Publications by authors named "Yvonne Pannekoek"

is among the leading causes of hospital-acquired infections. Critical to biology and pathogenesis are the cell wall-anchored glycopolymers wall teichoic acids (WTA). Approximately one-third of isolates decorates WTA with a mixture of α1,4- and β1,4--acetylglucosamine (GlcNAc), which requires the dedicated glycosyltransferases TarM and TarS, respectively.

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  • The study focuses on a critical infection-causing pathogen, examining a specific carbohydrate structure (GAC) essential for its disease-causing abilities and diagnostic recognition.* -
  • Researchers discovered genetic variations in the GAC biosynthesis genes among various strains, especially noting a premature stop codon that leads to the loss of a crucial side chain, affecting the bacterium's immune response.* -
  • The findings provide insights into how genetic variations influence the bacterium's ability to evade the human immune system and highlight the significance of GacH in maintaining the pathogen's structural integrity.*
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Phase variation allows a single strain to produce phenotypic diverse subpopulations. Phase-variable restriction modification (RM) systems are systems that allow for such phase variation via epigenetic regulation of gene expression levels. The phase-variable RM system SsuCC20p was found in multiple streptococcal species and was acquired by an emerging zoonotic lineage of .

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  • The study examines a globally distributed veterinary pathogen with zoonotic potential, highlighting challenges in isolating and culturing it which hinder the understanding of its genetic diversity, especially in avian hosts from Australia and New Zealand.
  • Researchers utilized culture-independent whole-genome sequencing to discover new genomes from various birds, including pigeons and parrots, revealing unique genetic sequences and characters.
  • The findings showcase significant genetic diversity, with specific strains identified in different bird species and environments, enhancing knowledge of the pathogen’s global diversity and its capability to thrive in multiple host species.
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  • In 2020, the International Committee on Systematics of Prokaryotes (ICSP) rejected a proposal to change the naming rules for prokaryotes to include gene sequences as a basis for nomenclature.
  • In 2022, an alternative naming system called SeqCode was introduced, allowing genome sequences to be used for naming species.
  • The ICSP's taxonomy subcommittee believes that using gene sequences could improve naming for hard-to-culture microorganisms, like chlamydiae, and suggests registering new names for uncultured prokaryotes in the SeqCode registry.
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Neisseria meningitidis (meningococcus) colonizes the human nasopharynx, primarily as a commensal, but sporadically causing septicemia and meningitis. During colonization and invasion, it encounters different niches with specific nutrient compositions. Small noncoding RNAs (sRNAs) are used to fine-tune expression of genes, allowing adaptation to their physiological differences.

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is a leading cause of skin and soft tissue infections and systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for nasal colonization, phage-mediated horizontal gene transfer, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with -acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP.

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  • MRSA is a significant health concern, recognized by the World Health Organization, creating an urgent need for new treatments.
  • Human group IIA-secreted phospholipase A2 (hGIIA) is highly effective against MRSA, and researchers found that a gene called lspA enables MRSA to resist hGIIA, making it a target for potential therapies.
  • By inhibiting LspA, researchers discovered that MRSA and other Gram-positive bacteria become more susceptible to hGIIA and the last-resort antibiotic daptomycin, suggesting that targeting LspA could improve treatment outcomes against these infections.
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  • The avian pathogen poses a risk to both animals and humans, particularly causing reproductive loss in horses and subsequent infections in humans who come into contact with them.
  • A study analyzed genomic data from various species, revealing that predominant strains (ST24) showed clonal characteristics across horses, birds, and humans, primarily in Australia, while also identifying significant genomic diversity in other groups.
  • Findings indicated that ST24 has distinct sub-lineages with recent population expansion, highlighting the potential for cross-species transmission within its various hosts.
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Unlabelled: or the meningococcus, can cause devasting diseases such as sepsis and meningitis. Its polysaccharide capsule, on which serogrouping is based, is the most important virulence factor. Non-encapsulated meningococci only rarely cause disease, due to their sensitivity to the host complement system.

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is traditionally regarded as a globally distributed avian pathogen that can cause zoonotic spill-over. Molecular research has identified an extended global host range and significant genetic diversity. However, Australia has reported a reduced host range (avian, horse, and human) with a dominance of clonal strains, denoted ST24.

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  • - Chlamydia gallinacea is a newly identified bacterium in the Chlamydiaceae family, commonly found in poultry, and may cause pneumonia in slaughterhouse workers, though infections typically appear asymptomatic in birds.
  • - Researchers isolated two closely related strains (NL_G47 and NL_F725) from healthy chickens, showing high similarity to the C. gallinacea Type strain, and conducted experiments to assess their pathogenic potential.
  • - Infection experiments in chicken embryos demonstrated lower mortality rates with C. gallinacea compared to a more harmful related bacterium, C. psittaci, but the presence of virulence factors suggests that C. gallinacea could be an opportunistic pathogen rather than harmless.
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  • Chlamydia abortus and Chlamydia psittaci are pathogens affecting livestock and birds, with the former evolving from the latter, indicating a close evolutionary link.
  • The study focused on the parrot-derived strain 84/2334, analyzing its genome, which showed that it clusters closely with C. abortus, particularly in genomic structure and evolutionary lineage.
  • Findings indicate strain 84/2334 possesses characteristics and diversity from both species, including an extrachromosomal plasmid typical of C. psittaci, supporting its classification as an intermediary strain between C. psittaci and C. abortus.
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In 2016, an outbreak of Chlamydia avium infection occurred among Picazuro pigeons (Patagioenas picazuro) living in an aviary in the Netherlands. Molecular typing revealed a unique strain of C. avium.

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Developed two decades ago as a molecular method to provide definite characterization of a bacterial isolate, Multilocus Sequence Typing (MLST) is today globally adopted as a universal fine-detailed molecular typing tool and has been applied to numerous pathogenic and nonpathogenic bacterial as well eukaryotic organisms. MLST utilizes DNA sequence of several conserved housekeeping (HK) genes which are assigned an allelic number, which then collectively constitute an allelic profile or sequence type (ST), a "molecular barcode" of the interrogated bacterial strain or a eukaryotic organism. Here, we describe the principles and molecular approaches for generating MLST data for an analysis of a bacteria in the order Chlamydiales, using a Chlamydia pecorum-specific MLST scheme as an example.

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Background: Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated.

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  • Chlamydia gallinacea is a newly identified bacterium primarily affecting chickens and has potential zoonotic implications for humans, as evidenced by its association with atypical pneumonia.
  • The genome of strain JX-1 is characterized by a 1,059,522-bp circular chromosome, which shows high sequence similarity to the type strain, and includes a unique plasmid found only in chicken field strains.
  • Comparative genomic analysis reveals conserved genetic regions in C. gallinacea strains, along with significant genetic diversity among different strains, particularly within Chinese populations.
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Background: Chlamydia suis is an important, globally distributed, highly prevalent and diverse obligate intracellular pathogen infecting pigs. To investigate the prevalence and genetic diversity of C. suis in China, 2,137 nasal, conjunctival, and rectal swabs as well as whole blood and lung samples of pigs were collected in 19 regions from ten provinces of China in this study.

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The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species.

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NrrF is a small regulatory RNA of the human pathogen . NrrF was previously shown to repress succinate dehydrogenase () under control of the ferric uptake regulator (Fur). Here, we provide evidence that cytochrome , encoded by the polycistronic mRNA , is a NrrF target as well.

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The conserved RNA-binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed-phase liquid chromatography combined with data-independent alternate scanning mass spectrometry (LC-MS) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal deletion mutant.

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Background: Streptococcus suis is a zoonotic pathogen, causing meningitis and septicemia. We previously demonstrated that the gastrointestinal tract (GIT) is an entry site for zoonotic S. suis infection.

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(the meningococcus) is primarily a commensal of the human oropharynx that sporadically causes septicemia and meningitis. Meningococci adapt to diverse local host conditions differing in nutrient supply, like the nasopharynx, blood, and cerebrospinal fluid, by changing metabolism and protein repertoire. However, regulatory transcription factors and two-component systems in meningococci involved in adaptation to local nutrient variations are limited.

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Many studies have aimed to set up boundaries for the classification and definition of prokaryotic genus and species classification; however, studies that focused on genus-level genomic differences for existing taxonomy systems are limited. Recently, a novel method was described for prokaryotic genus delineation using the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance (Qin et al. A proposed genus boundary for the prokaryotes based on genomic insights.

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