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Nurjadi D, Boutin S, Schmidt K, Ahmels M, Hasche D. Identification and Elimination of the Clinically Relevant Multi-Resistant Environmental Bacteria Ralstonia insidiosa in Primary Cell Culture. Microorganisms 2020; 8:microorganisms8101599. [PMID: 33080836 PMCID: PMC7603027 DOI: 10.3390/microorganisms8101599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/09/2023] Open
Abstract
In times of spreading multidrug-resistant bacteria, species identification and decontamination of cell cultures can be challenging. Here, we describe a mobile cell culture contaminant with “black dot”-like microscopic appearance in newly established irreplaceable hybridoma cell lines and its identification. Using 16S rRNA gene sequencing, species-specific PCRs, whole genome sequencing (WGS), and MALDI-TOF mass spectrometry, the contaminant was identified as the ubiquitous environmental and clinically relevant Gram-negative bacterium Ralstonia insidiosa (R. insidiosa), a strong biofilm producer. Further characterizations by transmission electron microscopy (TEM) and biochemical API test were not conclusive. Whole genome sequencing of our R. insidiosa isolate revealed numerous drug-resistance determinants. Genome-wide comparison to other Ralstonia species could not unambiguously designate our isolate to R. insidiosa (<95% average nucleotide identity) suggesting a potential novel species or subspecies, closely related to R. insidiosa and R. pickettii. After determining the antibiotic susceptibility profile, the hybridoma cell culture was successfully decontaminated with ciprofloxacin without affecting antibody production.
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Chiasson R, Aboulhouda I, Roy G, Boucher A, Gagnon MP, Boutin S, Kankindi B, Ouellet M. E-health, community housing and nursing interprofessional clinic for equity. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Problem
From a focus on transmittable diseases, attention to prevention and promotion has become a priority since 2011. Influenced by the Political Declaration of the High-level Meeting on the Prevention and Control of Non-communicable Diseases and The Rio Declaration on Social Determinants of Health, many countries across the world have identified targets aiming at chronic diseases prevention, preventable death and reduced morbidity. Individual behavior changes remain a challenge for health practitioners. Shanghai Declaration suggests that health literacy is a critical determinant for healthy choices and decisions.
Description
A healthy living program has been developed and offered in partnership between local public health and university Laval. We present the case of the community housing Mimosa du Quartier and its preventative nursing clinic. Eight-week Preventative circles and e-prevention interventions from kinesiologist, nutritionist and nurses are explored. IPads were provided to families and we used REACT technology.
Results
Discussion on e-health relevance, feasibility and impact is proposed. Program description, personalised action plan using SMART goals, health literacy and prevention gains are revealed. Relevance, feasibility and perceived impact are discussed. Learning about the user's experience, we can improve the telehealth program in support of continuity of care within the homes of families. This strategy is key to self-management and empowerment Lessons. Health promotion with e-prevention is strategic for sustainable family health. Combining strategies can improve outcomes. This pilot research shows promising results and practical considerations are given to the importance of the relational and alliance aspect of the care relationship even through technology use, to digital literacy capabilities, to family's motivation and engagement and finally to the advantages provided by the technology use.
Key messages
E-health prevention is an innovative avenue to fight chronic disease. Increased engagement in self-management leads to equity and less adverse outcomes for vulnerable families.
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Sörensen M, Kantorek J, Byrnes L, Boutin S, Mall MA, Lasitschka F, Zabeck H, Nguyen D, Dalpke AH. Corrigendum: Pseudomonas aeruginosa Modulates the Antiviral Response of Bronchial Epithelial Cells. Front Immunol 2020; 11:1453. [PMID: 32754158 PMCID: PMC7366873 DOI: 10.3389/fimmu.2020.01453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/04/2020] [Indexed: 11/28/2022] Open
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Kocer K, Boutin S, Probst K, Heeg K, Nurjadi D. Whole-genome sequencing disproves two suspected transmission events of bla NDM between Pseudomonas aeruginosa and Enterobacterales in hospitalized patients. J Hosp Infect 2020; 106:372-375. [PMID: 32652213 DOI: 10.1016/j.jhin.2020.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/06/2020] [Indexed: 11/18/2022]
Abstract
New Delhi metallo-β-lactamase (blaNDM) acquisition by Gram-negative bacteria is a primary concern due to its broad-host-range distribution. This study investigated two potential in-vivo horizontal gene transfers (HGTs) of blaNDM between Enterobacterales and Pseudomonas aeruginosa, initially indicated by polymerase chain reaction. Whole-genome sequencing showed independent parallel acquisition of two different blaNDM variants (NDM-1 and NDM-5) in P. aeruginosa and Enterobacterales, respectively. The data show that short-read sequencing provides the necessary resolution to confirm or dispute HGT by the comparison of genetic elements surrounding the gene of interest, and thus provide a timely response to potential outbreaks.
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Boutin S, Dalpke AH. The Microbiome: A Reservoir to Discover New Antimicrobials Agents. Curr Top Med Chem 2020; 20:1291-1299. [DOI: 10.2174/1568026620666200320112731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 02/01/2023]
Abstract
Nature offered mankind the first golden era of discovery of novel antimicrobials based on
the ability of eukaryotes or micro-organisms to produce such compounds. The microbial world proved
to be a huge reservoir of such antimicrobial compounds which play important functional roles in every
environment. However, most of those organisms are still uncultivable in a classical way, and therefore,
the use of extended culture or DNA based methods (metagenomics) to discover novel compounds
promises usefulness. In the past decades, the advances in next-generation sequencing and bioinformatics
revealed the enormous diversity of the microbial worlds and the functional repertoire available for
studies. Thus, data-mining becomes of particular interest in the context of the increased need for new
antibiotics due to antimicrobial resistance and the rush in antimicrobial discovery. In this review, an
overview of principles will be presented to discover new natural compounds from the microbiome. We
describe culture-based and culture-independent (metagenomic) approaches that have been developed to
identify new antimicrobials and the input of those methods in the field as well as their limitations.
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Heininger A, Zimmermann S, Bootsveld C, Boutin S, Nurjadi D. Low prevalence of combined linezolid- and vancomycin-resistant Enterococcus faecium from hospital admission screening in an endemic region in Germany. J Glob Antimicrob Resist 2020; 22:646-650. [PMID: 32439568 DOI: 10.1016/j.jgar.2020.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Accepted: 05/08/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The emergence and spread of linezolid and combined linezolid/vancomycin resistance in Enterococcus faecium (LVRE) is a major therapeutic challenge. Due to the unavailability of standardized selective culture media for LVRE screening, the detection of LVRE is laborious and costly. Systematic data on LVRE prevalence are scarce, and therefore, supportive evidence for the correct implementation of preemptive strategies is lacking. OBJECTIVE We investigated the prevalence of LVRE in a vancomycin-resistant enterococci (VRE) endemic area in Germany in admission screening of high-risk patients for multidrug-resistant organisms to assess the necessity of LVRE screening. METHODS We performed phenotypic testing for linezolid susceptibility in all patients (n = 2572) admitted to our hospital in the months of January, April, July and October 2018 with a positive VRE culture in their rectal admission screening swab. Eight isolates from seven patients with LVRE colonization were characterized by whole genome sequencing. RESULTS Twenty-eight percent (712/2572) of screened patients were colonized by VRE. Seventy percent (497/712) of the isolates were available for testing and whole genome sequencing. A total of 1.4% (7/497) of VRE were LVRE, predominantly due to mutations of 23S rRNA. optrA, poxtA or cfr genes were not detected. Patients with LVRE colonization did not develop LVRE infections during their stay. CONCLUSION LVRE prevalence was low, and there was no evidence for the dissemination of linezolid resistance genes. Due to the low prevalence and the low risk of infection due to endogenous LVRE, we do not see the immediate necessity to introduce routine LVRE screening in our hospital.
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Schmitt FCF, Lipinski A, Hofer S, Uhle F, Nusshag C, Hackert T, Dalpke AH, Weigand MA, Brenner T, Boutin S. Pulmonary microbiome patterns correlate with the course of the disease in patients with sepsis-induced ARDS following major abdominal surgery. J Hosp Infect 2020; 105:S0195-6701(20)30203-6. [PMID: 32339614 DOI: 10.1016/j.jhin.2020.04.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Patients with sepsis-induced Acute Respiratory Distress Syndrome (ARDS) are hallmarked by high mortality rates. Early, targeted antibiotic therapy is crucial for patients' survival. The clinical use of a Next Generation Sequencing (NGS)-based approach for pathogen identification may lead to an improved diagnostic performance. Therefore, the objective of this study was to examine changes in the pulmonary-microbiome and resulting influences on patients' outcome in septic ARDS, but also to compare NGS- and culture-based diagnostic methods for pathogen identification. METHODS In total, 30 patients in two groups were enrolled in the study: (1) 15 septic ARDS patients following major abdominal surgery and (2) 15 patients undergoing oesophageal resection serving as controls. In the ARDS group, blood samples were collected at ARDS onset as well as 5 days and 10 days afterwards. At the same timepoints, bronchoalveolar lavages (BAL) were performed to collect epithelial lining fluid for culture-, as well as NGS-based analyses and to evaluate longitudinal changes in the pulmonary microbiome. In the control group, only one BAL and one blood sample were collected. RESULTS ARDS patients showed a significantly reduced α-diversity (p=0.007**) and an increased dominance (p=0.012*) in their pulmonary-microbiome. The α-diversity-index correlated with the length of stay in the intensive care unit (p-value=0.015) and the need for mechanical ventilation (p-value=0.009). In 42.9% of all ARDS patients, culture-based results were negative, while NGS findings indicated bacterial colonization. CONCLUSION Sepsis-induced ARDS is associated with a significant dysbiosis of patients' pulmonary-microbiome, which is closely correlated with the clinical course of the disease. TRIAL REGISTRATION This prospective, observational pilot study was approved by the Ethics Committee of the Medical Faculty of Heidelberg (trial code no. S-063/2015) and was prospectively registered in the German clinical trials register (DRKS-ID: DRKS00008317 prospectively registered: 28.10.2015). All study patients or their legal representatives signed written informed consent.
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Studd EK, Menzies AK, Siracusa ER, Dantzer B, Lane JE, McAdam AG, Boutin S, Humphries MM. Optimisation of energetic and reproductive gains explains behavioural responses to environmental variation across seasons and years. Ecol Lett 2020; 23:841-850. [PMID: 32189469 DOI: 10.1111/ele.13494] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/09/2019] [Accepted: 02/21/2020] [Indexed: 12/31/2022]
Abstract
Animals switch between inactive and active states, simultaneously impacting their energy intake, energy expenditure and predation risk, and collectively defining how they engage with environmental variation and trophic interactions. We assess daily activity responses to long-term variation in temperature, resources and mating opportunities to examine whether individuals choose to be active or inactive according to an optimisation of the relative energetic and reproductive gains each state offers. We show that this simplified behavioural decision approach predicts most activity variation (R2 = 0.83) expressed by free-ranging red squirrels over 4 years, as quantified through accelerometer recordings (489 deployments; 5066 squirrel-days). Recognising activity as a determinant of energetic status, the predictability of activity variation aggregated at a daily scale, and the clear signal that behaviour is environmentally forced through optimisation of gain, provides an integrated approach to examine behavioural variation as an intermediary between environmental variation and energetic, life-history and ecological outcomes.
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Nurjadi D, Last K, Klein S, Boutin S, Schmack B, Mueller F, Heeg K, Ruhparwar A, Heininger A, Zanger P. Nasal colonization with Staphylococcus aureus is a risk factor for ventricular assist device infection in the first year after implantation: A prospective, single-centre, cohort study. J Infect 2020; 80:511-518. [PMID: 32112885 DOI: 10.1016/j.jinf.2020.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To assess, whether S. aureus nasal colonization is a risk factor for infections in patients with durable ventricular assist device (VAD). METHODS Prospective, single-centre, cohort study (i) ascertaining S. aureus nasal colonization status of patients admitted for VAD-implantation and detecting time to first episode of VAD-specific or -related infection according to International Society for Heart and Lung Transplantation criteria during follow-up and (ii) comparing whole genomes of S. aureus from baseline colonization and later infection. RESULTS Among 49 patients (17 colonized, 32 non-colonized), S. aureus VAD-infections occurred with long latency after implantation (inter quartile range 76-217 days), but occurred earlier (log-rank test P = 0.006) and were more common (9/17, 52.9% vs. 4/32, 12.5%, P = 0.005; incidence rates 2.81 vs. 0.61/1000 patient days; incidence rate ratio 4.65, 95% confidence interval 1.30-20.65, P = 0.009) among those nasally colonized with S. aureus before implantation. We found a similar but less pronounced effect of colonization status when analysing its effect on all types of VAD-infections (10/17, 58.8% vs. 7/32, 21.9%, P = 0.01). These findings remained robust when adjusting for potential confounders and restricting the analysis to 'proven infections'. 75% (6/8) of paired S. aureus samples from colonization and VAD-infection showed concordant whole genomes. CONCLUSIONS In patients with durable VAD, S. aureus nasal colonization is a source of endogenous infection, often occurring months after device-implantation and affecting mostly the driveline. Hygiene measures interrupting the endogenous route of transmission in VAD-patients colonized with S. aureus long-term may about half the burden of infections and require clinical scrutiny.
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Sörensen M, Kantorek J, Byrnes L, Boutin S, Mall MA, Lasitschka F, Zabeck H, Nguyen D, Dalpke AH. Pseudomonas aeruginosa Modulates the Antiviral Response of Bronchial Epithelial Cells. Front Immunol 2020; 11:96. [PMID: 32117250 PMCID: PMC7025480 DOI: 10.3389/fimmu.2020.00096] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/14/2020] [Indexed: 01/22/2023] Open
Abstract
Cystic fibrosis (CF) patients frequently acquire Pseudomonas aeruginosa infections that have been associated with a bad prognosis and an increased rate of pulmonary exacerbations. Respiratory viruses can cause exacerbations in chronic pulmonary diseases including COPD or asthma and have been suggested to contribute to exacerbations also in CF. In this study we investigated a possible link between P. aeruginosa infection and susceptibility to respiratory viruses. We show that P. aeruginosa is able to block the antiviral response of airway epithelial cells thereby promoting virus infection and spread. Mechanistically, P. aeruginosa secretes the protease AprA in a LasR dependent manner, which is able of directly degrading epithelial-derived IFNλ resulting in inhibition of IFN signaling. In addition, we correlate the virus infection status of CF patients with the ability of patients' P. aeruginosa isolates to degrade IFNλ. In line with this, the infection status of CF patients correlated significantly with the amount of respiratory viruses in sputum. Our data suggest that the interplay between P. aeruginosa and respiratory virus infections might partially explain the association of increased rates of pulmonary exacerbations and P. aeruginosa infections in CF patients.
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Kocer K, Boutin S, Dalpke AH, Heeg K, Mutters NT, Nurjadi D. Comparative genomic analysis reveals a high prevalence of inter-species in vivo transfer of carbapenem-resistance plasmids in patients with haematological malignancies. Clin Microbiol Infect 2019; 26:780.e1-780.e8. [PMID: 31654794 DOI: 10.1016/j.cmi.2019.10.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Conjugative gene transfer has been considered as one of the driving factors in the transmission and dissemination of multidrug resistance in bacteria. The abundance of antimicrobial resistance genes and bacteria in the gut microbiome may provide the ideal platform for plasmid exchange. Systematic data on in vivo horizontal gene transfer (HGT) and its frequency are scarce. MATERIALS AND METHODS One hundred and ninety-six carbapenem-resistant gram-negative bacilli (CRGNBs) from 179 patients (158 inpatients and 21 outpatients) between January 2016 and April 2017 were analysed retrospectively. Alignment of plasmid content for 32 isolates from 16 patients with multiple CRGNB species was performed from whole-genome sequencing (WGS) data. RESULTS Sixteen of the 179 patients (8.9%) were colonized and/or infected with more than one CRGNB species; 11/179 (6.1%) were colonized by multiple carbapenem-resistant Enterobacteriaceae (CREs) and 5/179 (2.8%) by carbapenem-resistant non-fermenters (CRNFs) and CREs. WGS suggested interspecies transfer as the predominant mechanism rather than independent acquisition in 8/10 patients (80%, one non-recoverable isolate) with multiple CREs but not in CRNF-CRE combinations; 30/158 inpatients (20%) had underlying haematological malignancies, and they are more likely to exhibit multiple CRGNB strains (OR 3.0, 95%CI 0.98-8.89, p 0.05) and CRE strains (OR 3.9, 95%CI 1.02-14.58, p 0.04) during hospital stay compared to other patient groups. CONCLUSION Our data give insight into the occurrence of natural in vivo HGT in a clinical setting. Better understanding of HGT will help optimize containment measures and may guide antibiotic stewardship programmes.
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DeMars C, Serrouya R, Mumma M, Gillingham M, McNay R, Boutin S. Moose, caribou, and fire: have we got it right yet? CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0319] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural disturbance plays a key role in shaping community dynamics. Within Canadian boreal forests, the dominant form of natural disturbance is fire, and its effects are thought to influence the dynamics between moose (Alces alces (Linnaeus, 1758)) and the boreal ecotype of woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)). Boreal caribou are considered “threatened” and population declines are attributed, at least in part, to disturbance-mediated apparent competition (DMAC) with moose. Here, we tested a primary prediction of the DMAC hypothesis: that moose respond positively to burns within and adjacent to the caribou range. We assessed moose selection for ≤25-year-old burns (when selection is predicted to be strongest) at multiple spatial scales and evaluated whether moose density was correlated with the extent of ≤40-year-old burns (a time frame predicted to negatively affect caribou). Against expectation, moose showed avoidance and low use of ≤25-year-old burns at all scales, regardless of burn age, season, and type of land cover burned. These findings mirrored the demographic response, as we found no correlation between ≤40-year-old burns and moose density. By contradicting the prevailing hypothesis linking fires to caribou population declines, our results highlight the need to understand regional variation in disturbance impacts on caribou populations.
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Eichel V, Papan C, Boutin S, Pöschl J, Heeg K, Nurjadi D. Alteration of antibiotic regimen as an additional control measure in suspected multi-drug-resistant Enterobacter cloacae outbreak in a neonatal intensive care unit. J Hosp Infect 2019; 104:144-149. [PMID: 31525448 DOI: 10.1016/j.jhin.2019.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Increased occurrence of a particular species of Gram-negative bacteria (GNB), especially when multi-drug-resistant (MDR), in routine screening surveillance in neonatal intensive care units (NICUs) can be evoked by selection pressure. AIM To evaluate adaptation of the empiric antibiotic regimen for its usefulness as a control measure in suspected outbreaks in the NICU. METHODS In a retrospective outbreak analysis, cases between 1st December 2017 and 31st March 2018 were identified through microbiology and hygiene surveillance records. Furthermore, risk factors for MDR-GNB colonization were collected. Whole-genome sequencing (WGS) was performed on all isolates. Control measure documentations and interviews were employed to define interventions. As well as infection control measures, administration of third-generation cephalosporins was avoided and replaced whenever clinically acceptable as part of the intervention bundle. FINDINGS In total, nine patients were found to have rectal colonization with third-generation cephalosporin-resistant Enterobacter cloacae in routine screening surveillance in the pre-intervention period. After implementation of an infection control bundle, the incidence declined rapidly. WGS analysis revealed that two MDR E. cloacae were transmitted, and the majority were new cases. The incidence density of MDR-GNB colonization was 7.94/1000 patient-days (PD) before the intervention and 1.68/1000 PD during the altered antibiotic regimen. No infections with MDR-GNB occurred during the study. CONCLUSIONS Altering the antibiotic regimen with regard to selection pressure may be considered as part of an intervention bundle to rapidly control the emergence of MDR-GNB in suspected outbreak situations in the NICU.
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Wolff D, Frese C, Schoilew K, Dalpke A, Wolff B, Boutin S. Amplicon-based microbiome study highlights the loss of diversity and the establishment of a set of species in patients with dentin caries. PLoS One 2019; 14:e0219714. [PMID: 31365560 PMCID: PMC6668773 DOI: 10.1371/journal.pone.0219714] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives To elicit patterns in pathogenic biofilm composition we characterized the oral microbiome present in patients with dentin caries in comparison to healthy subjects. Methods 16S amplicon sequencing was used to analyse a total of 56 patients; 19 samples of carious dentin (pooled from at least three teeth) and 37 supragingival samples (pooled from three healthy tooth surfaces). Oral and periodontal status and socio-demographic parameters were recorded. Group assignment, smoking and further socio-demographic parameters were used as explanatory variables in the microbiome composition analysis. Results Overall, a total of 4,110,020 DNA high-quality sequences were yielded. Using a threshold of similarity >97% for assigning operational taxonomic units (OTU), a total of 1,537 OTUs were identified. PERMANOVA showed significant differences in microbiome composition between the groups caries/healthy (p = 0.001), smoking/non-smoking (p = 0.007) and fluoride intake during childhood yes/no (tablets p = 0.003, salt p = 0.023). The healthy microbiome had a significantly higher diversity (alpha diversity, p<0.001) and a lower dominance (Berger-Parker index, p<0.001). It was dominated by Fusobacteria. A linear discriminant analysis effect size (LEfSe) yielded a set of 39 OTUs being more abundant in carious dentin samples, including Atopobium spp. (14.9 log2FoldChange), Lactobacillus casei (11.6), Acinetobacter spp. (10.8), Lactobacillus gasseri (10.6), Parascardovia denticolens (10.5), Olsenella profusa (10.4), and others. Also Propionibacterium acidifaciens (7.2) and Streptococcus mutans (5.2) were overabundant in caries lesions. Conclusions The healthy microbiome was highly diverse. The advanced caries microbiome was dominated by a set of carious associated bacteria where S. mutans played only a minor role. Smoking and fluoride intake during childhood influenced the microbiome composition significantly. Clinical significance The presented investigation adds knowledge to the still not fully comprehended patterns of oral microbiomes in caries compared with oral health. By analysing the genetics of biofilm samples from oral health and severe tooth decay we found distinct discriminating species which could be targets for future therapeutic approaches.
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Freund I, Buhl DK, Boutin S, Kotter A, Pichot F, Marchand V, Vierbuchen T, Heine H, Motorin Y, Helm M, Dalpke AH, Eigenbrod T. 2'- O-methylation within prokaryotic and eukaryotic tRNA inhibits innate immune activation by endosomal Toll-like receptors but does not affect recognition of whole organisms. RNA (NEW YORK, N.Y.) 2019; 25:869-880. [PMID: 31019095 PMCID: PMC6573781 DOI: 10.1261/rna.070243.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 05/10/2023]
Abstract
Bacterial RNA has emerged as an important activator of innate immune responses by stimulating Toll-like receptors TLR7 and TLR8 in humans. Guanosine 2'-O-methylation at position 18 (Gm18) in bacterial tRNA was shown to antagonize tRNA-induced TLR7/8 activation, suggesting a potential role of Gm18 as an immune escape mechanism. This modification also occurs in eukaryotic tRNA, yet a physiological immune function remained to be tested. We therefore set out to investigate the immune modulatory role of Gm18 in both prokaryotic and eukaryotic microorganisms, Escherichia coli and Saccharomyces cerevisiae, and in human cells. Using RiboMethSeq analysis we show that mutation of trmH in E. coli, trm3 in S. cereviase, and CRISPR/Cas9-induced knockout of TARBP1 in H. sapiens results in loss of Gm18 within tRNA. Lack of Gm18 across the kingdoms resulted in increased immunostimulation of peripheral blood mononuclear cells when activated by tRNA preparations. In E. coli, lack of 2'-O-methyltransferase trmH also enhanced immune stimulatory properties by whole cellular RNA. In contrast, lack of Gm18 in yeasts and human cells did not affect immunostimulation by whole RNA preparations. When using live E. coli bacteria, lack of trmH did not affect overall immune stimulation although we detected a defined TLR8/RNA-dependent gene expression signature upon E. coli infection. Together, these results demonstrate that Gm18 is a global immune inhibitory tRNA modification across the kingdoms and contributes to tRNA recognition by innate immune cells, but as an individual modification has insufficient potency to modulate recognition of the investigated microorganisms.
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Schoilew K, Ueffing H, Dalpke A, Wolff B, Frese C, Wolff D, Boutin S. Bacterial biofilm composition in healthy subjects with and without caries experience. J Oral Microbiol 2019; 11:1633194. [PMID: 31275531 PMCID: PMC6598481 DOI: 10.1080/20002297.2019.1633194] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 01/03/2023] Open
Abstract
Objective:The composition of the oral microbiome differs distinctively between subjects with and without active caries. Still, caries research has mainly been focused on states of disease; aspects about how biofilm composition and structure maintain oral health still remain widely unclear. Therefore, the aim of the study was to compare the healthy oral microbiome of caries-free adult subjects with and without former caries experience using next generation sequencing methods. Methods: 46 samples were collected from subjects without any signs of untreated active caries. Samples of pooled supragingival plaque from 19 subjects without caries experience (NH; DMFT = 0) and 27 subjects with 'caries experience' ( CE; DMFT > 0 [F(T)> 0; D(T)= 0]) were analyzed by 16S ribosomal RNA amplicon sequencing. Results: Subjects with caries experience did not exhibit a dramatically modified supragingival plaque microbiome. However, we observed a slight and significant modification between the two groups, validated by PERMANOVA ( NH vs. CE: R2 0.04; p= 0.039). The composition of the microbiome of subjects with caries experience indicates a tendency to lower α-diversity and richness. Subjects without caries experience showed a significant higher evenness compared to patients with previous caries. LDA effect size (LEfSe) analysis demonstrated that the genus Haemophilus is significantly more frequent in patients with caries experience. For the group without caries experience LefSe analysis showed a set of 11 genera being significantly more frequent, including Corynebacterium, Fusobacterium, Capnocytophaga, Porphyromonas, Prevotella,and Leptotrichia. Conclusion: The analysis of the oral microbiome of subjects with and without caries experience indicates specific differences. With the presence of Corynebacterium and Fusobacterium subjects without caries experience exhibited more frequently organisms that are considered to be main actors in structural plaque formation and integration. The abundance of Corynebacterium might be interpreted as a signature for dental health.
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Gross DA, Leborgne C, Chappert P, Masurier C, Leboeuf M, Monteilhet V, Boutin S, Lemonnier FA, Davoust J, Kichler A. Induction of tumor-specific CTL responses using the C-terminal fragment of Viral protein R as cell penetrating peptide. Sci Rep 2019; 9:3937. [PMID: 30850685 PMCID: PMC6408526 DOI: 10.1038/s41598-019-40594-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/14/2018] [Indexed: 12/30/2022] Open
Abstract
The discovery of tumor-associated antigens recognized by T lymphocytes opens the possibility of vaccinating cancer patients with defined antigens. However, one of the major limitation of peptide-based vaccines is the low immunogenicity of antigenic peptides. Interestingly, if these epitopes are directly delivered into the cytoplasm of antigen presenting cells, they can be efficiently presented via the direct MHC class I presentation pathway. To improve antigen entry, one promising approach is the use of cell penetrating peptides (CPPs). However, most studies use a covalent binding of the CPP with the antigen. In the present study, we focused on the C-terminal domain of Vpr which was previously demonstrated to efficiently deliver plasmid DNA into cells. We provide evidence that the peptides Vpr55-91 and Vpr55-82 possess the capacity of delivering proteins and epitopes into cell lines as well as into human primary dendritic cells, without the necessicity for a chemical linkage. Moreover, immunization of HLA-A2 transgenic mice with Vpr55-91 as the sole adjuvant is able to induce antigen-specific cytotoxic T lymphocytes against multiple tumor epitopes.
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Schmitt FCF, Brenner T, Uhle F, Loesch S, Hackert T, Ulrich A, Hofer S, Dalpke AH, Weigand MA, Boutin S. Gut microbiome patterns correlate with higher postoperative complication rates after pancreatic surgery. BMC Microbiol 2019; 19:42. [PMID: 30777006 PMCID: PMC6379976 DOI: 10.1186/s12866-019-1399-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/23/2019] [Indexed: 12/12/2022] Open
Abstract
Background Postoperative complications are of great relevance in daily clinical practice, and the gut microbiome might play an important role by preventing pathogens from crossing the intestinal barrier. The two aims of this prospective clinical pilot study were: (1) to examine changes in the gut microbiome following pancreatic surgery, and (2) to correlate these changes with the postoperative course of the patient. Results In total, 116 stool samples of 32 patients undergoing pancreatic surgery were analysed by 16S-rRNA gene next-generation sequencing. One sample per patient was collected preoperatively in order to determine the baseline gut microbiome without exposure to surgical stress and/or antibiotic use. At least two further samples were obtained within the first 10 days following the surgical procedure to observe longitudinal changes in the gut microbiome. Whenever complications occurred, further samples were examined. Based on the structure of the gut microbiome, the samples could be allocated into three different microbial communities (A, B and C). Community B showed an increase in Akkermansia, Enterobacteriaceae and Bacteroidales as well as a decrease in Lachnospiraceae, Prevotella and Bacteroides. Patients showing a microbial composition resembling community B at least once during the observation period were found to have a significantly higher risk for developing postoperative complications (B vs. A, odds ratio = 4.96, p < 0.01**; B vs. C, odds ratio = 2.89, p = 0.019*). Conclusions The structure of the gut microbiome is associated with the development of postoperative complications. Electronic supplementary material The online version of this article (10.1186/s12866-019-1399-5) contains supplementary material, which is available to authorized users.
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Héry-Arnaud G, Boutin S, Cuthbertson L, Elborn SJ, Tunney MM. The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis? J Cyst Fibros 2018; 18:13-21. [PMID: 30487080 DOI: 10.1016/j.jcf.2018.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
The 15th European Cystic Fibrosis Society (ECFS) Basic Science pre-conference Symposium focused on the topic of the microbiome, asking the question "The lung and gut microbiome: what has to be considered for cystic fibrosis (CF)?" This review gives an overview of the main points raised during the symposium, which dealt with the technical considerations, pathophysiology and clinical implications of the microbiome in CF.
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Braun MS, Wang E, Zimmermann S, Boutin S, Wagner H, Wink M. Kocuria tytonicola, new bacteria from the preen glands of American barn owls (Tyto furcata). Syst Appl Microbiol 2018; 42:198-204. [PMID: 30514593 DOI: 10.1016/j.syapm.2018.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 10/25/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926T. In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species. The same conclusion was drawn from MALDI-TOF MS analyses. Once again, the new bacterial strains were very similar to one another, but exhibited substantial differences when compared to the most closely related species. Besides, the results of the biochemical tests, optimum growth conditions and pigmentation differed from closely related Kocuria spp. Finally, ANIb values of less than 87% provided striking evidence that the isolates recovered from American barn owls represent a hitherto undescribed species, for which we propose the name Kocuria tytonicola sp. nov. The type strain is 489T (DSM 104133T=LMG 29945T, taxonumber TA00340).
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Nurjadi D, Fleck R, Lindner A, Schäfer J, Gertler M, Mueller A, Lagler H, Van Genderen PJJ, Caumes E, Boutin S, Kuenzli E, Gascon J, Kantele A, Grobusch MP, Heeg K, Zanger P. Import of community-associated, methicillin-resistant Staphylococcus aureus to Europe through skin and soft-tissue infection in intercontinental travellers, 2011-2016. Clin Microbiol Infect 2018; 25:739-746. [PMID: 30315958 DOI: 10.1016/j.cmi.2018.09.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/21/2018] [Accepted: 09/30/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Recently, following import by travel and migration, epidemic community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has caused nosocomial outbreaks in Europe, sometimes with a fatal outcome. We describe clinico-epidemiological characteristics of CA-MRSA detected by the European Network for the Surveillance of imported S. aureus (www.staphtrav.eu) from May 2011 to November 2016. METHODS Sentinel surveillance at 13 travel clinics enrolling patients with travel-associated skin and soft-tissue infection (SSTI) and analysing lesion and nose swabs at one central laboratory. RESULTS A total of 564 independent case-patients with SSTI were enrolled and had 374 (67%) S. aureus-positive lesions, of which 14% (51/374) were MRSA. The majority of CA-MRSA isolates from SSTI were Panton-Valentine leucocidin (PVL) -positive (43/51, 84%). The risk of methicillin-resistance in imported S. aureus varied by travel region (p <0.001) and was highest in Latin America (16/57, 28%, 95% CI 17.0-41.5) and lowest in Sub-Saharan Africa (4/121, 3%, 95% CI 0.9-8.3). Major epidemic clones (USA300 / USA300 Latin-American Variant, Bengal Bay, South Pacific) accounted for more than one-third (19/51, 37%) of CA-MRSA imports. CA-MRSA SSTI in returnees was complicated (31/51 multiple lesions, 61%; 22/50 recurrences, 44%), led to health-care contact (22/51 surgical drainage, 43%; 7/50 hospitalization, 14%), was transmissible (13/47 reported similar SSTI in non-travelling contacts, 28%), and associated with S. aureus nasal colonization (28 of 51 CA-MRSA cases, 55%; 24 of 28 colonized with identical spa-type in nose and lesion, 85%). CONCLUSIONS Travel-associated CA-MRSA SSTI is a transmissible condition that leads to medical consultations and colonization of the infected host.
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Boutin S, Weitnauer M, Hassel S, Graeber SY, Stahl M, Dittrich AS, Mall MA, Dalpke AH. One time quantitative PCR detection of Pseudomonas aeruginosa to discriminate intermittent from chronic infection in cystic fibrosis. J Cyst Fibros 2018; 17:348-355. [PMID: 29336943 DOI: 10.1016/j.jcf.2017.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Chronic airway infection with Pseudomonas aeruginosa is a major risk factor of progression of lung disease in patients with cystic fibrosis (CF). Chronic P. aeruginosa infection evolves from intermittent infection that is amenable to antibiotic eradication, whereas chronically adapted P. aeruginosa becomes resistant to antibiotic therapy. Discrimination of intermittent versus chronic infection is therefore of high therapeutic relevance, yet the available diagnostic methods are only partly satisfactory. The aim of the present study was, therefore, to evaluate the usage of quantitative PCR (qPCR) to measure pathogen abundance and to discriminate between intermittent and chronic Pseudomonas infection in patients with CF. METHOD Using an established qPCR protocol, we analyzed the abundance of P. aeruginosa in 141 throats swabs and 238 sputa from CF patients with intermittent or chronic infection with P. aeruginosa, as determined by standard culture based diagnostics. RESULTS We observed a large increase of abundance of P. aeruginosa in throat swabs and sputum samples from patients with chronic compared to intermittent infections with P. aeruginosa. The data show that abundance of P. aeruginosa as measured by qPCR is a valuable tool to discriminate intermittent from chronic infection. Of note, P. aeruginosa burden seems more sensitive than mucoidity phenotype to discriminate chronic from intermittent strains. Furthermore we observed that molecular detection in throat swabs was linked to a viable culture in the sputum when sputum was available. This result is of special interest in young patients with cystic fibrosis that often cannot expectorate sputum. We also observed that qPCR in comparison to culture detected the infection earlier. CONCLUSION The results suggest that qPCR detection and quantification of P. aeruginosa is a precious tool to be added to the diagnostic toolbox in cystic fibrosis.
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Braun MS, Wang E, Zimmermann S, Boutin S, Wink M. Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov., isolated from the preen glands of Great Spotted Woodpeckers (Dendrocopos major). Syst Appl Microbiol 2017; 41:38-43. [PMID: 29169691 DOI: 10.1016/j.syapm.2017.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/22/2017] [Accepted: 09/01/2017] [Indexed: 11/18/2022]
Abstract
Two new species of Gram-positive cocci were isolated from the uropygial glands of wild woodpeckers (Dendrocopos major) originating from different locations in Germany. A polyphasic approach confirmed the affiliation of the isolates to the genus Kocuria. Phylogenetic analysis based on the 16S rRNA gene showed high degree of similarity to Kocuria koreensis DSM 23367T (99.0% for both isolates). However, low ANIb values of <80% unequivocally separated the new species from K. koreensis. This finding was further corroborated by DNA fingerprinting and analysis of polar lipid profiles. Furthermore, growth characteristics, biochemical tests, MALDI-TOF MS analysis, and G+C contents clearly differentiated the isolates from their known relatives. Besides, the woodpecker isolates significantly differed from each other in their whole-cell protein profiles, DNA fingerprints, and ANIb values. In conclusion, the isolated microorganisms constitute members of two new species, for which the names Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov. are proposed. The type strains are 36T (DSM 101740T=LMG 29265T) and 257T (=DSM 101741T=LMG 29266T) for K. uropygialis sp. nov. and K. uropygioeca sp. nov., respectively.
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Boutin S, Graeber SY, Stahl M, Dittrich AS, Mall MA, Dalpke AH. Chronic but not intermittent infection with Pseudomonas aeruginosa is associated with global changes of the lung microbiome in cystic fibrosis. Eur Respir J 2017; 50:50/4/1701086. [PMID: 28982777 DOI: 10.1183/13993003.01086-2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/04/2017] [Indexed: 11/05/2022]
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Chan K, Boutin S, Hossie TJ, Krebs CJ, O'Donoghue M, Murray DL. Improving the assessment of predator functional responses by considering alternate prey and predator interactions. Ecology 2017; 98:1787-1796. [PMID: 28369822 DOI: 10.1002/ecy.1828] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/22/2017] [Accepted: 03/03/2017] [Indexed: 11/11/2022]
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