLST data. This scheme has demonstrated high discriminatory power, with the analysis showing the presence of genetically distant and divergent clusters of isolates predominantly associated with geographical origins.

scholarly journals Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex

2013 ◽  
Vol 79 (23) ◽  
pp. 7220-7228 ◽  
Author(s):  
Padmini Ramachandran ◽  
David W. Lacher ◽  
Erika A. Pfeiler ◽  
Christopher A. Elkins
Keyword(s):  
Lactobacillus Acidophilus ◽  
Multilocus Sequence Typing ◽  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Housekeeping Genes ◽  
Nucleotide Substitutions ◽  
Content Type ◽  
Mlst Scheme ◽  
Pcr Rflp ◽  
Pcr Targeting

ABSTRACTMembers of theLactobacillus acidophiluscomplex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of theL. acidophiluscomplex (L. acidophilus,L. amylovorus,L. crispatus,L. gallinarum,L. gasseri, andL. johnsonii) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of thehsp60gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genesfusA,gpmA,gyrA,gyrB,lepA,pyrG, andrecA, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of theL. acidophiluscomplex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection ofLactobacillusspecies.

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens

Microbiology ◽  
2011 ◽  
Vol 157 (7) ◽  
pp. 1990-2003 ◽  
Author(s):  
Andrew McDowell ◽  
Anna Gao ◽  
Emma Barnard ◽  
Colin Fink ◽  
Philip I. Murray ◽  
...  
Keyword(s):  
Cell Surface ◽  
Multilocus Sequence Typing ◽  
Propionibacterium Acnes ◽  
Antigenic Variation ◽  
Dna Typing ◽  
Single Locus ◽  
Type I ◽  
Mlst Scheme ◽  
Type Ia

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 64 % of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants, which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore support an association between acne and P. acnes strains from the type IA cluster and highlight the role of a widely disseminated clonal genotype in this condition. Characterization of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

scholarly journals Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Preetha Shibu ◽  
Frazer McCuaig ◽  
Anne L. McCartney ◽  
Magdalena Kujawska ◽  
Lindsay J. Hall ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. bla OXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis . Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii . The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four ( K. oxytoca , K. pasteurii , K. grimontii , K. michiganensis ) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

scholarly journals Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov.

2020 ◽  
Vol 70 (4) ◽  
pp. 2288-2297 ◽  
Author(s):  
Sabrina Duranti ◽  
Gabriele Andrea Lugli ◽  
Alice Viappiani ◽  
Leonardo Mancabelli ◽  
Giulia Alessandri ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Bifidobacterium Bifidum ◽  
Content Type ◽  
Link Type ◽  
Callimico Goeldii ◽  
Goeldi's Monkey ◽  
Type Strains ◽  
Rrna Sequences

Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.

scholarly journals Characterization of HypermutatorPseudomonas aeruginosaIsolates from Patients with Cystic Fibrosis in Australia

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Vanessa E. Rees ◽  
Deanna S. Deveson Lucas ◽  
Carla López-Causapé ◽  
Yuling Huang ◽  
Tom Kotsimbos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Health Care ◽  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type

ABSTRACTHypermutablePseudomonas aeruginosaisolates (hypermutators) have been identified in patients with cystic fibrosis (CF) and are associated with reduced lung function. Hypermutators display a greatly increased mutation rate and an enhanced ability to become resistant to antibiotics during treatment. Their prevalence has been established among patients with CF, but it has not been determined for patients with CF in Australia. This study aimed to determine the prevalence of hypermutableP. aeruginosaisolates from adult patients with CF from a health care institution in Australia and to characterize the genetic diversity and antibiotic susceptibility of these isolates. A total of 59 P. aeruginosaclinical isolates from patients with CF were characterized. For all isolates, rifampin (RIF) mutation frequencies and susceptibility to a range of antibiotics were determined. Of the 59 isolates, 13 (22%) were hypermutable. Whole-genome sequences were determined for all hypermutable isolates. Core genome polymorphisms were used to assess genetic relatedness of the isolates, both to each other and to a sample of previously characterizedP. aeruginosastrains. Phylogenetic analyses showed that the hypermutators were from divergent lineages and that hypermutator phenotype was mostly the result of mutations inmutLor, less commonly, inmutS. Hypermutable isolates also contained a range of mutations that are likely associated with adaptation ofP. aeruginosato the CF lung environment. Multidrug resistance was more prevalent in hypermutable than nonhypermutable isolates (38% versus 22%). This study revealed that hypermutableP. aeruginosastrains are common among isolates from patients with CF in Australia and are implicated in the emergence of antibiotic resistance.

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