Genomic stability among O3:K6 V. parahaemolyticus pandemic strains isolated between 1996 to 2012 in American countries

Abstract Background The V. parahaemolyticus pandemic clone, results in the development of gastrointestinal illness in humans. Toxigenic strains of this species are frequently isolated from aquatic habitats and organisms such as mollusks and crustaceans. Reports on the isolation of the pandemic clone started in 1996, when a new O3:K6 clone was identified in Asia, that rapidly spread worldwide, becoming the predominant clone isolated from clinical cases. In this study whole genome sequencing was accomplished with an Illumina MiniSeq platform, upon six novel V. parahaemolyticus strains, that have been isolated in Mexico since 1998 and three representative genomes of strains that were isolated from reported outbreaks in other American countries, and were deposited in the GenBank. These nine genomes were compared against the reference sequence of the O3:K6 pandemic strain (RIMD 2210633), which was isolated in 1996, to determine sequence differences within American isolates and between years of isolation. Results The results indicated that strains that were isolated at different times and from different countries, were highly genetically similar, among them as well as to the reference strain RIMD 2210633, indicating a high level of genetic stability among the strains from American countries between 1996 to 2012, without significant genetic changes relative to the reference strain RIMD 2210633, which was isolated in 1996 and was considered to be representative of a novel O3:K6 pandemic strain. Conclusions The genomes of V. parahaemolyticus strains isolated from clinical and environmental sources in Mexico and other American countries, presented common characteristics that have been reported for RIMD 2210633 O3:K6 pandemic strain. The major variations that were registered in this study corresponded to genes non associated to virulence factors, which could be the result of adaptations to different environmental conditions. Nevertheless, results do not show a clear pattern with the year or locality where the strains were isolated, which is an indication of a genomic stability of the studied strains.

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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

Scientific Reports ◽

10.1038/s41598-021-82565-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jung-Hyun Kim ◽

Vladimir N. Noskov ◽

Aleksey Y. Ogurtsov ◽

Ramaiah Nagaraja ◽

Nikolai Petrov ◽

...

Keyword(s):

Genomic Structure ◽

Organizer Region ◽

Nucleolar Organizer Region ◽

Nucleolar Organizer ◽

Chromosome 21 ◽

Reference Sequence ◽

Chromosome 22 ◽

Rdna Variation ◽

High Level ◽

Tar Cloning

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.

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Draft Genome Sequence of the Serratia rubidaea CIP 103234 T Reference Strain, a Human-Opportunistic Pathogen

Genome Announcements ◽

10.1128/genomea.01340-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 7

Author(s):

Rémy A. Bonnin ◽

Delphine Girlich ◽

Dilek Imanci ◽

Laurent Dortet ◽

Thierry Naas

Keyword(s):

Genome Sequence ◽

Reference Strain ◽

Draft Genome ◽

Opportunistic Pathogen ◽

Draft Genome Sequence ◽

Reference Sequence ◽

Serratia Rubidaea

We provide here the first genome sequence of a Serratia rubidaea isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the Serratia genus.

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A patient with respiratory toxigenic diphtheria in Greece after more than 30 years

Epidemiology and Infection ◽

10.1017/s0950268820002605 ◽

2020 ◽

Vol 148 ◽

Author(s):

T. Georgakopoulou ◽

K. Tryfinopoulou ◽

A. Doudoulakakis ◽

F. Nikolaou ◽

I. Magaziotou ◽

...

Keyword(s):

Health Management ◽

Asymptomatic Carrier ◽

Fatal Outcome ◽

Asymptomatic Carriage ◽

Laboratory Confirmation ◽

Toxigenic Strains ◽

Susceptible Populations ◽

High Level ◽

Close Contacts

Abstract The introduction of treatment and systematic vaccination has significantly reduced diphtheria mortality; however, toxigenic strains continue to circulate worldwide. The emergence of an indigenous diphtheria case with fatal outcome in Greece, after 30 years, raised challenges for laboratory confirmation, clinical and public health management. Toxigenic Corynebacterium diphtheriae was isolated from an incompletely vaccinated 8-year-old boy with underlying conditions. The child passed away due to respiratory distress syndrome, before the administration of diphtheria antitoxin (DAT). All close contacts in family, school and hospital settings were investigated. Pharyngeal swabs were obtained to determine asymptomatic carriage. Chemoprophylaxis was given for 7 days to all close contacts and a booster dose to those incompletely vaccinated. Testing revealed a classmate, belonging to a subpopulation group (Roma), and incompletely vaccinated, as an asymptomatic carrier with an indistinguishable toxigenic strain (same novel multilocus sequence type, designated ST698). This case highlights the role of asymptomatic carriage, as the entry of toxigenic strains into susceptible populations can put individuals and their environment at risk. Maintenance of high-level epidemiological and microbiological surveillance, implementation of systematic vaccination in children and adults with primary and booster doses, availability of a DAT stockpile, and allowing timely administration are the cornerstone to prevent similar incidents in the future.

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A Novel Application of Levenshtein Distance for Assessment of High-Level Motor Planning Underlying Performance During Learning of Complex Motor Sequences

Journal of Motor Learning and Development ◽

10.1123/jmld.2018-0060 ◽

2020 ◽

Vol 8 (1) ◽

pp. 67-86 ◽

Cited By ~ 1

Author(s):

Theresa C. Hauge ◽

Garrett E. Katz ◽

Gregory P. Davis ◽

Kyle J. Jaquess ◽

Matthew J. Reinhard ◽

...

Keyword(s):

Mental Workload ◽

Motor Planning ◽

Reference Sequence ◽

Levenshtein Distance ◽

Complex Action ◽

Action Sequence ◽

Motor Efficiency ◽

Practice Performance ◽

Action Sequences ◽

High Level

Few studies have examined high-level motor plans underlying cognitive-motor performance during practice of complex action sequences. These investigations have assessed performance through fairly simple metrics without examining how practice affects the structures of action sequences. By adapting the Levenshtein distance (LD) method to the motor domain, we propose a computational approach to accurately capture performance dynamics during practice of action sequences. Practice performance dynamics were assessed by computing the LD based on the number of insertions, deletions, and substitutions of actions needed to transform any sequence into a reference sequence (having a minimal number of actions to complete the task). Also, combining LD-based performance with mental workload metrics allowed assessment of cognitive-motor efficiency dynamics. This approach was tested on the Tower of Hanoi task. The findings revealed that throughout practice this method could capture: i) action sequence performance improvements as indexed by a reduced LD (decrease of insertions and substitutions), ii) structural modifications of the high-level plans, iii) an attenuation of mental workload, and iv) enhanced cognitive-motor efficiency. This effort complements prior work examining the practice of complex action sequences in healthy adults and has potential for probing cognitive-motor impairment in clinical populations as well as the development/assessment of cognitive robotic controllers.

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Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence

Virus Evolution ◽

10.1093/ve/veaa067 ◽

2020 ◽

Vol 6 (2) ◽

Author(s):

Christopher Ruis ◽

Lisa C Lindesmith ◽

Michael L Mallory ◽

Paul D Brewer-Jensen ◽

Josephine M Bryant ◽

...

Keyword(s):

Strong Evidence ◽

Host Population ◽

Antigenic Drift ◽

Genetic Changes ◽

Pandemic Strain ◽

Population Immunity ◽

Virus Capsids ◽

Global Spread ◽

Ancestral Virus ◽

Conventional Models

Abstract The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesized that new GII.4 pandemic viruses arise when previously circulating pandemic or pre-pandemic variants undergo substitutions in antigenic regions that enable evasion of host population immunity, as described by conventional models of antigenic drift. In contrast, we show here that the acquisition of new genetic and antigenic characteristics cannot be the proximal driver of new pandemics. Pandemic GII.4 viruses diversify and spread over wide geographical areas over several years prior to simultaneous pandemic emergence of multiple lineages, indicating that the necessary sequence changes must have occurred before diversification, years prior to pandemic emergence. We confirm this result through serological assays of reconstructed ancestral virus capsids, demonstrating that by 2003, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics.

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An Hcp100 gene fragment reveals Histoplasma capsulatum presence in lungs of Tadarida brasiliensis migratory bats

Epidemiology and Infection ◽

10.1017/s0950268811002585 ◽

2011 ◽

Vol 140 (11) ◽

pp. 1955-1963 ◽

Cited By ~ 6

Author(s):

A. E. GONZÁLEZ-GONZÁLEZ ◽

C. M. ALIOUAT-DENIS ◽

L. E. CARRETO-BINAGHI ◽

J. A. RAMÍREZ ◽

G. RODRÍGUEZ-ARELLANES ◽

...

Keyword(s):

Reference Strain ◽

Histoplasma Capsulatum ◽

Gene Fragment ◽

Sequence Analyses ◽

Tadarida Brasiliensis ◽

Environmental Distribution ◽

Fungal Isolation ◽

Fungal Burden ◽

High Level ◽

New Evidence

SUMMARYHistoplasma capsulatum was sampled in lungs from 87 migratory Tadarida brasiliensis bats captured in Mexico (n=66) and Argentina (n=21). The fungus was screened by nested-PCR using a sensitive and specific Hcp100 gene fragment. This molecular marker was detected in 81·6% [95% confidence interval (CI) 73·4–89·7] of all bats, representing 71 amplified bat lung DNA samples. Data showed a T. brasiliensis infection rate of 78·8% (95% CI 68·9–88·7) in bats captured in Mexico and of 90·4% (95% CI 75·2–100) in those captured in Argentina. Similarity with the H. capsulatum sequence of a reference strain (G-217B) was observed in 71 Hcp100 sequences, which supports the fungal findings. Based on the neighbour-joining and maximum parsimony Hcp100 sequence analyses, a high level of similarity was found in most Mexican and all Argentinean bat lung samples. Despite the fact that 81·6% of the infections were molecularly evidenced, only three H. capsulatum isolates were cultured from all samples tested, suggesting a low fungal burden in lung tissues that did not favour fungal isolation. This study also highlighted the importance of using different tools for the understanding of histoplasmosis epidemiology, since it supports the presence of H. capsulatum in T. brasiliensis migratory bats from Mexico and Argentina, thus contributing new evidence to the knowledge of the environmental distribution of this fungus in the Americas.

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The inheritance of DDT-resistance in the cattle tick, Boophilus microplus

Australian Journal of Agricultural Research ◽

10.1071/ar9620984 ◽

1962 ◽

Vol 13 (5) ◽

pp. 984 ◽

Cited By ~ 15

Author(s):

BF Stone

Keyword(s):

Resistant Strain ◽

Reference Strain ◽

Boophilus Microplus ◽

Autosomal Gene ◽

Cattle Tick ◽

Adult Females ◽

Ddt Resistance ◽

High Level ◽

Multiresistant Strain

Adults of a DDT-resistant strain of the cattle tick from central Queensland were crossed with adults of a susceptible reference strain, by means of cardboard mating boxes glued to the skins of cattle. F1, backcross, and F2 larvae were tested for resistance to DDT by enclosure of larvae in filter paper packets impregnated with oil solutions of pp'-DDT. F1 and backcross engorged adult females were tested for resistance by injection with oil solutions of pp'-DDT. There was no evidence of departure from a 1 : 1 ratio in the backcrosses or from a 1 : 2 : 1 ratio in the F2, and there was little difference between the compositions of the F1 reciprocal crosses or among the backcrosses derived from them. Therefore DDT resistance in this strain was considered to be due to a single, incompletely recessive, autosomal gene. Engorged nymphs of the resistant strain moulted later in vitro than nymphs of the susceptible strain, and resistant engorged adult females detached from the host later than susceptible engorged adult females. After 13 generations of DDT-free culturing of a multiresistant strain, the percentage of homozygous DDT-resistant ticks in the strain had fallen from a high level to about 55%. This figure remained constant for a further 10 generations.

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Evidence for history-dependence of influenza pandemic emergence

Scientific Reports ◽

10.1038/srep43623 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 2

Author(s):

Edward M. Hill ◽

Michael J. Tildesley ◽

Thomas House

Keyword(s):

Influenza A ◽

Influenza Pandemic ◽

Influenza A Viruses ◽

History Dependence ◽

Influenza Pandemics ◽

Gamma Distributions ◽

Time Periods ◽

Pandemic Strains ◽

Modelling Assumptions ◽

High Level

Abstract Influenza A viruses have caused a number of global pandemics, with considerable mortality in humans. Here, we analyse the time periods between influenza pandemics since 1700 under different assumptions to determine whether the emergence of new pandemic strains is a memoryless or history-dependent process. Bayesian model selection between exponential and gamma distributions for these time periods gives support to the hypothesis of history-dependence under eight out of nine sets of modelling assumptions. Using the fitted parameters to make predictions shows a high level of variability in the modelled number of pandemics from 2010–2110. The approach we take here relies on limited data, so is uncertain, but it provides cheap, safe and direct evidence relating to pandemic emergence, a field where indirect measurements are often made at great risk and cost.

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Characterisation of Staphylococcus argenteus carried by healthy Royal Marines: a molecular epidemiology case-study

10.1101/2021.06.03.21257959 ◽

2021 ◽

Author(s):

Elita Jauneikaite ◽

Bruno Pichon ◽

Mia Mosavie ◽

Joanne L. Fallowfield ◽

Trish Davey ◽

...

Keyword(s):

Military Training ◽

Common Source ◽

Snp Analysis ◽

Genetic Changes ◽

Asymptomatic Carriage ◽

High Level ◽

A Prospective Study ◽

Spa Type ◽

Future Outbreak

Objectives: During a prospective study of S. aureus carriage in Royal Marines (RM) recruits, six S. argenteus strains were identified in four recruits undertaking military training together. As S. argenteus sepsis leads to mortality similar to S. aureus, we determined the potential for person-to-person transmission, to evaluate future outbreak risk. Methods: We used whole-genome sequencing to characterise S. argenteus and investigate phylogenetic relationships between isolates. Participant colonisation with S. aureus and skin and soft tissue infection acquisition were recorded. Results: All six S. argenteus strains were spa-type t5078, ST2250. Strains were detected in 4/40 recruits in the same troop (training cohort) in weeks 1, 6 or 15 of training. No mec, tsst or LukPV genes were detected. We identified differences of 10-35 core SNPs between S. argenteus from different recruits. In two recruits, two S. argenteus strains were isolated; these could be distinguished by 3 and 15 core SNPs in each case. S. argenteus was not identified in any one of the other 21 participating troops (1,012 recruits). Conclusions: The identification of S. argenteus within a single troop from the total recruit population supports a common source for transmission, supported by SNP analysis. The high number of SNPs between some isolates may indicate a common source of diverse isolates or a high level of S. argenteus mutation in carriage. S. argenteus ST2250 is a newly recognised lineage; a better understanding of the frequency of genetic changes during transmission and transition from asymptomatic carriage to disease is required.

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Ribotypes of clinical Vibrio cholerae non-O1 non-O139 strains in relation to O-serotypes

Epidemiology and Infection ◽

10.1017/s0950268898001654 ◽

1998 ◽

Vol 121 (3) ◽

pp. 535-545 ◽

Cited By ~ 9

Author(s):

A. DALSGAARD ◽

A. FORSLUND ◽

H. F. MORTENSEN ◽

T. SHIMADA

Keyword(s):

Vibrio Cholerae ◽

The United States ◽

Dice Coefficient ◽

Clonal Line ◽

Genetic Changes ◽

Low Degree ◽

Clonal Origin ◽

High Level ◽

Degree Of Similarity ◽

Different Levels

The emergence of Vibrio cholerae O139 in 1992 and reports of an increasing number of other non-O1 serogroups being associated with diarrhoea, stimulated us to characterize V. cholerae non-O1 non-O139 strains received at the National Institute of Infectious Diseases, Japan for serotyping. Ribotyping with the restriction enzyme BglI of 103 epidemiological unrelated mainly clinical strains representing 10 O-serotypes yielded 67 different typing patterns. Ribotype similarity within each serotype was compared by using the Dice coefficient (Sd) and different levels of homogeneity were observed (serotypes O5, O41 and O17, Sd between 82 and 90%; serotypes O13 and O141 Sd of 72; and O2, O6, O7, O11, O24 Sd of 62–66%). By cluster analysis, the strains were divided into several clusters of low similarity suggesting a high level of genetic diversity. A low degree of similarity between serotypes and ribotypes was found as strains within a specific serotypes often did not cluster but clustered with strains from other serotypes. However, epidemiological unrelated O5 strains showed identical or closely related ribotypes suggesting that these strains have undergone few genetic changes and may correspond to a clonal line. Surprisingly, 10 of 16 O141 strains studied contained a cholera toxin (CT) gene, including 7 strains recovered from stool and water samples in the United States. This is to our knowledge the first report of CT-positive clinical O141 strains. The closely related ribotypes shown by eight CT-positive strains is disturbing and suggest that these strains may be of a clonal origin and have the potential to cause cholera-like disease. Despite the low degree of correlation found between ribotypes and serotypes, both methods appears to be valuable techniques in studying the epidemiology of emerging serotypes of V. cholerae.

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