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Article ; Online: Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection.

Dekker, John P

2023 Volume 19, Page(s) 203–226

Abstract: Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can ... ...

Abstract	Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.
MeSH term(s)	Humans ; Persistent Infection ; Immune Evasion
Language	English
Publishing date	2023-10-13
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2227429-7
ISSN	1553-4014 ; 1553-4006
ISSN (online)	1553-4014
ISSN	1553-4006
DOI	10.1146/annurev-pathmechdis-051122-111408
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Article ; Online: Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality.

Dekker, John P

Journal of clinical microbiology

2018 Volume 56, Issue 9

Abstract: Metagenomics approaches based on shotgun next-generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these ... ...

Abstract	Metagenomics approaches based on shotgun next-generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these approaches to transform how clinical pathogen identification and analysis are performed. In an article in this issue of the
MeSH term(s)	Communicable Diseases/diagnosis ; Communicable Diseases/microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Laboratories/economics ; Laboratories/standards ; Metagenomics ; Molecular Diagnostic Techniques/methods ; Pathology, Molecular/methods ; Sequence Analysis, DNA
Language	English
Publishing date	2018-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.00850-18
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Article ; Online: Visual hallucinations induced by Ganzflicker and Ganzfeld differ in frequency, complexity, and content.

Shenyan, Oris / Lisi, Matteo / Greenwood, John A / Skipper, Jeremy I / Dekker, Tessa M

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2353

Abstract: Visual hallucinations can be phenomenologically divided into those of a simple or complex nature. Both simple and complex hallucinations can occur in pathological and non-pathological states, and can also be induced experimentally by visual stimulation ... ...

Abstract	Visual hallucinations can be phenomenologically divided into those of a simple or complex nature. Both simple and complex hallucinations can occur in pathological and non-pathological states, and can also be induced experimentally by visual stimulation or deprivation-for example using a high-frequency, eyes-open flicker (Ganzflicker) and perceptual deprivation (Ganzfeld). Here we leverage the differences in visual stimulation that these two techniques involve to investigate the role of bottom-up and top-down processes in shifting the complexity of visual hallucinations, and to assess whether these techniques involve a shared underlying hallucinatory mechanism despite their differences. For each technique, we measured the frequency and complexity of the hallucinations produced, utilising button presses, retrospective drawing, interviews, and questionnaires. For both experimental techniques, simple hallucinations were more common than complex hallucinations. Crucially, we found that Ganzflicker was more effective than Ganzfeld at eliciting simple hallucinations, while complex hallucinations remained equivalent across the two conditions. As a result, the likelihood that an experienced hallucination was complex was higher during Ganzfeld. Despite these differences, we found a correlation between the frequency and total time spent hallucinating in Ganzflicker and Ganzfeld conditions, suggesting some shared mechanisms between the two methodologies. We attribute the tendency to experience frequent simple hallucinations in both conditions to a shared low-level core hallucinatory mechanism, such as excitability of visual cortex, potentially amplified in Ganzflicker compared to Ganzfeld due to heightened bottom-up input. The tendency to experience complex hallucinations, in contrast, may be related to top-down processes less affected by visual stimulation.
MeSH term(s)	Humans ; Retrospective Studies ; Hallucinations/etiology ; Visual Cortex
Language	English
Publishing date	2024-01-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-52372-1
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Article ; Online: Molecular Assay Validation Using Genomic Sequence Databases.

Dekker, John P

Journal of clinical microbiology

2016 Volume 54, Issue 12, Page(s) 2854–2856

Abstract: Whole-genome sequence databases offer new in silico approaches for designing and validating PCR assays in the clinical microbiology laboratory. An article in this issue of the Journal of Clinical Microbiology (M. J. Jansen van Rensburg, C. Swift, A. J. ... ...

Abstract	Whole-genome sequence databases offer new in silico approaches for designing and validating PCR assays in the clinical microbiology laboratory. An article in this issue of the Journal of Clinical Microbiology (M. J. Jansen van Rensburg, C. Swift, A. J. Cody, C. Jenkins, and M. C. J. Maiden, J Clin Microbiol, 54:2882-2890, 2016, http://dx.doi.org/10.1128/JCM.01522-16) demonstrates the use of publicly available genomic sequence data to evaluate a PCR assay for distinguishing Campylobacter species.
MeSH term(s)	Base Sequence ; Campylobacter/classification ; Campylobacter/genetics ; Campylobacter/isolation & purification ; Campylobacter Infections/diagnosis ; Campylobacter Infections/drug therapy ; Campylobacter Infections/microbiology ; Databases, Genetic ; Gastroenteritis/diagnosis ; Gastroenteritis/microbiology ; Genome, Bacterial/genetics ; Humans ; Molecular Diagnostic Techniques/methods ; Multilocus Sequence Typing/methods ; Real-Time Polymerase Chain Reaction/methods ; Sequence Analysis, DNA
Language	English
Publishing date	2016-12
Publishing country	United States
Document type	Journal Article ; Validation Studies
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01797-16
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Article ; Online: Adjunctive clindamycin therapy in invasive β-haemolytic streptococcal infections - Authors' reply.

Babiker, Ahmed / Dekker, John P / Danner, Robert L / Kadri, Sameer S

The Lancet. Infectious diseases

2021 Volume 21, Issue 6, Page(s) 762–763

MeSH term(s)	Anti-Bacterial Agents/therapeutic use ; Clindamycin/therapeutic use ; Cohort Studies ; Hospitals ; Humans ; Retrospective Studies ; Streptococcal Infections/drug therapy ; beta-Lactams
Chemical Substances	Anti-Bacterial Agents ; beta-Lactams ; Clindamycin (3U02EL437C)
Language	English
Publishing date	2021-05-16
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(21)00259-0
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Article ; Online: Republication of "Osteochondral Lesions of the Talus: Current Concepts in Diagnosis and Treatment".

Steele, John R / Dekker, Travis J / Federer, Andrew E / Liles, Jordan L / Adams, Samuel B / Easley, Mark E

Foot & ankle orthopaedics

2023 Volume 8, Issue 3, Page(s) 24730114231192961

Abstract: Osteochondral lesions of the talus (OLTs) are a difficult pathologic entity to treat. They require a strong plan. Lesion size, location, chronicity, and characteristics such as displacement and the presence of subchondral cysts help dictate the ... ...

Abstract	Osteochondral lesions of the talus (OLTs) are a difficult pathologic entity to treat. They require a strong plan. Lesion size, location, chronicity, and characteristics such as displacement and the presence of subchondral cysts help dictate the appropriate treatment required to achieve a satisfactory result. In general, operative treatment is reserved for patients with displaced OLTs or for patients who have failed nonoperative treatment for 3 to 6 months. Operative treatments can be broken down into cartilage repair, replacement, and regenerative strategies. There are many promising treatment options, and research is needed to elucidate which are superior to minimize the morbidity from OLTs.
Language	English
Publishing date	2023-08-06
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2473-0114
ISSN (online)	2473-0114
DOI	10.1177/24730114231192961
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Article ; Online: Smoking cessation care during pregnancy: A qualitative exploration of midwives' challenging role.

Kalamkarian, Anna / Hoon, Elizabeth / Chittleborough, Catherine R / Dekker, Gustaaf / Lynch, John W / Smithers, Lisa G

Women and birth : journal of the Australian College of Midwives

2022 Volume 36, Issue 1, Page(s) 89–98

Abstract: Problem: The majority of South Australian pregnant women who smoke do not quit during pregnancy. Additionally, the prevalence of smoking is higher among pregnant women living in socially disadvantaged areas.: Background: Understanding challenges in ... ...

Abstract	Problem: The majority of South Australian pregnant women who smoke do not quit during pregnancy. Additionally, the prevalence of smoking is higher among pregnant women living in socially disadvantaged areas. Background: Understanding challenges in midwives' provision of smoking cessation care can elucidate opportunities to facilitate women's smoking cessation. Aim: We aimed to understand midwives' perspectives on current practices, perceived barriers and facilitators to delivery of smoking cessation care, and potential improvements to models of smoking cessation care. Methods: An exploratory qualitative research methodology and thematic analysis was used to understand the perspectives of midwives in five focus groups. Findings: Four themes were generated from the data on how midwives perceived their ability to provide smoking cessation care: Tensions between providing smoking cessation care and maternal care; Organisational barriers in the delivery of smoking cessation care; Scepticism and doubt in the provision of smoking cessation care; and Opportunities to enable midwives' ability to provide smoking cessation care. Discussion: A combination of interpersonal, organisational and individual barriers impeded on midwives' capacities to approach, follow-up and prioritise smoking cessation care. Working with women living with disadvantage and high rates of smoking, the midwife's role was challenging as it balanced delivering smoking cessation care without jeopardising antenatal care. Conclusion: Providing midwives with resources and skills may alleviate the sense of futility that surrounds smoking cessation care. Provision of routine training and education could also improve understandings of the current practice guidelines.
MeSH term(s)	Female ; Pregnancy ; Humans ; Midwifery/methods ; Smoking Cessation/methods ; Australia ; Pregnant Women ; Prenatal Care/methods ; Qualitative Research ; Nurse Midwives
Language	English
Publishing date	2022-03-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2235085-8
ISSN	1878-1799 ; 1871-5192
ISSN (online)	1878-1799
ISSN	1871-5192
DOI	10.1016/j.wombi.2022.03.005
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Article ; Online: Isolation, marginalisation and disempowerment - understanding how interactions with health providers can influence smoking cessation in pregnancy.

Fletcher, Cherise / Hoon, Elizabeth / Gialamas, Angela / Dekker, Gustaaf / Lynch, John / Smithers, Lisa

BMC pregnancy and childbirth

2022 Volume 22, Issue 1, Page(s) 396

Abstract: Background: Maternal smoking during pregnancy can lead to serious adverse health outcomes for both women and their infants. While smoking in pregnancy has declined over time, it remains consistently higher in women with lower socioeconomic circumstances. ...

Abstract	Background: Maternal smoking during pregnancy can lead to serious adverse health outcomes for both women and their infants. While smoking in pregnancy has declined over time, it remains consistently higher in women with lower socioeconomic circumstances. Furthermore, fewer women in this group will successfully quit during pregnancy. Aim: This study explores the barriers to smoking cessation experienced by socially disadvantaged pregnant women and investigates how interactions with health providers can influence their smoking cessation journey. Methods: Women (either pregnant or birthed in the previous 10 years, who smoked or quit smoking in pregnancy) were recruited from a metropolitan public hospital antenatal clinic in South Australia and community organisations in surrounding suburbs. Seventeen women participated in qualitative semi-structured small focus groups or interviews. The focus groups and interviews were recorded, transcribed and thematically analysed. Findings: Four interconnected themes were identified: 1) smoking embedded in women's challenging lives and pregnancies, 2) cyclic isolation and marginalisation, 3) feeling disempowered, and 4) autonomy and self-determination. Themes 3 and 4 are characterised as being two sides of a single coin in that they coexist simultaneously and are inseparable. A key finding is a strong unanimous desire for smoking cessation in pregnancy but women felt they did not have the necessary support from health providers or confidence and self-efficacy to be successful. Conclusion: Women would like improvements to antenatal care that increase health practitioners' understanding of the social and contextual healthcare barriers faced by women who smoke in pregnancy. They seek improved interventions from health providers to make informed choices about smoking cessation and would like women-centred care. Women feel that with greater support, more options for cessation strategies and consistency and encouragement from health providers they could be more successful at antenatal smoking cessation. If such changes were made, then South Australian practice could align more with best practice international guidelines for addressing smoking cessation in pregnancy, and potentially improve outcomes for women and their children.
MeSH term(s)	Australia ; Child ; Delivery of Health Care ; Female ; Humans ; Pregnancy ; Pregnant Women ; Prenatal Care ; Smoking Cessation
Language	English
Publishing date	2022-05-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2059869-5
ISSN	1471-2393 ; 1471-2393
ISSN (online)	1471-2393
ISSN	1471-2393
DOI	10.1186/s12884-022-04720-0
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Article ; Online: Association between piperacillin/tazobactam MIC and survival among hospitalized patients with Enterobacterales infections: retrospective cohort analysis of electronic health records from 161 US hospitals.

Strich, Jeffrey R / Lawandi, Alexander / Warner, Sarah / Demirkale, Cumhur Y / Sarzynski, Sadia / Babiker, Ahmed / Dekker, John P / Kadri, Sameer S

JAC-antimicrobial resistance

2023 Volume 5, Issue 2, Page(s) dlad041

Abstract: Introduction: A recent randomized trial has suggested an increased risk of mortality for ceftriaxone-non-susceptible Enterobacterales infections treated with piperacillin/tazobactam compared with meropenem despite MICs within the susceptible range.: ... ...

Abstract	Introduction: A recent randomized trial has suggested an increased risk of mortality for ceftriaxone-non-susceptible Enterobacterales infections treated with piperacillin/tazobactam compared with meropenem despite MICs within the susceptible range. Methods: We conducted a retrospective cohort study of clinical encounters within the Cerner Health Facts database to identify all encounters between 2001 and 2017 in which Enterobacterales infections were treated empirically with piperacillin/tazobactam and for which MICs to the drug were available. Multivariate regression analysis was performed to enable partitioning of MICs into discrete strata based on statistically significant difference in mortality risk. Results: During the study period, 10 101 inpatient encounters were identified meeting inclusion criteria. The crude in-hospital mortality for the entire cohort was 16.5%. Partitioning analysis identified a breakpoint of ≤16/4 mg/L that dichotomized encounters into lower versus higher mortality risk strata in the primary cohort of overall infections. This finding persisted in sequentially granular subsets where specific MICs ≤8/4 mg/L were reported (in lieu of ranges) as well as in the high-reliability subset with bloodstream infections. A higher clinical breakpoint of ≥128/4 mg/L dichotomized encounters with respiratory tract infection. No breakpoint was identified when restricting to encounters with urinary tract infections, ICU admits or upon restricting analysis to encounters with ceftriaxone-resistant isolates. Conclusions: Clinical data suggest improved outcomes when piperacillin/tazobactam is prescribed for Enterobacterales infections with an MIC of ≤16/4 mg/L compared with ≥32/4 mg/L.
Language	English
Publishing date	2023-04-06
Publishing country	England
Document type	Journal Article
ISSN	2632-1823
ISSN (online)	2632-1823
DOI	10.1093/jacamr/dlad041
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Article ; Online: A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint.

Sánchez, Humberto / Liu, Zhaowei / van Veen, Edo / van Laar, Theo / Diffley, John F X / Dekker, Nynke H

Nature communications

2023 Volume 14, Issue 1, Page(s) 6735

Abstract: Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ...

Abstract	Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.
MeSH term(s)	Origin Recognition Complex/genetics ; Origin Recognition Complex/metabolism ; Nucleosomes ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Cell Cycle Proteins/metabolism ; DNA/metabolism ; DNA Replication ; Minichromosome Maintenance Proteins/genetics ; Minichromosome Maintenance Proteins/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Replication Origin
Chemical Substances	Origin Recognition Complex ; Nucleosomes ; Cell Cycle Proteins ; DNA (9007-49-2) ; Minichromosome Maintenance Proteins (EC 3.6.4.12) ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2023-10-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42524-8
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