Search

OBJECTIVES Hospital-acquired pneumonia in non-ventilated patients (nvHAP) belongs to the most common healthcare-associated infections. This study aimed to investigate risk factors for nvHAP in patients outside the intensive care unit, focusing on modifiable risk factors. METHODS All inpatients admitted to an academic teaching hospital in Switzerland between 2017 and 2018 were included. NvHAP was defined according to European Centre for Disease Prevention and Control criteria. Patient days during and after ICU stay were excluded. Candidate risk factors - both constant and time-varying - were included in uni- and multivariable Cox proportional hazards models. The decay ratio and the characteristic time of influence of HRs was estimated by adopting a linear decay in the Cox model. RESULTS A total of 66,001 hospitalizations with 314 (0.48%) nvHAP and 471,401 patient days were included. Median age was 57 years (interquartile range: 38-71 years) and 32,253 (48.9%) patients were male. Among non-modifiable risk factors, age (adjusted-HR 2.66 for age ≥60 years, 95%CI 1.59-4.45) and male sex (aHR 1.71, 95%CI 1.34-2.18) were independently associated with nvHAP. Time-varying exposures showing strongest independent association with nvHAP were tube feeding (aHR 3.24, 95%CI 2.17-4.83), impaired consciousness (aHR 2.32, 95%CI 1.63-3.31), and severely impaired activity and mobility (aHR 2.06, 95%CI 1.50-2.84). The association with nvHAP decayed within 7.1 - 13.2 days after these exposures ended. CONCLUSIONS The risk for nvHAP varies with time, depending on the patient's medical condition and medical interventions. Several risk factors for nvHAP represent potential targets for specific prevention measures.

Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs—so far thought to transfer effectors only into eukaryotic cells—to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture.

Objectives This study aimed to investigate the faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in Switzerland and to genetically characterize the isolates. Methods A total of 399 stool samples from healthy individuals employed in different food-processing plants were cultured on a selective medium containing 10 mg/L florfenicol. Resulting enterococci were screened by PCR for the presence of cfr, optrA and poxtA. A hybrid approach combining short-read and long-read WGS was used to analyse the genetic context of the cfr, optrA and poxtA genes. Results Enterococcus faecalis (n = 6), Enterococcus faecium (n = 6), Enterococcus gallinarum (n = 1) and Enterococcus hirae (n = 2) were detected in 15/399 (3.8%) of the faecal samples. They carried cfr + poxtA, optrA, optrA + poxtA or poxtA. Four E. faecalis harbouring optrA and one E. faecium carrying poxtA were resistant to linezolid (8 mg/L). In most optrA-positive isolates, the genetic environments of optrA were highly variable, but often resembled previously described platforms. In most poxtA-positive isolates, the poxtA gene was flanked on both sides by IS1216E elements and located on medium-sized plasmids. Conclusions Faecal carriage of Enterococcus spp. harbouring cfr, optrA and poxtA in healthy humans associated with the food-production industry demonstrates the possibility of spread of oxazolidinone resistance genes into the community. Given the importance of linezolid as a last-resort antibiotic for the treatment of serious infections caused by Gram-positive pathogens, the detection of the oxazolidinone resistance determinants in enterococci from healthy humans is of concern for public health.

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK., Nature Microbiology, 7 (8), ISSN:2058-5276

A previous study showed that investigation of children with invasive pneumococcal disease (IPD) revealed an immunodeficiency in up to 10% of cases. Following this report, we implemented a protocol to investigate children with IPD, to assess the proportion with an immunodeficiency in our setting.We retrospectively identified patients who presented with IPD from January 2015 to November 2020 and collected data from medical records. Immunological investigations included complement C3 and C4 levels, classical and alternative pathway complement function, IgG, IgA and IgM levels, specific IgG levels (H. influenza B, tetanus and pneumococcal serotypes), peripheral blood film, lymphocyte subsets, and CD62L-shedding upon activation with Toll-like receptor-agonists in selected cases.We identified a total of 68 children with IPD, with a mortality of 6%. Immunological investigations were performed in 51 children. Four children (8%) had abnormal findings that were deemed of clinical significance. Two children had complement deficiencies (Factor I and C2 deficiency), one child had specific antibody deficiency, and another child had low IgM, low NK-cells and poor persistence of serotype-specific anti-pneumococcal IgG concentrations. Of the 17 children with IPD who were not tested for immunodeficiencies, 4 died and four had possible explanations for the infection.We identified clinically relevant abnormal immunological findings in 4/51 (8%) of children with IPD. Our results support the recommendation to perform immunological investigations in children with IPD, since this might reveal underlying immunodeficiencies, allowing for necessary preventive measures and close follow-up.

IntroductionTuberculosis (TB) is an infectious disease caused by the group of bacterial pathogens Mycobacterium tuberculosis complex (MTBC) and is one of the leading causes of death worldwide. Timely diagnosis and treatment of drug-resistant TB is a key pillar of WHO’s strategy to combat global TB. The time required to carry out drug susceptibility testing (DST) for MTBC via the classic culture method is in the range of weeks and such delays have a detrimental effect on treatment outcomes. Given that molecular testing is in the range of hours to 1 or 2 days its value in treating drug resistant TB cannot be overstated. When developing such tests, one wants to optimize each step so that tests are successful even when confronted with samples that have a low MTBC load or contain large amounts of host DNA. This could improve the performance of the popular rapid molecular tests, especially for samples with mycobacterial loads close to the limits of detection. Where optimizations could have a more significant impact is for tests based on targeted next generation sequencing (tNGS) which typically require higher quantities of DNA. This would be significant as tNGS can provide more comprehensive drug resistance profiles than the relatively limited resistance information provided by rapid tests. In this work we endeavor to optimize pre-treatment and extraction steps for molecular testing.MethodsWe begin by choosing the best DNA extraction device by comparing the amount of DNA extracted by five commonly used devices from identical samples. Following this, the effect that decontamination and human DNA depletion have on extraction efficiency is explored.ResultsThe best results were achieved (i.e., the lowest Ct values) when neither decontamination nor human DNA depletion were used. As expected, in all tested scenarios the addition of decontamination to our workflow substantially reduced the yield of DNA extracted. This illustrates that the standard TB laboratory practice of applying decontamination, although being vital for culture-based testing, can negatively impact the performance of molecular testing. As a complement to the above experiments, we also considered the best Mycobacterium tuberculosis DNA storage method to optimize molecular testing carried out in the near- to medium-term. Comparing Ct values following three-month storage at 4 °C and at −20 °C and showed little difference between the two.DiscussionIn summary, for molecular diagnostics aimed at mycobacteria this work highlights the importance of choosing the right DNA extraction device, indicates that decontamination causes significant loss of mycobacterial DNA, and shows that samples preserved for further molecular testing can be stored at 4 °C, just as well at −20 °C. Under our experimental settings, human DNA depletion gave no significant improvement in Ct values for the detection of MTBC.

Bacteria communicate with each other through a plethora of small, diffusible organic molecules called autoinducers. This cell-density-dependent regulatory principle is termed quorum sensing, and in many cases the process indeed coordinates group behavior of bacterial populations. Yet, even clonal bacterial populations are not uniform entities; rather, they adopt phenotypic heterogeneity to cope with consecutive, rapid, and frequent environmental fluctuations (bet-hedging) or to concurrently interact with each other by exerting different, often complementary, functions (division of labor). Quorum sensing is mainly regarded as a coordinator of bacterial collective behavior. However, it can also be a driver or a target of individual phenotypic heterogeneity. Hence, quorum sensing increases the overall fitness of a bacterial community by orchestrating group behavior as well as individual traits.

Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. Results We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. Conclusion We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom.

Bacteria communicate and coordinate their behaviour at the intra- and interspecies levels by producing and sensing diverse extracellular small molecules called autoinducers. Autoinducer 2 (AI-2) is produced and detected by a variety of bacteria and thus plays an important role in interspecies communication and chemotaxis. Although AI-2 is a major autoinducer molecule present in the mammalian gut and can influence the composition of the murine gut microbiota, its role in bacteria-bacteria and bacteria-host interactions during gut colonization remains unclear. Combining competitive infections in C57BL/6 mice with microscopy and bioinformatic approaches, we show that chemotaxis (cheY) and AI-2 signalling (via lsrB) promote gut colonization by Escherichia coli, which is in turn connected to the ability of the bacteria to utilize fructoselysine (frl operon). We further show that the genomic diversity of E. coli strains with respect to AI-2 signalling allows ecological niche segregation and stable co-existence of different E. coli strains in the mammalian gut., Nature Microbiology, 8 (2), ISSN:2058-5276

Alveolar (AE) and cystic echinococcosis (CE) are severe parasitic zoonoses caused by the larval stages of Echinococcus multilocularis and E. granulosus sensu lato, respectively. A panel of 7 monoclonal antibodies (mAbs) was selected against major diagnostic epitopes of both species. The binding capacity of the mAbs to Echinococcus spp. excretory/secretory products (ESP) was analyzed by sandwich-ELISA, where mAb Em2G11 and mAb EmG3 detected in vitro extravesicular ESP of both E. multilocularis and E. granulosus s.s. These findings were subsequently confirmed by the detection of circulating ESP in a subset of serum samples from infected hosts including humans. Extracellular vesicles (EVs) were purified, and the binding to mAbs was analyzed by sandwich-ELISA. Transmission electron microscopy (TEM) was used to confirm the binding of mAb EmG3 to EVs from intravesicular fluid of Echinococcus spp. vesicles. The specificity of the mAbs in ELISA corresponded to the immunohistochemical staining (IHC-S) patterns performed on human AE and CE liver sections. Antigenic small particles designated as ‘‘spems’’ for E. multilocularis and ‘‘spegs’’ for E. granulosus s.l. were stained by the mAb EmG3IgM, mAb EmG3IgG1, mAb AgB, and mAb 2B2, while mAb Em2G11 reacted with spems and mAb Eg2 with spegs only. The laminated layer (LL) of both species was strongly visualized by using mAb EmG3IgM, mAb EmG3IgG1, mAb AgB, and mAb 2B2. The LL was specifically stained by mAb Em2G11 in E. multilocularis and by mAb Eg2 in E. granulosus s.l. In the germinal layer (GL), including the protoscoleces, a wide staining pattern with all structures of both species was observed with mAb EmG3IgG1, mAb EmG3IgM, mAb AgB, mAb 2B2, and mAb Em18. In the GL and protoscoleces, the mAb Eg2 displayed a strong E. granulosus s.l. specific binding, while mAb Em2G11 exhibited a weak granular E. multilocularis specific reaction. The most notable staining pattern in IHC-S was found with mAb Em18, which solely bound to the GL and protoscoleces of Echinococcus species and potentially to primary cells. To conclude, mAbs represent valuable tools for the visualization of major antigens in the most important Echinococcus species, as well as providing insights into parasite-host interactions and pathogenesis.

BACKGROUND Anaesthesia induction is a fast-paced, complex activity that involves a high density of hand-to-surface exposures. Hand hygiene (HH) adherence has been reported to be low, which bears the potential for unnoticed pathogen transmission between consecutive patients. Therefore, we aimed to study the fit of the WHO's five moments of HH concept to the anaesthesia induction workflow. METHODS We analysed video recordings of 59 anaesthesia inductions according to the WHO HH observation method considering each hand-to-surface exposure of every involved anaesthesia provider. Binary logistic regression was used to determine risk factors for non-adherence, i.e., professional category, gender, task role, gloves, holding of objects, team size and HH moment. Additionally, we re-coded half of the videos for self-touching behaviour for quantitative and qualitative analysis. RESULTS Overall, 2240 HH opportunities were met by 105 HH actions (4.7%). The drug administrator role (OR=2.2), the senior physician status (OR=2.1), donning (OR=2.6) and doffing (OR=3.6) of gloves were associated with higher HH adherence. Notably, 47.2% of all HH opportunities were caused by self-touching behaviour. Provider clothes, face, and patient skin were the most frequently touched surfaces. CONCLUSIONS The high density of hand-to-surface exposures, a high cognitive load, prolonged glove use, carried mobile objects, self-touching, and personal behaviour patterns were potential causes for non-adherence. A purpose-designed HH concept based on these results, involving the introduction of designated objects and provider clothes to the patient zone, could mitigate HH adherence and microbiologic safety.

Purpose The risk of secondary zoonotic transmission of SARS-CoV-2 from pet animals remains unclear. Here, we report on a 44 year old Caucasian male presenting to our clinic with COVID-19 pneumonia, who reported that his dog displayed respiratory signs shortly prior to his infection. The dog tested real-time-PCR (RT-PCR) positive for SARS-CoV-2 RNA and the timeline of events suggested a transmission from the dog to the patient. Methods RT-PCR and serological assays were used to confirm SARS-CoV-2 infection in the nasopharyngeal tract in the dog and the patient. We performed SARS-CoV-2-targeted amplicon-based next generation sequencing of respiratory samples from the dog and patient for sequence comparisons. Results SARS-CoV-2 infection of the dog was confirmed by three independent PCR-positive pharyngeal swabs and subsequent seroconversion. Sequence analysis identified two separate SARS-CoV-2 lineages in the canine and the patient’s respiratory samples. The timeline strongly suggested dog-to-human transmission, yet due to the genetic distance of the canine and the patient’s samples paired-transmission was highly unlikely. Conclusion The results of this case support current knowledge about the low risk of secondary zoonotic dog-to-human transmissions of SARS-CoV-2 and emphasizes the strength of genomic sequencing in deciphering viral transmission chains.

Since its discovery six decades ago, the predatory bacterium Bdellovibrio bacteriovorus has sparked recent interest as a potential remedy to the antibiotic resistance crisis. Here we give a comprehensive historical overview from discovery to progressive developments in microscopy and molecular mechanisms. Research on B. bacteriovorus has moved from curiosity to a new model organism, revealing over time more details on its physiology and fascinating predatory life cycle with the help of a variety of methods. Based on recent findings in cryo-electron tomography, we recapitulate on the intricate molecular details known in the predatory life cycle including how this predator searches for its prey bacterium, to how it attaches, grows, and divides all from within the prey cell. Finally, the newly developed B. bacteriovorus progeny leave the prey cell remnants in the exit phase. While we end with some unanswered questions remaining in the field, new imaging technologies and quantitative, systematic advances will likely help to unravel them in the next decades.

Objectives The global dissemination of vancomycin-resistant enterococci (VRE) has become a serious public-health concern. Although outbreaks are typically caused by nosocomial transmission, contaminated food and water may contribute to the spread of VRE. The aim of this study was to assess the presence of VRE in flowing surface water bodies in Switzerland and to characterise the isolates. Methods Surface water was sampled from rivers, streams and canals throughout Switzerland and was screened for the presence of VRE. Whole-genome sequencing was used to identify antimicrobial resistance genes and the phylogenetic similarity of the obtained isolates. Results VRE were detected in 6 (3.1%) of 191 water samples. The six VRE-containing samples were all collected near treated wastewater discharge sites. The six isolates were identified as Enterococcus faecium sequence type 133 (ST133) and harboured the vancomycin resistance-conferring vanA gene cluster on transposon Tn1546. They showed a close phylogenetic relationship to ST133 swine faecal isolates obtained during a previously reported screening in Switzerland. Conclusion Our results suggest that surface water contributes to the environmental dissemination of VRE. Repeated identification of ST133 clones in geographically distinct water sampling sites and swine faecal samples collected in slaughterhouses may indicate a local dominance of this VRE lineage in Switzerland.

Pandemics are caused by novel pathogens to which pre-existing antibody immunity is lacking. Under these circumstances, the body must rely on innate interferon-mediated defenses to limit pathogen replication and allow development of critical humoral protection. Here, we highlight studies on disease susceptibility during H1N1 influenza and COVID-19 (SARS-CoV-2) pandemics. An emerging concept is that genetic and non-genetic deficiencies in interferon system components lead to uncontrolled virus replication and severe illness in a subset of people. Intriguingly, new findings suggest that individuals with autoantibodies neutralizing the antiviral function of interferon are at increased risk of severe COVID-19. We discuss key questions surrounding how such autoantibodies develop and function, as well as the general implications of diagnosing interferon deficiencies for personalized therapies.

Background With the increasing dimensions of the international cardiac surgery-associated Mycobacterium chimaera outbreak the hypothesis of a point source arose. Objectives To review the published evidence of clonality among cardiac surgery-associated M. chimaera isolates evaluated by whole-genome sequencing (WGS) and to perform an integrative genomic analysis of available genome data. Data sources We searched PubMed and EMBASE for studies applying WGS on cardiac surgery-associated M. chimaera isolates. Study eligibility criteria We included studies that applied WGS on more than a single M. chimaera isolate. Methods Two authors independently extracted data from included studies. Available genome data from published studies were subjected to a joint analysis. Results Of 121 identified articles, nine studies were included. M. chimaera isolates from LivaNova heater–cooler devices (HCDs) had a high level of genetic similarity, but were genetically distant from isolates from HCDs produced by other manufacturers. With the exception of a single (11.1%) study, the remaining eight (89.9%) studies reported a high level of genetic proximity between the majority of M. chimaera isolates derived from cardiac surgery-associated patients and LivaNova HCDs. In-depth analysis revealed involvement of three distinct M. chimaera subgroups in the outbreak (1.1, 1.8, 2.1), with 1.1 suggested as causative of the outbreak. Samples taken at the LivaNova production site supported contamination with strains of subgroups 1.1 and 1.8. In the combined analysis of 526 publicly available WGS data sets, nearly all isolates from cardiac surgery-associated patients contained strain 1.1 (50/52, 96.2%), and at least one of the outbreak strains was found in almost all LivaNova HCDs (241/257, 93.8%), with strain 1.1 in particular present in 198/257 (77.0%). Conclusions HCD contamination during production seems plausible as the predominant point source for the global M. chimaera outbreak. Although HCDs can be contaminated with mixed populations, M. chimaera strains of the subgroup 1.1 caused most infections.

Introduction Antimicrobial resistance (AMR) is an emerging global threat. It increases mortality and morbidity and strains healthcare systems. Health care professionals can counter the rising AMR by promoting antibiotic stewardship and facilitating new drug development. Even with the economic and scientific challenges, it is reassuring that new agents continue to be developed. Methods This review addresses new antibiotics in the pipeline. We conducted a review of the literature including Medline, Clinicaltrials.org, and relevant pharmaceutical companies for approved and in pipeline antibiotics in phase 3 or new drug application (NDA). Results We found a number of new antibiotics and reviewed their current development status, mode of action, spectra of activity, and indications for which they have been approved. The included studies from phase 3 clinical trials were mainly utilized for the treatment of acute bacterial skin and skin structure infections, community-acquired bacterial pneumonia, and pneumonia acquired in the healthcare settings. The number of these agents is limited against high priority organisms. The identified antibiotics were based mainly on previously known molecules or pre-existing antimicrobial agents. Conclusion There are a limited number of antibiotics against high priority organisms such as multi-drug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Enterobacteriaceae. New antimicrobial agents directed against the top priority organisms as classified by the World Health Organization are urgently needed.

The most prevalent infections encountered in neonatal care are healthcare-associated infections (HAIs). The majority of HAIs are considered preventable by evidence-based infection prevention and control (IPC) practices, but substantial knowledge gaps exist in IPC implementation in neonatal care. Furthermore, knowledge of factors that facilitate or challenge IPC programme uptake and sustainment in neonatal units is limited. The integration of implementation science approaches within IPC programmes in neonatal care aims to address these problems.The aim of this narrative review was to identify determinants that have been reported to influence the implementation of IPC programmes and best practices in inpatient neonatal care settings.A literature search was conducted in PubMed, MEDLINE and CINAHL in May 2022. Primary study reports published since 2000 in English, French, German, Spanish, Portuguese, Italian, Danish, Swedish, or Norwegian were eligible for inclusion. Included studies focused on IPC practices in inpatient neonatal care settings and reported determinants that influenced implementation processes.The Consolidated Framework for Implementation Research was used to identify and cluster reported determinants to the implementation of IPC practices and programmes in neonatal care. Most studies reported challenges and facilitators at the organisational level as particularly relevant to implementation processes. Commonly reported determinants included staffing levels, work- and caseloads, as well as aspects of organisational culture, such as communication and leadership.The presented knowledge about factors influencing neonatal IPC can support the design, implementation, and evaluation of IPC practices.

Of 1,118 patients with COVID-19 at a university hospital in Switzerland during October 2020-June 2021, we found 83 (7.4%) had probable or definite healthcare-associated COVID-19. After in-hospital exposure, we estimated secondary attack rate at 23.3%. Transmission was associated with longer contact times and with lower cycle threshold values among index patients.

Reptarenaviruses cause boid inclusion body disease (BIBD), a poten- tially fatal disease, occurring in captive constrictor snakes boas and pythons worldwide. Classical BIBD, characterized by the formation of pathognomonic cyto- plasmic inclusion bodies (IBs), occurs mainly in boas, whereas in pythons, for example, reptarenavirus infection most often manifests as central nervous system signs with limited IB formation. The natural hosts of reptarenaviruses are unknown, although free-ranging/wild constrictor snakes are among the suspects. Here, we report BIBD with reptarenavirus infection in indigenous captive and wild boid snakes in Costa Rica using histology, immunohistology, transmission electron microscopy, and next-generation sequencing (NGS). The snakes studied represented diagnostic post- mortem cases of captive and wild-caught snakes since 1989. The results from NGS on archival paraffin blocks confirm that reptarenaviruses were already present in wild boa constrictors in Costa Rica in the 1980s. Continuous sequences that were de novo assembled from the low-quality RNA obtained from paraffin-embedded tissue allowed the identification of a distinct pair of reptarenavirus S and L segments in all studied animals; in most cases, reference assembly could recover almost complete segments. Sampling of three prospective cases in 2018 allowed an examination of fresh blood or tissues and resulted in the identification of additional reptarenavirus segments and hartmanivirus coinfection. Our results show that BIBD is not only a disease of captive snakes but also occurs in indigenous wild constrictor snakes in Costa Rica, suggesting boa constrictors to play a role in natural reptarenavirus circulation. Los reptarenavirus causan la enfermedad del cuerpo de inclusión de las boas (BIBD), una enfermedad potencialmente mortal que se produce en las serpientes constrictoras cautivas, boas y pitones, de las serpientes constrictoras en cautividad, las boas y las pitones, en todo el mundo. La BIBD clásica, caracterizada por la formación de cuerpos de inclusión cito de inclusión patognomónicos, se da principalmente en las boas, mientras que en las pitones, por ejemplo, la infección por reptarenavirus se manifiesta más a menudo como con una formación limitada de IB. Los huéspedes naturales de los reptarenavirus son desconocidos, aunque las serpientes constrictoras salvajes y en libertad están entre los sospechosos. En este caso, informamos de la existencia de de reptarenavirus en serpientes constrictoras autóctonas y silvestres de Costa Rica. Costa Rica utilizando histología, inmunohistología, microscopía electrónica de transmisión y secuenciación de próxima generación (NGS). Las serpientes estudiadas representaban casos de diagnóstico post de diagnóstico de serpientes cautivas y silvestres desde 1989. Los resultados de la NGS en de parafina de archivo confirman que los reptarenavirus ya estaban presentes en las boas en Costa Rica en la década de 1980. Las secuencias continuas que se ensamblaron de novo a partir del ARN de baja calidad obtenido de los tejidos embebidos en parafina, permitieron identificar un par de segmentos S y L del reptarenavirus en todos los animales estudiados. En la mayoría de los casos, el ensamblaje de referencia pudo recuperar segmentos casi completos. El muestreo de tres casos prospectivos en 2018 permitió un examen de sangre o tejidos y dio lugar a la identificación de segmentos adicionales de reptarenavirus y coinfección por hartmanivirus. Nuestros resultados muestran que la BIBD no es solo una enfermedad de las serpientes cautivas sino que también se da en las serpientes constrictoras silvestres de Costa Rica, lo que sugiere que las boas constrictoras desempeñan un papel en la circulación natural de reptarenavirus. Universidad Nacional, Costa Rica Escuela de Medicina Veterinaria

Infections with Mycobacterium microti, a member of the M. tuberculosis complex, have been increasingly reported in humans and in domestic and free-ranging wild animals. At postmortem examination, infected animals may display histopathologic lesions indistinguishable from those caused by M. bovis or M. caprae, potentially leading to misidentification of bovine tuberculosis. We report 3 cases of M. microti infections in free-ranging red deer (Cervus elaphus) from western Austria and southern Germany. One diseased animal displayed severe pyogranulomatous pleuropneumonia and multifocal granulomas on the surface of the pericardium. Two other animals showed alterations of the lungs and associated lymph nodes compatible with parasitic infestation. Results of the phylogenetic analysis including multiple animal strains from the study area showed independent infection events, but no host-adapted genotype. Personnel involved in bovine tuberculosis–monitoring programs should be aware of the fastidious nature of M. microti, its pathogenicity in wildlife, and zoonotic potential.

Pigeon paramyxovirus-1 (PPMV-1) is predominantly isolated from pigeons or doves and forms a separate group of viral strains within Avian Orthoavulavirus-1, the causative agent of Newcastle disease in poultry. Since the introduction of PPMV-1 into Europe in 1981, these strains have rapidly spread all over Europe, and are nowadays considered to be enzootic in feral and hobby pigeons (Columba livia domestica). Infections with PPMV-1 can range from asymptomatic to fatal. To assess whether PPMV-1 continuously circulates in healthy feral pigeons, 396 tissue samples of pigeons from the city of Zurich were tested by reverse transcriptase real-time PCR over the period of one year. PPMV-1-RNA was detected in 41 feral pigeons (10.35%), determined as the dominant European genotype VI.2.1.1.2.2. In 38 of the 41 pigeons where organ samples tested positive, PPMV-1-RNA was also detected in either choana or cloaca swabs. There were no significant differences in positivity rates between seasons, age, and sex. The current study shows that feral pigeons without clinical signs of disease can harbour and most likely excrete PPMV-1. Spill-over into free-range holdings of chickens are therefore possible, as observed in a recent outbreak of Newcastle disease in laying hens due to PPMV-1 genotype VI.2.1.1.2.2. in the canton of Zurich in January 2022.

Objectives:In 2017, a point-prevalence survey was conducted with 12,931 patients in 96 hospitals across Switzerland as part of the national strategy to prevent healthcare-associated infections (HAIs). We present novel statistical methods to assess incidence proportions of HAI and attributable length-of-stay (LOS) in point-prevalence surveys.Methods:Follow-up data were collected for a subsample of patients and were used to impute follow-up data for all remaining patients. We used weights to correct length bias in logistic regression and multistate analyses. Methods were also tested in simulation studies.Results:The estimated incidence proportion of HAIs during hospital stay and not present at admission was 2.3% (95% confidence intervals [CI], 2.1–2.6), the most common type being lower respiratory tract infections (0.8%; 95% CI, 0.6–1.0). Incidence proportion was highest in patients with a rapidly fatal McCabe score (7.8%; 95% CI, 5.7–10.4). The attributable LOS for all HAI was 6.4 days (95% CI, 5.6–7.3) and highest for surgical site infections (7.1 days, 95% CI, 5.2–9.0). It was longest in the age group of 18–44 years (9.0 days; 95% CI, 5.4–12.6). Risk-factor analysis revealed that McCabe score had no effect on the discharge hazard after infection (hazard ratio [HR], 1.21; 95% CI, 0.89–1.63). Instead, it only influenced the infection hazard (HR, 1.84; 95% CI, 1.39–2.43) and the discharge hazard prior to infection (HR, 0.73; 95% CI, 0.66–0.82).Conclusions:In point-prevalence surveys with limited follow-up data, imputation and weighting can be used to estimate incidence proportions and attributable LOS that would otherwise require complete follow-up data.

Mammarenaviruses cause a persistent infection in their natural rodent and bat hosts. Reptarenaviruses cause boid inclusion body disease (BIBD) in constrictor snakes, but it is unclear whether snakes are the natural host of these viruses. Mammarenaviruses establish a persistent infection in their rodent and bat hosts, and the evidence suggests that reptarenaviruses and hartmaniviruses found in captive snakes act similarly. In snakes, reptarenaviruses cause boid inclusion body disease (BIBD), which is often associated with secondary infections. Snakes with BIBD usually carry more than a single pair of reptarenavirus S and L segments and occasionally demonstrate hartmanivirus coinfection. Here, we reported the generation of cell lines persistently infected with a single or two reptarenavirus(es) and a cell line with persistent reptarenavirus-hartmanivirus coinfection. By RT-PCR we demonstrated that the amount of viral RNA within the persistently infected cells remains at levels similar to those observed following initial infection. Using antibodies against the glycoproteins (GPs) and nucleoprotein (NP) of reptarenaviruses, we studied the levels of viral protein in cells passaged 10 times after the original inoculation and observed that the expression of GPs declines dramatically during persistent infection, unlike the expression of NP. Immunofluorescence (IF) staining served to demonstrate differences in the distribution of NP within the persistently infected compared to freshly infected cells. IF staining of cells inoculated with the viruses secreted from the persistently infected cell lines produced similar NP staining compared to cells infected with a traditionally passaged virus, suggesting that the altered NP expression pattern of persistently infected cells does not relate to changes in the virus. The cell cultures described herein can serve as tools for studying the coinfection and superinfection interplay between reptarenaviruses and studying the BIBD pathogenesis mechanisms. IMPORTANCE Mammarenaviruses cause a persistent infection in their natural rodent and bat hosts. Reptarenaviruses cause boid inclusion body disease (BIBD) in constrictor snakes, but it is unclear whether snakes are the natural host of these viruses. In this study, we showed that reptarenaviruses established a persistent infection in cultured Boa constrictor cells and that the persistently infected cells continued to produce infectious virus. Our results showed that persistent infection results from subsequent passaging of cells inoculated with a single reptarenavirus, two reptarenaviruses, or even when inoculating the cells with reptarenavirus and hartmanivirus (another arenavirus genus). The results further suggested that coinfection would not result in overt competition between the different reptarenaviruses, thus helping to explain the frequent reptarenavirus coinfections in snakes with BIBD. The established cell culture models of persistent infection could help to elucidate the role of coinfection and superinfection and potential immunosuppression as the pathogenic mechanisms behind BIBD.

The recently identified bacterium Tannerella serpentiformis is the closest phylogenetic relative of Tannerella forsythia, whose presence in oral biofilms is associated with periodontitis. Conversely, T. serpentiformis is considered health-associated. This discrepancy was investigated in a comparative study of the two Tannerella species. The biofilm behavior was analyzed upon their addition and of Porphyromonas gingivalis-each bacterium separately or in combinations-to an in vitro five-species oral model biofilm. Biofilm composition and architecture was analyzed quantitatively using real-time PCR and qualitatively by fluorescence in situ hybridization/confocal laser scanning microscopy, and by scanning electron microscopy. The presence of T. serpentiformis led to a decrease of the total cell number of biofilm bacteria, while P. gingivalis was growth-promoting. This effect was mitigated by T. serpentiformis when added to the biofilm together with P. gingivalis. Notably, T. serpentiformis outcompeted T. forsythia numbers when the two species were simultaneously added to the biofilm compared to biofilms containing T. forsythia alone. Tannerella serpentiformis appeared evenly distributed throughout the multispecies biofilm, while T. forsythia was surface-located. Adhesion and invasion assays revealed that T. serpentiformis was significantly less effective in invading human gingival epithelial cells than T. forsythia. Furthermore, compared to T. forsythia, a higher immunostimulatory potential of human gingival fibroblasts and macrophages was revealed for T. serpentiformis, based on mRNA expression levels of the inflammatory mediators interleukin 6 (IL-6), IL-8, monocyte chemoattractant protein-1 and tumor necrosis factor α, and production of the corresponding proteins. Collectively, these data support the potential of T. serpentiformis to interfere with biological processes relevant to the establishment of periodontitis.

Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.

International audience; Introduction Little is known about the bloodstream infection (BSI) risk associated with short-term peripheral venous catheters (PVCs) and no large study investigated the insertion site-related risk for PVC-BSI. Methods We performed a cohort study at the University of Geneva Hospitals using the prospective hospital-wide BSI surveillance database. We analyzed the association between insertion site and risk of PVC-BSI on the upper extremity using univariable and multivariable marginal Cox models. Results Between 2016 and 2020, utilization of 403′206 peripheral venous catheters were prospectively recorded in a 2000-bed hospital consortium with ten sites. Twenty-seven percent of PVC (n = 109′686) were inserted in the hand. After adjustment for confounding factors, hand insertion was associated with a decreased PVC-BSI risk (adjusted hazard ratio [HR] 0.42, 95% CI 0.18–0.98, p = 0.046) compared to more proximal insertion sites. In a sensitivity analysis for PVCs with ≥ 3 days of dwell time, we confirmed a decreased PVC-BSI risk after hand insertion (HR 0.37, 95% CI 0.15–0.93, p = 0.035). Conclusion Hand insertion should be considered for reducing PVC infections, especially for catheters with an expected dwell time of more than 2 days.

Neuro- and nephrotoxicity of polymyxins are known but clinical studies in horses are lacking. The aim of this study was to describe neurogenic and nephrogenic side effects of hospitalized horses receiving Polymyxin B (PolyB) as part of their treatment plan. Twenty horses diagnosed with surgical colic (n = 11), peritonitis (n = 5), typhlocolitis (n = 2), pneumonia, and pyometra (each n = 1) were included. Antimicrobial treatment was randomized to GENTA (gentamicin 10 mg/kg bwt q24 h IV, penicillin 30.000 IU/kg q6 h IV) or NO GENTA (marbofloxacin 2 mg/kg bwt q24 h IV, penicillin 30.000 IU/kg q6 h IV). The duration of PolyB treatment ranged from 1 to 4 days. Clinical and neurological examinations were performed, and serum PolyB concentrations were measured daily during and three days following PolyB treatment. Urinary analysis, plasma creatinine, urea and SDMA were assessed every other day. Video recordings of neurological examinations were graded by three blinded observers. All horses showed ataxia during PolyB treatment in both groups (median maximum ataxia score of 3/5, range 1–3/5). Weakness was detected in 15/20 (75%) horses. In 8/14 horses, the urinary γ-glutamyltransferase (GGT)/creatinine ratio was elevated. Plasma creatinine was mildly elevated in 1/16 horses, and SDMA in 2/10 horses. Mixed-model analysis showed a significant effect of time since last PolyB dose (p = 0.0001, proportional odds: 0.94) on the ataxia score. Ataxia and weakness should be considered as reversible adverse effects in hospitalized horses receiving PolyB. Signs of tubular damage occurred in a considerable number of horses; therefore, the nephrotoxic effect of polymyxins should be considered and urinary function monitored.

Microtubules and specialized microtubule-containing structures are assembled from tubulins, an ancient superfamily of essential eukaryotic proteins. Here, we use bioinformatic approaches to analyze features of tubulins in organisms from the phylum Apicomplexa. Apicomplexans are protozoan parasites that cause a variety of human and animal infectious diseases. Individual species harbor one to four genes each for α- and β-tubulin isotypes. These may specify highly similar proteins, suggesting functional redundancy, or exhibit key differences, consistent with specialized roles. Some, but not all apicomplexans harbor genes for δ- and ε-tubulins, which are found in organisms that construct appendage-containing basal bodies. Critical roles for apicomplexan δ- and ε-tubulin are likely to be limited to microgametes, consistent with a restricted requirement for flagella in a single developmental stage. Sequence divergence or the loss of δ- and ε-tubulin genes in other apicomplexans appears to be associated with diminished requirements for centrioles, basal bodies, and axonemes. Finally, because spindle microtubules and flagellar structures have been proposed as targets for anti-parasitic therapies and transmission-blocking strategies, we discuss these ideas in the context of tubulin-based structures and tubulin superfamily properties.

Switzerland began a national lockdown on March 16, 2020, in response to the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We assessed the prevalence of SARS-CoV-2 infection among patients admitted to 4 hospitals in the canton of Zurich, Switzerland, in April 2020. These 4 acute care hospitals screened 2,807 patients, including 2,278 (81.2%) who did not have symptoms of coronavirus disease (COVID-19). Overall, 529 (18.8%) persons had >1 symptom of COVID-19, of whom 60 (11.3%) tested positive for SARS-CoV-2. Eight asymptomatic persons (0.4%) also tested positive for SARS-CoV-2. Our findings indicate that screening on the basis of COVID-19 symptoms, regardless of clinical suspicion, can identify most SARS-CoV-2–positive persons in a low-prevalence setting.

A nationwide outbreak of human listeriosis in Switzerland was traced to persisting environmental contamination of a cheese dairy with Listeria monocytogenes serotype 4b, sequence type 6, cluster type 7488. Whole-genome sequencing was used to match clinical isolates to a cheese sample and to samples from numerous sites within the production environment.

Fungi are an important part of the microbiota in healthy barrier tissues. Fungal dysbiosis in turn is associated with local and distal inflammatory diseases. Recent advances have shed light on the antigen-specific IL-17-dependent mechanisms that regulate fungal commensalism and prevent fungal overgrowth during homeostasis. Progress in our understanding of species-specific differences in fungus-host interactions provides new hypotheses of why Candida albicans-targeting T cells exceed those directed against other fungal species in the human T cell repertoire. Importantly, C. albicans-specific Th17 cells can also contribute to immune pathology in distant organs such as the lung via cross-reaction with heterologous antigens.

The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by NextGeneration Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases., Microorganisms, 10 (6)

Filifactor alocis is a Gram-positive asaccharolytic, obligate anaerobic rod that has been isolated from a variety of oral infections including periodontitis, peri-implantitis, and odontogenic abscesses. As a newly emerging pathogen, its type strain has been investigated for pathogenic properties, yet little is known about its virulence variations among strains. We previously screened the whole genome of nine clinical oral isolates and a reference strain of F. alocis, and they expressed a novel RTX toxin, FtxA. In the present study, we aimed to use label-free quantification proteomics to characterize the full proteome of those ten F. alocis strains. A total of 872 proteins were quantified, and 97 among them were differentially expressed in FtxA-positive strains compared with the negative strains. In addition, 44 of these differentially expressed proteins formed 66 pairs of associations based on their predicted functions, which included clusters of proteins with DNA repair/mediated transformation and catalytic activity-related function, indicating different biosynthetic activities among strains. FtxA displayed specific interactions with another six intracellular proteins, forming a functional cluster that could discriminate between FtxA-producing and non-producing strains. Among them were FtxB and FtxD, predicted to be encoded by the same operon as FtxA. While revealing the broader qualitative and quantitative proteomic landscape of F. alocis, this study also sheds light on the deeper functional inter-relationships of FtxA, thus placing this RTX family member into context as a major virulence factor of this species., Pathogens, 11 (5), ISSN:2076-0817

Background Traditionally, hand hygiene (HH) interventions do not identify the observed healthcare workers (HWCs) and therefore, reflect HH compliance only at population level. Intensive care units (ICUs) in seven European hospitals participating in the “Prevention of Hospital Infections by Intervention and Training” (PROHIBIT) study provided individual HH compliance levels. We analysed these to understand the determinants and dynamics of individual change in relation to the overall intervention effect. Methods We included HCWs who contributed at least two observation sessions before and after intervention. Improving, non-changing, and worsening HCWs were defined with a threshold of 20% compliance change. We used multivariable linear regression and spearman’s rank correlation to estimate determinants for the individual response to the intervention and correlation to overall change. Swarm graphs visualized ICU-specific patterns. Results In total 280 HCWs contributed 17,748 HH opportunities during 2677 observation sessions. Overall, pooled HH compliance increased from 43.1 to 58.7%. The proportion of improving HCWs ranged from 33 to 95% among ICUs. The median HH increase per improving HCW ranged from 16 to 34 percentage points. ICU wide improvement correlated significantly with both the proportion of improving HCWs (ρ = 0.82 [95% CI 0.18–0.97], and their median HH increase (ρ = 0.79 [0.08–0.97]). Multilevel regression demonstrated that individual improvement was significantly associated with nurse profession, lower activity index, higher nurse-to-patient ratio, and lower baseline compliance. Conclusions Both the proportion of improving HCWs and their median individual improvement differed substantially among ICUs but correlated with the ICUs’ overall HH improvement. With comparable overall means the range in individual HH varied considerably between some hospitals, implying different transmission risks. Greater insight into improvement dynamics might help to design more effective HH interventions in the future.

Enterotoxins (SEs) produced by Staphylococcus aureus are the cause of serious food intoxications. Staphylococcal enterotoxin C (SEC) is one of the main contributors, as it is often highly expressed. S. aureus possesses a competitive growth advantage over accompanying bacterial flora under stress conditions encountered in foods, such as high NaCl concentrations. However, the influence of NaCl as an external stressor on SEC expression is still unclear. We investigated the influence of 4.5% NaCl on sec mRNA and SEC protein levels. A qRT-PCR assay revealed that NaCl stress leads to time-dependently decreased or elevated sec mRNA levels for most strains. SEC protein levels were generally decreased under NaCl stress. Our findings suggest that NaCl stress lowers overall SEC concentration and time-dependently affects sec mRNA levels., Frontiers in Microbiology, 13, ISSN:1664-302X

9 páginas, 4 figuras, 1 tabla., Background: Molecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: A candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: 15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: This first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes. Funding: UNITAID, Wellcome, MRC, BMGF., Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC), which is accompanied by or without production of copious amounts of gas, has been linked to the acetone–butyrate–ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. The reconstruction and comparison of intra- and interspecies metabolic pathways linked to meat spoilage at the genomic level can unravel the genetic basis for the variable phenotype. However, this is hindered by unavailability of CEC genomes, which in addition, has hampered the determination of genetic diversity and its drivers within CEC. Therefore, the current study aimed at determining the diversity of CEC through comprehensive comparative genomics. Fifty CEC genomes from 11 CEC species were compared. Recombination and gene gain/loss events were identified as important sources of natural variation within CEC, with the latter being pronounced in genomospecies2 that has lost genes related to flagellar assembly and signaling. Pan-genome analysis revealed variations in carbohydrate metabolic and hydrogenases genes within the complex. Variable inter- and intraspecies gas production in meat by C. estertheticum and Clostridium tagluense were associated with the distribution of the [NiFe]-hydrogenase hyp gene cluster whose absence or presence was associated with occurrence or lack of pack distention, respectively. Through comparative genomics, we have shown CEC species exhibit high genetic diversity that can be partly attributed to recombination and gene gain/loss events. We have also shown genetic basis for variable gas production in meat can be attributed to the presence/absence of the hyp gene cluster.

Background The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples. Results A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02–14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress. Conclusions A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with ‘lake snow’ particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum.

There is now considerable evidence that in Europe, babesiosis is an emerging infectious disease, with some of the causative species spreading as a consequence of the increasing range of their tick vector hosts. In this review, we summarize both the historic records and recent findings on the occurrence and incidence of babesiosis in 20 European countries located in southeastern Europe (Bosnia and Herzegovina, Croatia, and Serbia), central Europe (Austria, the Czech Republic, Germany, Hungary, Luxembourg, Poland, Slovakia, Slovenia, and Switzerland), and northern and northeastern Europe (Lithuania, Latvia, Estonia, Iceland, Denmark, Finland, Sweden, and Norway), identified in humans and selected species of domesticated animals (cats, dogs, horses, and cattle). Recorded cases of human babesiosis are still rare, but their number is expected to rise in the coming years. This is because of the widespread and longer seasonal activity of Ixodes ricinus as a result of climate change and because of the more extensive use of better molecular diagnostic methods. Bovine babesiosis has a re-emerging potential because of the likely loss of herd immunity, while canine babesiosis is rapidly expanding in central and northeastern Europe, its occurrence correlating with the rapid, successful expansion of the ornate dog tick (Dermacentor reticulatus) populations in Europe. Taken together, our analysis of the available reports shows clear evidence of an increasing annual incidence of babesiosis across Europe in both humans and animals that is changing in line with similar increases in the incidence of other tick-borne diseases. This situation is of major concern, and we recommend more extensive and frequent, standardized monitoring using a “One Health” approach.

The Chlamydiae are a phylum of obligate intracellular, Gram-negative bacteria with a biphasic lifecycle [...]

Objective:Nosocomial transmission of influenza is a major concern for infection control. We aimed to dissect transmission dynamics of influenza, including asymptomatic transmission events, in acute care.Design:Prospective surveillance study during 2 influenza seasons.Setting:Tertiary-care hospital.Participants:Volunteer sample of inpatients on medical wards and healthcare workers (HCWs).Methods:Participants provided daily illness diaries and nasal swabs for influenza A and B detection and whole-genome sequencing for phylogenetic analyses. Contacts between study participants were tracked. Secondary influenza attack rates were calculated based on spatial and temporal proximity and phylogenetic evidence for transmission.Results:In total, 152 HCWs and 542 inpatients were included; 16 HCWs (10.5%) and 19 inpatients (3.5%) tested positive for influenza on 109 study days. Study participants had symptoms of disease on most of the days they tested positive for influenza (83.1% and 91.9% for HCWs and inpatients, respectively). Also, 11(15.5%) of 71 influenza-positive swabs among HCWs and 3 (7.9%) of 38 influenza-positive swabs among inpatients were collected on days without symptoms; 2 (12.5%) of 16 HCWs and 2 (10.5%) of 19 inpatients remained fully asymptomatic. The secondary attack rate was low: we recorded 1 transmission event over 159 contact days (0.6%) that originated from a symptomatic case. No transmission event occurred in 61 monitored days of contacts with asymptomatic influenza-positive individuals.Conclusions:Influenza in acute care is common, and individuals regularly shed influenza virus without harboring symptoms. Nevertheless, both symptomatic and asymptomatic transmission events proved rare. We suggest that healthcare-associated influenza prevention strategies that are based on preseason vaccination and barrier precautions for symptomatic individuals seem to be effective.