scholarly journals Differentiation of Campylobacter Populations as Demonstrated by Flagellin Short Variable Region Sequences

2005 ◽  
Vol 71 (10) ◽  
pp. 6368-6374 ◽  
Author(s):  
Richard J. Meinersmann ◽  
Robert W. Phillips ◽  
Kelli L. Hiett ◽  
Paula Fedorka-Cray
Keyword(s):  
Population Structure ◽  
Synonymous Codon ◽  
Variable Region ◽  
Synonymous Codon Usage ◽  
Relative Synonymous Codon Usage ◽  
Clonal Population ◽  
Significant Differentiation ◽  
Clonal Population Structure ◽  
Usage Analysis ◽  
Short Variable Region

ABSTRACT The DNA sequence of the flaA short variable region (SVR) was used to analyze a random population of Campylobacter isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of C. jejuni and C. coli isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both C. jejuni and C. coli strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified C. jejuni, and the second group was characteristic for C. coli and the disparate alleles were not clustered. The data show that there is significant differentiation of Campylobacter populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from Campylobacter species other than C. jejuni and C. coli. It is evident that recombination within the flaA SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.

scholarly journals "Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions

2005 ◽  
Vol 102 (48) ◽  
pp. 17388-17393 ◽  
Author(s):  
F. G. Razakandrainibe ◽  
P. Durand ◽  
J. C. Koella ◽  
T. De Meeus ◽  
F. Rousset ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Population Structure ◽  
Clonal Population ◽  
High Infection ◽  
Clonal Population Structure

scholarly journals PyClone: statistical inference of clonal population structure in cancer

2014 ◽  
Vol 11 (4) ◽  
pp. 396-398 ◽  
Author(s):  
Andrew Roth ◽  
Jaswinder Khattra ◽  
Damian Yap ◽  
Adrian Wan ◽  
Emma Laks ◽  
...  
Keyword(s):  
Population Structure ◽  
Statistical Inference ◽  
Clonal Population ◽  
Clonal Population Structure

scholarly journals Clonal population structure of encapsulated Haemophilus influenzae.

1988 ◽  
Vol 56 (8) ◽  
pp. 1837-1845 ◽  
Author(s):  
J M Musser ◽  
J S Kroll ◽  
E R Moxon ◽  
R K Selander
Keyword(s):  
Population Structure ◽  
Haemophilus Influenzae ◽  
Clonal Population ◽  
Clonal Population Structure

Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

2021 ◽  
Author(s):  
Yanan Fu ◽  
Yanping Huang ◽  
Jingjing Rao ◽  
Feng Zeng ◽  
Ruiping Yang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Binding Affinity ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Host Adaptation ◽  
Synonymous Codon Usage ◽  
Mutation Pressure ◽  
Usage Analysis ◽  
Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

Trypanosoma vivax displays a clonal population structure

2009 ◽  
Vol 39 (13) ◽  
pp. 1475-1483 ◽  
Author(s):  
Craig W. Duffy ◽  
Liam J. Morrison ◽  
Alana Black ◽  
Gina L. Pinchbeck ◽  
Robert M. Christley ◽  
...  
Keyword(s):  
Population Structure ◽  
Trypanosoma Vivax ◽  
Clonal Population ◽  
Clonal Population Structure

The clonal population structure and serosubtypes of Neisseria meningitidis serogroup A isolated in China

1991 ◽  
pp. 159-164
Author(s):  
Li Xinwu ◽  
Hu Xujing ◽  
Gao Lihui ◽  
Xi Wenlong ◽  
Ji Yinduo ◽  
...  
Keyword(s):  
Population Structure ◽  
Neisseria Meningitidis ◽  
Clonal Population ◽  
Clonal Population Structure

scholarly journals Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys

2007 ◽  
Vol 73 (7) ◽  
pp. 2156-2164 ◽  
Author(s):  
C. B. D'lima ◽  
W. G. Miller ◽  
R. E. Mandrell ◽  
S. L. Wright ◽  
R. M. Siletzky ◽  
...  
Keyword(s):  
North Carolina ◽  
Population Structure ◽  
Multidrug Resistant ◽  
Source Tracking ◽  
Campylobacter Coli ◽  
Clonal Population ◽  
Antimicrobial Resistance Profile ◽  
Clonal Population Structure ◽  
Commercial Turkey ◽  
Sequence Types

ABSTRACT Commercial turkey flocks in North Carolina have been found to be colonized frequently with Campylobacter coli strains that are resistant to several antimicrobials (tetracycline, streptomycin, erythromycin, kanamycin, and ciprofloxacin/nalidixic acid). Such strains have been designated multidrug resistant (MDR). However, the population structure of MDR C. coli from turkeys remains poorly characterized. In this study, an analysis of multilocus sequence typing (MLST)-based sequence types (STs) of 59 MDR strains from turkeys revealed that the majority of these strains corresponded to one of 14 different STs, with three STs accounting for 41 (69%) of the strains. The major STs were turkey specific, and most (87%) of the strains with these STs were resistant to the entire panel of antibiotics mentioned above. Some (13%) of the strains with these STs were susceptible to just one or two of the antibiotics in this panel. Further subtyping using fla typing and pulsed-field gel electrophoresis with SmaI and KpnI revealed that the major MDR STs corresponded to strains of related but distinct subtypes, providing evidence for genomic diversification within these STs. These findings suggest that MDR strains of C. coli from turkeys have a clonal population structure characterized by the presence of a relatively small number of clonal groups that appear to be disseminated in the turkey production system. In addition, the observed correlation between STs and the MDR profiles of the microbes indicates that MLST-based typing holds potential for source-tracking applications specific to the animal source (turkeys) and the antimicrobial resistance profile (MDR status) of C. coli.

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