scholarly journals Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Rebecca J. Bennett ◽  
Kate S. Baker
Keyword(s):  
Ancient Dna ◽  
Culture Collection ◽  
Health Concern ◽  
Human History ◽  
Bacterial Genomes ◽  
Content Type ◽  
Retrospective Diagnosis ◽  
Sequencing Technologies ◽  
Sequencing Studies ◽  
Unique Source

ABSTRACT Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.

scholarly journals Complete Genome Sequence of Paradevosia shaoguanensis Type Strain J5-3, Obtained Using Nanopore and Illumina Sequencing Technologies

2021 ◽  
Vol 10 (23) ◽  
Author(s):  
Yang Wang ◽  
Songxue Wang
Keyword(s):  
Genome Sequence ◽  
Illumina Sequencing ◽  
Genome Analysis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Culture Collection ◽  
Comparative Genome Analysis ◽  
Content Type ◽  
Sequencing Technologies

The complete genome sequence of Paradevosia shaoguanensis J5-3 T (China General Microbiological Culture Collection Center [CGMCC] 1.12430 T ) is presented here. The complete genome sequence of P . shaoguanensis J5-3 T will provide valuable references for classification and comparative genome analysis.

scholarly journals The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

2020 ◽  
Vol 54 (1) ◽  
pp. 563-581
Author(s):  
Ludovic Orlando
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Economic Value ◽  
Domestic Horse ◽  
Human History ◽  
Archaeological Remains ◽  
Animal Kingdom ◽  
Sequencing Technologies ◽  
Sport Industry ◽  
Horse Domestication

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500–10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.

scholarly journals Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Fabrício S. Campos ◽  
Fernando B. Cerqueira ◽  
Gil R. Santos ◽  
Eliseu J. G. Pereira ◽  
Roberto F. T. Corrêia ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Crucial Role ◽  
Bacterial Genomes ◽  
Content Type ◽  
Complete Sequences

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.

scholarly journals A Putative Cro-Like Repressor Contributes to Arylomycin Resistance in Staphylococcus aureus

2015 ◽  
Vol 59 (6) ◽  
pp. 3066-3074 ◽  
Author(s):  
Arryn Craney ◽  
Floyd E. Romesberg
Keyword(s):  
Staphylococcus Aureus ◽  
Ex Vivo ◽  
Transcriptional Regulator ◽  
Signal Peptidase ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Type I ◽  
Wall Teichoic Acid ◽  
Content Type ◽  
Wide Range

ABSTRACTAntibiotic-resistant bacteria are a significant public health concern and motivate efforts to develop new classes of antibiotics. One such class of antibiotics is the arylomycins, which target type I signal peptidase (SPase), the enzyme responsible for the release of secreted proteins from their N-terminal leader sequences. Despite the essentiality, conservation, and relative accessibility of SPase, the activity of the arylomycins is limited against some bacteria, including the important human pathogenStaphylococcus aureus. To understand the origins of the limited activity againstS. aureus, we characterized the susceptibility of a panel of strains to two arylomycin derivatives, arylomycin A-C16and its more potent analog arylomycin M131. We observed a wide range of susceptibilities to the two arylomycins and found that resistant strains were sensitized by cotreatment with tunicamycin, which inhibits the first step of wall teichoic acid synthesis. To further understand howS. aureusresponds to the arylomycins, we profiled the transcriptional response ofS. aureusNCTC 8325 to growth-inhibitory concentrations of arylomycin M131 and found that it upregulates the cell wall stress stimulon (CWSS) and an operon consisting of a putative transcriptional regulator and three hypothetical proteins. Interestingly, we found that mutations in the putative transcriptional regulator are correlated with resistance, and selection for resistanceex vivodemonstrated that mutations in this gene are sufficient for resistance. The results begin to elucidate howS. aureuscopes with secretion stress and how it evolves resistance to the inhibition of SPase.

scholarly journals Expression, Purification, and Biological Characterization of Babesia microti Apical Membrane Antigen 1

2015 ◽  
Vol 83 (10) ◽  
pp. 3890-3901 ◽  
Author(s):  
Prasun Moitra ◽  
Hong Zheng ◽  
Vivek Anantharaman ◽  
Rajdeep Banerjee ◽  
Kazuyo Takeda ◽  
...  
Keyword(s):  
Apical Membrane ◽  
The United States ◽  
Host Cells ◽  
Health Concern ◽  
Babesia Microti ◽  
Type I ◽  
Content Type ◽  
Apical Membrane Antigen 1 ◽  
Apical Membrane Antigen ◽  
Extracellular Region

The intraerythrocytic apicomplexanBabesia microti, the primary causative agent of human babesiosis, is a major public health concern in the United States and elsewhere. Apicomplexans utilize a multiprotein complex that includes a type I membrane protein called apical membrane antigen 1 (AMA1) to invade host cells. We have isolated the full-lengthB. microtiAMA1 (BmAMA1) gene and determined its nucleotide sequence, as well as the amino acid sequence of the AMA1 protein. This protein contains an N-terminal signal sequence, an extracellular region, a transmembrane region, and a short conserved cytoplasmic tail. It shows the same domain organization as the AMA1 orthologs from piroplasm, coccidian, and haemosporidian apicomplexans but differs from all other currently known piroplasmida, including otherBabesiaandTheileriaspecies, in lacking two conserved cysteines in highly variable domain III of the extracellular region. Minimal polymorphism was detected in BmAMA1 gene sequences of parasite isolates from six babesiosis patients from Nantucket. Immunofluorescence microscopy studies showed that BmAMA1 is localized on the cell surface and cytoplasm near the apical end of the parasite. Native BmAMA1 from parasite lysate and refolded recombinant BmAMA1 (rBmAMA1) expressed inEscherichia colireacted with a mouse anti-BmAMA1 antibody using Western blotting.In vitrobinding studies showed that both native BmAMA1 and rBmAMA1 bind to human red blood cells (RBCs). This binding is trypsin and chymotrypsin treatment sensitive but neuraminidase independent. Incubation ofB. microtiparasites in human RBCs with a mouse anti-BmAMA1 antibody inhibited parasite growth by 80% in a 24-h assay. Based on its antigenically conserved nature and potential role in RBC invasion, BmAMA1 should be evaluated as a vaccine candidate.

Women’s health concern in Jordan: knowledge, practice and barriers toward cervical cancer screening

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Roqia Saleem Maabreh ◽  
Raya Yousef Al-Husban ◽  
Hekmat Yousef Al-Akash ◽  
Noha Al-Shdayfat
Keyword(s):  
Risk Factors ◽  
Cervical Cancer ◽  
Pap Smear ◽  
Cervical Screening ◽  
Health Concern ◽  
Cancer Awareness ◽  
Early Screening ◽  
Cross Sectional ◽  
Content Type ◽  
Knowledge Barriers

Purpose Cervical cancer (CC) is one of the most important health issues faced by women worldwide. The purpose of this study is to identify Jordanian women’s knowledge, barriers and measures pertaining to risk factors and screening choices of CC (Pap smear tests). Design/methodology/approach This study applied a cross sectional design by collecting data from a convenient sample of 200 women between 20 and 70 years of age in health and public centers in Jordan. Data was then analyzed using the descriptive statistical tools of SPSS, version 21. Findings The findings revealed that 55.5% of the participants had no information about the Pap smear, and 75% did not know the risk factors. Moreover, 50% of the sample did not know where to take the test, and 50% reported a lack of encouragement from the husband to undertake the test. More than half of the participants (56.5%) expressed fear that cervical screening would be a painful examination even though they reported not having any previous experience with the test. Originality/value Based on these findings, public education about CC screening is essential, including advertising and a campaign similar to the breast cancer awareness programs in Jordan, as a way of encouraging early screening to improve the health of women.

scholarly journals Development and Validation of a High-Resolution Melting Assay To Detect Azole Resistance in Aspergillus fumigatus

2017 ◽  
Vol 61 (12) ◽  
Author(s):  
L. Bernal-Martínez ◽  
H. Gil ◽  
O. Rivero-Menéndez ◽  
S. Gago ◽  
M. Cuenca-Estrella ◽  
...  
Keyword(s):  
High Resolution ◽  
Aspergillus Fumigatus ◽  
Tandem Repeats ◽  
High Resolution Melting ◽  
Screening Method ◽  
Melting Curve ◽  
Health Concern ◽  
Azole Resistance ◽  
Content Type ◽  
Selection Of

ABSTRACT The global emergence of azole-resistant Aspergillus fumigatus strains is a growing public health concern. Different patterns of azole resistance are linked to mutations in cyp51A. Therefore, accurate characterization of the mechanisms underlying azole resistance is critical to guide selection of the most appropriate antifungal agent for patients with aspergillosis. This study describes a new sequencing-free molecular screening tool for early detection of the most frequent mutations known to be associated with azole resistance in A. fumigatus. PCRs targeting cyp51A mutations at positions G54, Y121, G448, and M220 and targeting different tandem repeats (TRs) in the promoter region were designed. All PCRs were performed simultaneously, using the same cycling conditions. Amplicons were then distinguished using a high-resolution melting assay. For standardization, 30 well-characterized azole-resistant A. fumigatus strains were used, yielding melting curve clusters for different resistance mechanisms for each target and allowing detection of the most frequent azole resistance mutations, i.e., G54E, G54V, G54R, G54W, Y121F, M220V, M220I, M220T, M220K, and G448S, and the tandem repeats TR34, TR46, and TR53. Validation of the method was performed using a blind panel of 80 A. fumigatus azole-susceptible or azole-resistant strains. All strains included in the blind panel were properly classified as susceptible or resistant with the developed method. The implementation of this screening method can reduce the time needed for the detection of azole-resistant A. fumigatus isolates and therefore facilitate selection of the best antifungal therapy in patients with aspergillosis.

scholarly journals Ancient DNA set to rewrite human history

Nature ◽  
2010 ◽  
Vol 465 (7295) ◽  
pp. 148-148 ◽  
Author(s):  
Rex Dalton
Keyword(s):  
Ancient Dna ◽  
Human History

scholarly journals Fathers experiences of sleeping problems in children with autism

2017 ◽  
Vol 3 (2) ◽  
pp. 100-111 ◽  
Author(s):  
Carol Ann Potter
Keyword(s):  
Sleep Onset ◽  
Children With Autism ◽  
Health Concern ◽  
Structured Interviews ◽  
Negative Effects ◽  
Night Time ◽  
Content Type ◽  
Sleeping Problems ◽  
Significant Public Health ◽  
The Impact

Purpose The purpose of this paper is to explore the role of fathers in the management of sleeping problems in children with autism and their perspectives of the impact of these difficulties on family life. Design/methodology/approach Semi-structured interviews with 25 UK-based fathers of children with autism were undertaken. Findings Two-thirds of fathers reported that their children experienced severe sleeping problems in the areas of bed-time resistance, sleep onset and night-time waking. Fathers were significantly involved in the management of these difficulties and reported a range of associated deleterious impacts on the family, including significant negative effects on paternal and maternal health, father’s employment, couple relationship and sibling experiences. Research limitations/implications The interview sample cannot be said to be representative of all fathers of children with autism since the backgrounds of those taking part were relatively homogeneous in respect of ethnicity, marital status and level of education. Practical implications Improvements in effective, family-centred provision are urgently needed which employ a co-parenting, gender-differentiated methodology. Social implications Given the severity and frequency of difficulties, sleeping problems in children with autism should be viewed as a significant public health concern. Originality/value This is one of the first studies, qualitative or quantitative, to explore the role and perspectives of fathers of children with autism in the important area of sleep management.

scholarly journals Could Dampening Expression of theNeisseria gonorrhoeaemtrCDE-Encoded Efflux Pump Be a Strategy To Preserve Currently or Resurrect Formerly Used Antibiotics To Treat Gonorrhea?

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Shaochun Chen ◽  
Kristie L. Connolly ◽  
Corinne Rouquette-Loughlin ◽  
Alexander D’Andrea ◽  
Ann E. Jerse ◽  
...  
Keyword(s):  
Genital Tract ◽  
Efflux Pump ◽  
Health Concern ◽  
Third Generation ◽  
Global Public Health ◽  
Beta Lactam ◽  
Beta Lactams ◽  
Genital Tract Infection ◽  
Infected Female ◽  
Content Type

ABSTRACTNeisseria gonorrhoeaehas developed resistance to every antibiotic introduced for treatment of gonorrhea since 1938, and concern now exists that gonorrheal infections may become refractory to all available antibiotics approved for therapy. The current recommended dual antibiotic treatment regimen of ceftriaxone (CRO) and azithromycin (AZM) is threatened with the emergence of gonococcal strains displaying resistance to one or both of these antibiotics. Non-beta-lactamase resistance to penicillin and third-generation cephalosporins, as well as low-level AZM resistance expressed by gonococci, requires overexpression of themtrCDE-encoded efflux pump, which in wild-type (WT) strains is subject to transcriptional repression by MtrR. Since earlier studies showed that loss of MtrCDE renders gonococci hypersusceptible to beta-lactams and macrolides, we hypothesized that transcriptional dampening ofmtrCDEwould render an otherwise resistant strain susceptible to these antibiotics as assessed by antibiotic susceptibility testing and during experimental infection. In order to test this hypothesis, we ectopically expressed a WT copy of themtrRgene, which encodes the repressor of themtrCDEefflux pump operon, inN. gonorrhoeaestrain H041, the first reported gonococcal strain to cause a third-generation-cephalosporin-resistant infection. We now report that MtrR production can repress the expression ofmtrCDE, increase antimicrobial susceptibilityin vitro, and enhance beta-lactam efficacy in eliminating gonococci as assessed in a female mouse model of lower genital tract infection. We propose that strategies that target the MtrCDE efflux pump should be considered to counteract the increasing problem of antibiotic-resistant gonococci.IMPORTANCEThe emergence of gonococcal strains resistant to past or currently used antibiotics is a global public health concern, given the estimated 78 million infections that occur annually. The dearth of new antibiotics to treat gonorrhea demands that alternative curative strategies be considered to counteract antibiotic resistance expressed by gonococci. Herein, we show that decreased expression of a drug efflux pump that participates in gonococcal resistance to antibiotics can increase gonococcal susceptibility to beta-lactams and macrolides under laboratory conditions, as well as improve antibiotic-mediated clearance of gonococci from the genital tract of experimentally infected female mice.

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