Simplified Spectrum Score (S3) app for pathogen-agnostic antimicrobial drug spectrum ranking to assess for antimicrobial de-escalation events

Antimicrobial/antibiotic de-escalation (ADE) is a key feature of antimicrobial stewardship programs (ASP) that relies mainly on individual panels for determining ADE events based on subjective ranking of antibiotics' spectrum activity. The lack of consensus among ASP experts leads to reproducibility issues in the measure of this clinical outcome, making difficult to assess its real impact on patient care. The S3 score (Simplified Spectrum Score) app was developed to allow an objective ranking of antibiotics. Ranking was achieved by developing a database harboring pairs of bacteria-antibiotics for which each molecule was assigned a score based on published and clinically validated data from a recognized international committee. S3 score shows a strong correlation relationship and substantial agreement to a clinically validated spectrum score, and its framework enables any person to use it for ADE detection without assuming prior knowledge or training. In addition, its design enables regular updates and sustainability.

Case report: Chronic Candida albicans meningitis: a rare entity diagnosed by metagenomic next-generation sequencing

The aetiology of chronic aseptic meningitis is difficult to establish. Candida meningitis in particular is often diagnosed late, as cerebrospinal fluid (CSF) work-up and imaging findings are nonspecific. A 35-year-old patient with chronic aseptic meningitis, for which repeated microbiological testing of CSF was unrevealing, was finally diagnosed with Candida albicans (C. albicans) meningitis with cauda equina involvement using metagenomic next-generation sequencing (mNGS). This report highlights the diagnostic challenges and the difficulties of treating shunt-associated fungal meningitis.

Significance of colonization by antibiotic-resistant organisms prior to congenital heart disease surgery in children from low- to middle-income countries sent by non-governmental organizations to Switzerland

PURPOSE

Children with congenital heart disease (CHD) from low- to middle-income countries (LMIC) are suspected to have a high prevalence of antibiotic-resistant microorganisms (ARMOs) carriage, but data are currently lacking. Carriage of ARMOs could impact the post-operative course in pediatric intensive care unit (PICU). The aim of the study was to assess the prevalence of ARMOs carriage in children with CHD from LMIC and its impact on post-operative outcomes.

METHODS

This was a retrospective monocentric study from 01/2019 to 12/2022. Included patients were children (0-18 years) from a LMIC admitted after CHD surgery and with AMRO screening performed the week before. Infections and post-operative evolution were compared based on ARMOs carriage status.

FINDINGS

Among 224 surgeries (median age 38.5 months (IQR 22-85.5)), ARMOs carriage was evidenced in 95 cases (42.4%). Main organisms isolated were Extended Spectrum Beta-Lactamase (ESBL) producing E. coli (75/224) 33.5%)) and ESBL-K. pneumoniae (30/224) 13.4%)). Median mechanical ventilation duration was 1 day (IQR 0-1), PICU stay 3 days (IQR 2-4) and hospital stay 6.5 days (IQR 5-10). A total of 17 infectious episodes occurred in 15 patients, mostly consisting in hospital-acquired pneumonia (HAP) (12/17). Only two infections were caused by a colonizing ARMO. Occurrence of infections and patients' outcome were similar between ARMO carriers and non-carriers. Higher use of carbapenems (6 (6.3%) vs 1 (0.8%), p = 0.04) and a trend to a higher use of vancomycin (14 (13.7%) vs 9 (6.9%), p = 0.04) in case of ARMOs carriage. Applying current guidelines, negative swab screening could have led to sparing most of empirical vancomycin therapy (11/12) for HAP based on current guidelines.

CONCLUSION

Prevalence of AMROs carriage is high in children from LMIC and has a limited impact on patients' outcome. However, ARMOs carriage leads to higher consumption of antibiotics. Screening may help saving use of broad-spectrum antibiotic in non-carrier patients.

Evaluation of PhenoMATRIX and PhenoMATRIX PLUS for the screening of MRSA from nasal and inguinal/perineal swabs using chromogenic media

The objective of this study was to assess the clinical performances of PhenoMATRIX and PhenoMATRIX PLUS for the screening of methicillin-resistant Staphylococcus aureus (MRSA) from nasal and inguinal/perineal ESwabs using chromogenic media. The automated performances were compared to the manual reading. Additionally, we evaluated PhenoMATRIX PLUS for the automatic release of the negative results to the Laboratory Information System (LIS) and the automatic discharge of the negative plates from the incubators. A total of 6,771 non-duplicate specimens were used by PhenoMATRIX as a machine learning model. The validation of these settings was performed on 17,223 non-duplicate specimens. The MRSA positivity rate was 5% (866/17,223). Validated settings were then used by PhenoMATRIX PLUS on another 1,409 non-duplicate specimens. The sensitivities of PhenoMATRIX and PhenoMATRIX PLUS were 99.8% [95% confidence interval (CI), 99.2%-99.9%] and 100% (95% CI, 92.1%-100%), respectively. The specificities of PhenoMATRIX and PhenoMATRIX PLUS were 99.1% (95% CI, 99.0%-99.2%) and 95.2% (95% CI, 93.8%-96.1%), respectively. All the 1,297 MRSA-negative specimens analyzed by PhenoMATRIX PLUS were automatically released and sent to the LIS immediately after availability of the culture image on the WASPLab (100% accuracy). All negative media plates were automatically discarded. PhenoMATRIX PLUS decreases the time spent by technologists on negative plates and ensures optimal usage of the incubators' capacity.

A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia

IMPORTANCE

The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.

Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study

BACKGROUND

Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise.

METHODS

This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients.

RESULTS

A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test.

CONCLUSIONS

This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.

Oral and intestinal dysbiosis in Parkinson's disease

The suspicion of an origin of Parkinson's disease (PD) at the periphery of the body and the involvement of environmental risk factors in the pathogenesis of PD have directed the attention of the scientific community towards the microbiota. The microbiota represents all the microorganisms residing both in and on a host. It plays an essential role in the physiological functioning of the host. In this article, we review the dysbiosis repeatedly demonstrated in PD and how it influences PD symptoms. Dysbiosis is associated with both motor and non-motor PD symptoms. In animal models, dysbiosis only promotes symptoms in individuals genetically susceptible to Parkinson's disease, suggesting that dysbiosis is a risk factor but not a cause of Parkinson's disease. We also review how dysbiosis contributes to the pathophysiology of PD. Dysbiosis induces numerous and complex metabolic changes, resulting in increased intestinal permeability, local and systemic inflammation, production of bacterial amyloid proteins that promote α-synuclein aggregation, as well as a decrease in short-chain fatty acid-producing bacteria that have anti-inflammatory and neuroprotective potential. In addition, we review how dysbiosis decreases the efficacy of dopaminergic treatments. We then discuss the interest of dysbiosis analysis as a biomarker of Parkinson's disease. Finally, we give an overview of how interventions modulating the gut microbiota such as dietary interventions, pro-biotics, intestinal decontamination and fecal microbiota transplantation could influence the course of PD.

Mycoplasma genitalium Endocarditis in Prosthetic Aortic Valve

We report a case of Mycoplasma genitalium endocarditis in a prosthetic heart valve of a woman who sought care in Switzerland for acute aortic valve dysfunction 3 years after valve replacement. This unusual manifestation of infection with this bacterium was diagnosed using broad-range PCR despite suspicion of a mechanical disinsertion.

IVDR: Analysis of the Social, Economic, and Practical Consequences of the Application of an Ordinance of the In Vitro Diagnostic Ordinance in Switzerland

IVDR regulation represents a major challenge for diagnostic microbiology laboratories. IVDR complicates a broad range of aspects and poses a risk given the high diversity of pathogens (including rare but highly virulent microbes) and the large variety of samples submitted for analysis. The regular emergence of new pathogens (including Echovirus E-11, Adenovirus 41, Monkeypox virus, Alongshan virus, and Enterovirus D68, as recent examples in Europe in the post SARS-CoV-2 era) is another factor that makes IVDR regulation risky, because its detrimental effect on production of in-house tests will negatively impact knowledge and expertise in the development of new diagnostic tests. Moreover, such regulations negatively impact the availability of diagnostic tests, especially for neglected pathogens, and has a detrimental effect on the overall costs of the tests. The increased regulatory burden of IVDR may thereby pose an important risk for public health. Taken together, it will have a negative impact on the financial balance of diagnostic microbiology laboratories (especially small ones). The already-high standards of quality management of all ISO-accredited and Swissmedic-authorized laboratories render IVDR law of little value, at least in Switzerland, while tremendously increasing the regulatory burden and associated costs. Eventually, patients will need to pay for diagnostic assays outside of the framework of their insurance in order to obtain a proper diagnostic assessment, which may result in social inequity. Thus, based on the risk assessment outlined above, the coordinated commission for clinical microbiology proposes adjusting the IvDO ordinance by (i) introducing an obligation to be ISO 15189 accredited and (ii) not implementing the IvDO 2028 milestone.

[Summary of the 8th Symposium "Feeding the microbiota": prebiotics and probiotics]

The microbiota represents all the microorganisms including viruses, bacteria, fungi, and parasites, that have a symbiotic relationship with their host and that are present in a particular system (or niche) of the human body such as the skin, the respiratory tract, the urogenital tract or the digestive tract. This paper is a narrative review of all talks given at the 8th edition of the « Feeding the Microbiota » symposium organized at the Geneva University Hospitals. The symposium gathered 346 participants, both onsite and online, from 23 countries all-around the world. The main thematic of this edition focused on the composition of the gut microbiota as affected by prebiotics and postbiotics and their effects on various diseases.

Postpartum septic arthritis of pubic symphysis due to Sneathia sanguinegens, Sneathia vaginalis, and Mageeibacillus indolicus: Contribution of clinicalmetagenomics

Sneathia sanguinegens, Sneathia vaginalis, and Mageeibacillus indolicus have been recently described in the female genital tract. We present the first case of a postpartum septic arthritis of the pubic symphysis due to these organisms, identified by next generation sequencing.

The Swiss Pathogen Surveillance Platform - towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata

The Swiss Pathogen Surveillance Platform (SPSP) is a shared secure surveillance platform between human and veterinary medicine, to also include environmental and foodborne isolates. It enables rapid and detailed transmission monitoring and outbreak surveillance of pathogens using whole genome sequencing data and associated metadata. It features controlled data access, complex dynamic queries, dedicated dashboards and automated data sharing with international repositories, providing actionable results for public health and the vision to improve societal well-being and health.

Dry alginate beads for fecal microbiota transplantation: from model strains to fecal samples

Clostridioides difficile infection (CDI) is a critical nosocomial infection with more than 124,000 cases per year in Europe and a mortality rate of 15-17%. The standard of care (SoC) is antibiotic treatment. Unfortunately, the relapse rate is high (∼35%) and SoC is significantly less effective against recurrent infection (rCDI). Fecal microbiota transplantation (FMT) is a recommended treatment against rCDI from the second recurrence episode and has an efficacy of 90%. The formulation of diluted donor stool deserves innovation because its actual administration routes deserve optimization (naso-duodenal/jejunal tubes, colonoscopy, enema or several voluminous oral capsules). Encapsulation of model bacteria strains in gel beads were first investigated. Then, the encapsulation method was applied to diluted stools. Robust spherical gel beads were obtained. The mean particle size was around 2 mm. A high loading of viable microorganisms was obtained for model strains and fecal samples. For plate-counting, values ranged from 10¹⁵ to 10¹⁷ CFU/g for single and mixed model strains, and 10⁶ to 10⁸ CFU/g for fecal samples. This corresponded to a viability of 30% to 60% as assessed by flow cytometry. This novel formulation is promising as the technology is applicable to both model strains and bacteria contained in the gut microbiota.

Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become tolerant, and could turn into agricultural or medical problems, for example, due to climate change or in immunocompromised individuals. However, quantitative data about fungicide sensitivity of environmental fungi is mostly lacking. Aureobasidium species are widely distributed and frequently isolated yeast-like fungi. One species, A. pullulans, is used as a biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared 16 clinical and 30 agricultural Aureobasidium isolates based on whole-genome data and by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to the species A. pullulans. These isolates clustered with other Aureobasidium species, including A. melanogenum, a recently separated species that expresses virulence traits that are mostly lacking in A. pullulans. Interestingly, the clinical Aureobasidium isolates were significantly more fungicide sensitive than many isolates from agricultural samples, which implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems. IMPORTANCE Environmental microbiota are regularly found in clinical samples and can cause disease, in particular, in immunocompromised individuals. Organisms of the genus Aureobasidium belonging to this group are highly abundant, and some species are even described as pathogens. Many A. pullulans isolates from agricultural samples are tolerant to different fungicides, and it seems inevitable that such strains will eventually appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for species A. melanogenum, which is also found in the environment and exhibits virulence traits. Based on our observation and the strains tested here, clinical Aureobasidium isolates are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species, such as A. pullulans and A. melanogenum, and to consider the development of fungicide tolerance in the evaluation process of fungicides.

Targeted mupirocin-based decolonization for Staphylococcus aureus carriers and the subsequent risk of mupirocin resistance in haemodialysis patients - a longitudinal study over 20 years

Mupirocin-based decolonization of Staphylococcus aureus carriers undergoing haemodialysis is not widely implemented due to concerns of mupirocin resistance. In our haemodialysis unit, a strategy combining universal S. aureus screening with targeted mupirocin-based decolonization has been introduced two decades ago. In this study of haemodialysis patients, mupirocin resistance was assessed in blood and colonizing S. aureus isolates during two periods. Mupirocin resistance in S. aureus was infrequent in both blood and colonizing isolates. Furthermore, in the years 2003-2021, a decreasing trend of the annual rate of S. aureus bloodstream infections was observed. Targeted mupirocin-based decolonization of S. aureus carriers undergoing haemodialysis is a sustainable measure for preventing healthcare-associated infections.

Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains

OBJECTIVES

Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it.

METHODS

For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared.

RESULTS

At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test).

DISCUSSION

We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.

Performance of the HiberGene Group B Streptococcus kit, a loop-mediated isothermal amplification-based assay for GBS screening during pregnancy

Timely and accurate detection of Group B Streptococcus (GBS) carriage in pregnant women allows for targeted peripartum prophylaxis. Replacing culture-based screening by molecular biology assays enables faster results obtention, better targeted antibiotic prophylaxis, and reduces the laboratory workload. Here, we present a comparative analysis between a Loop Mediated Isothermal Amplification assay (HiberGene GBS kit) and culture (gold-standard). The HiberGene GBS kit showed a sensitivity of 97.9% and a specificity of 96.8% compared with culture. The limit of detection was estimated at 10³ cfu/ml and results were obtained within 30 min. HiberGene GBS assay can be used for peripartum GBS screening and targeted antibiotic prophylaxis provided sample processing can be swiftly performed around the clock.

Diagnostic test accuracy of an automated device for the MALDI target preparation for microbial identification

The objective of this study was to evaluate the performance of the Copan Colibrí™ against the manual preparation of the MALDI targets. We analyzed 416 (31 different species) non-duplicate strains covering the most important species identified in clinical routine. We also assessed the intra-strain repeatability between the comparable methods. We then analyzed the performance of this new method after implementation in routine on 12,253 aerobic bacterial isolates and yeasts, encompassing a total of 42 different species. Among the 416 strains analyzed, 6.3% (26/416) and 10.8% (45/416) had a score value < 2 when processed by the Colibri™ and manual method, respectively. Only 5.9% (9/152) of the Gram positive rods and cocci had a score values < 2 by the Colibri™ versus 20.4% (31/152) by the manual method. We confirmed that this relative superiority observed for the Colibri™ was due primarily in the use of the formic acid protocol. For the Gram-negative bacteria, the results of both methods were comparable; 6.6% (17/256) and 4.7% (12/256) had a score value < 2 by the Colibri™ and the manual method, respectively. After implementation in routine, the results according to the Biotyper score cut-off values were distributed as follows: < 1.70: 2.5% (304/12,253), 1.70-1.79: 1.9% (227/12,253), 1.80-1.89: 3.1% (377/12,253), 1.90-1.99: 6.7% (825/12,253), and ≥ 2: 85.9% (10,520/12,253). The Colibrí™ coupled to MALDI-TOF/MS revealed good performances and higher intra-strain repeatability as compared to the manual preparation of the MALDI targets.

Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing

Before implementing metagenomic next-generation sequencing (mNGS) in the routine diagnostic laboratory, several challenges need to be resolved. To address strengths and limitations of mNGS in bacterial detection and quantification in samples with overwhelming host DNA abundance, we used the pig muscle tissue spiked with a home-made bacterial mock community, consisting of four species from different phyla. From the spiked tissue, we extracted DNA using: (i) a procedure based on mechanical/chemical lysis (no bacterial DNA enrichment); (ii) the Ultra-Deep Microbiome Prep (Molzym) kit for bacterial DNA enrichment; and (iii) the same enrichment kit but replacing the original proteinase K treatment for tissue solubilization by a collagenases/thermolysin digestion and cell filtration. Following mNGS, we determined bacterial: 'host' read ratios and taxonomic abundance profiles. We calculated the load of each mock-community member by combining its read counts with read counts and microscopically-determined cell counts of other co-spiked bacteria. In unenriched samples, bacterial quantification and taxonomic profiling were fairly accurate but at the expense of the sensitivity of detection. The removal of 'host' DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.

An interventional quasi-experimental study to evaluate the impact of a rapid screening strategy in improving control of nosocomial extended-spectrum beta-lactamase-producing Enterobacterales and carbapenemase-producing organisms in critically ill patients

Introduction

Rapid molecular tests could accelerate the control of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenemase-producing organisms (CPO) in intensive care units (ICUs).

Objective and methods

This interventional 12-month cohort study compared a loop-mediated isothermal amplification (LAMP) assay performed directly on rectal swabs with culturing methods (control period, 6 months), during routine ICU screening. Contact precautions (CP) were implemented for CPO or non-E. coli ESBL-producing Enterobacterales (nEcESBL-PE) carriers. Using survival analysis, we compared the time intervals from admission to discontinuation of unnecessary preemptive CP among patients at-risk and the time intervals from screening to implementation of CP among newly identified carriers. We also compared diagnostic performances, and nEcESBL-PE/CPO acquisition rates. This study is registered, ISRCTN 23588440.

Results

We included 1043 patients. During the intervention and control phases, 92/147 (62.6%) and 47/86 (54.7%) of patients at-risk screened at admission were candidates for early discontinuation of preemptive CP. The LAMP assay had a positive predictive value (PPV) of 44.0% and a negative predictive value (NPV) of 99.9% for CPO, and 55.6% PPV and 98.2% NPV for nEcESBL-PE. Due to result notification and interpretation challenges, the median time from admission to discontinuation of preemptive CP increased during the interventional period from 80.5 (95% CI 71.5–132.1) to 88.3 (95% CI 57.7–103.7) hours (p = 0.47). Due to the poor PPV, we had to stop using the LAMP assay to implement CP. No difference was observed regarding the incidence of nEcESBL-PE and CPO acquisition.

Conclusion

A rapid screening strategy with LAMP assays performed directly on rectal swabs had no benefit for infection control in a low-endemicity setting.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13054-022-04027-8.

The central and biodynamic role of gut microbiota in critically ill patients

Gut microbiota plays an essential role in health and disease. It is constantly evolving and in permanent communication with its host. The gut microbiota is increasingly seen as an organ, and its failure, reflected by dysbiosis, is seen as an organ failure associated with poor outcomes. Critically ill patients may have an altered gut microbiota, namely dysbiosis, with a severe reduction in “health-promoting” commensal intestinal bacteria (such as Firmicutes or Bacteroidetes) and an increase in potentially pathogenic bacteria (e.g. Proteobacteria). Many factors that occur in critically ill patients favour dysbiosis, such as medications or changes in nutrition patterns. Dysbiosis leads to several important effects, including changes in gut integrity and in the production of metabolites such as short-chain fatty acids and trimethylamine N-oxide. There is increasing evidence that gut microbiota and its alteration interact with other organs, highlighting the concept of the gut–organ axis. Thus, dysbiosis will affect other organs and could have an impact on the progression of critical diseases. Current knowledge is only a small part of what remains to be discovered. The precise role and contribution of the gut microbiota and its interactions with various organs is an intense and challenging research area that offers exciting opportunities for disease prevention, management and therapy, particularly in critical care where multi-organ failure is often the focus. This narrative review provides an overview of the normal composition of the gut microbiota, its functions, the mechanisms leading to dysbiosis, its consequences in an intensive care setting, and highlights the concept of the gut–organ axis.

Caution when using 1,3, β-D-glucan in the CSF as a biomarker of Candida albicans meningitis

Relying on a biomarker to diagnose or follow-up the treatment of a Candida albicans meningitis would have an impact on patient management. The biomarker 1,3, β-D-glucan (BDG), developed for serum testing, shows inconsistent values when applied on cerebro-spinal fluid (CSF), and its use with the current protocol on CSF samples warrants caution.

Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections

Bone and joint infections (BJIs) are complex infections that require precise microbiological documentation to optimize antibiotic therapy. Currently, diagnosis is based on microbiological culture, sometimes complemented by amplification and sequencing of the 16S rDNA gene. Clinical metagenomics (CMg), that is, the sequencing of the entire nucleic acids in a sample, was previously shown to identify bacteria not detected by conventional methods, but its actual contribution to the diagnosis remains to be assessed, especially with regard to 16S rDNA sequencing. In the present study, we tested the performance of CMg in 34 patients (94 samples) with suspected BJIs, as compared to culture and 16S rDNA sequencing. A total of 94 samples from 34 patients with suspicion of BJIs, recruited from two sites, were analyzed by (i) conventional culture, (ii) 16S rDNA sequencing (Sanger method), and (iii) CMg (Illumina Technology). Two negative controls were also sequenced by CMg for contamination assessment. Based on the sequencing results of negative controls, 414 out of 539 (76.7%) bacterial species detected by CMg were considered as contaminants and 125 (23.2%) as truly present. For monomicrobial infections (13 patients), the sensitivity of CMg was 83.3% as compared to culture, and 100% as compared to 16S rDNA. For polymicrobial infections (13 patients), the sensitivity of CMg was 50% compared to culture, and 100% compared to 16S rDNA. For samples negative in culture (8 patients, 21 samples), CMg detected 11 bacteria in 10 samples from 5 different patients. In 5/34 patients, CMg brought a microbiological diagnosis where conventional methods failed, and in 16/34 patients, CMg provided additional information. Finally, 99 antibiotic resistance genes were detected in 24 patients (56 samples). Provided sufficient genome coverage (87.5%), a correct inference of antibiotic susceptibility was achieved in 8/8 bacteria (100%). In conclusion, our study demonstrated that the CMg provides complementary and potentially valuable data to conventional methods of BJIs diagnosis.

Bacteremia Detection in Second or Subsequent Blood Cultures Among Hospitalized Patients in a Tertiary Care Hospital

This cohort study assesses the likelihood of detecting microbiological positivity or bacteremia in second or subsequent blood cultures among hospitalized patients while the first culture is still incubating after 24 hours.

Total Laboratory Automation for Rapid Detection and Identification of Microorganisms and Their Antimicrobial Resistance Profiles

At a time when diagnostic bacteriological testing procedures have become more complex and their associated costs are steadily increasing, the expected benefits of Total laboratory automation (TLA) cannot just be a simple transposition of the traditional manual procedures used to process clinical specimens. In contrast, automation should drive a fundamental change in the laboratory workflow and prompt users to reconsider all the approaches currently used in the diagnostic work-up including the accurate identification of pathogens and the antimicrobial susceptibility testing methods. This review describes the impact of TLA in the laboratory efficiency improvement, as well as a new fully automated solution for AST by disk diffusion testing, and summarizes the evidence that implementing these methods can impact clinical outcomes.

Changes in the gut bacterial communities in colon cancer surgery patients: an observational study

Background

Colon surgery has been shown to modulate the intestinal microbiota. Our objective was to characterize these changes using state-of-the-art next generation sequencing techniques.

Methods

We performed a single-centre prospective observational cohort study to evaluate the changes in the gut microbiota, i.e., taxon distribution, before and after elective oncologic colon surgery in adult patients with different antimicrobial prophylaxis regimens (standard prophylaxis with cefuroxime/metronidazole versus carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] carriers). We obtained rectal samples on the day of surgery, intraoperative luminal samples, and rectal or stoma samples 3 days after surgery. We performed metataxonomic analysis based on sequencing of the bacterial 16S rRNA gene marker. Similarities and differences between bacterial communities were assessed using Bray–Curtis similarity, visualised using principal coordinates analysis and statistically tested by PERMANOVA. Comparison of taxa relative abundance was performed using ANCOM.

Results

We included 27 patients between March 27, 2019 and September 17, 2019. The median age was 63.6 years (IQR 56.4–76.3) and 44% were females. Most (81%) patients received standard perioperative prophylaxis as they were not ESBL carriers. There was no significant association between ESBL carriage and differences in gut microbiome. We observed large and significant increases in the genus Enterococcus between the preoperative/intraoperative samples and the postoperative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae.

Conclusion

This hypothesis-generating study showed rapid changes in the rectal microbiota following colon cancer surgery.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00477-7.

Mycobacterium chelonae Infection Identified by Metagenomic Next-Generation Sequencing as the Probable Cause of Acute Contained Rupture of a Biological Composite Graft-A Case Report

We present the case of a 72-year-old female patient with acute contained rupture of a biological composite graft, 21 months after replacement of the aortic valve and the ascending aorta due to an aortic dissection. Auramine-rhodamine staining of intraoperative biopsies showed acid-fast bacilli, but classical culture and molecular methods failed to identify any organism. Metagenomic analysis indicated infection with Mycobacterium&nbsp;chelonae, which was confirmed by target-specific qPCR. The complexity of the sample required a customized bioinformatics pipeline, including cleaning steps to remove sequences of human, bovine ad pig origin. Our study underlines the importance of multiple testing to increase the likelihood of pathogen identification in highly complex samples.

Nontuberculous Mycobacteria under Scrutiny in the Geneva Area (2015-2020)

BACKGROUND

Nontuberculous mycobacteria (NTM) are increasingly identified in industrialized countries, and their role as pathogens is more frequently recognized. The relative prevalence of NTM strains shows an important geographical variability. Thus, establishing the local relative prevalence of NTM strains is relevant and useful for clinicians.

METHODS

Retrospective analysis (2015-2020) of a comprehensive database was conducted including all results of cultures for mycobacteria in a University Hospital (Geneva, Switzerland), covering a population of approximately 500,000 inhabitants. All NTM culture-positive patients were included in the analyses. Patients' characteristics, NTM strains, and time to culture positivity were reported.

RESULTS

Among 38,065 samples analyzed during the study period, 411 were culture-positive for NTM, representing 236 strains, and 231 episodes of care which occurred in 222 patients. Patients in whom NTM were identified were predominantly female (55%), with a median age of 62 years, and a low BMI (median: 22.6 kg/m2). The Mycobacterium avium complex (MAC) was the most frequently identified group (37% of strains) followed by Mycobacterium gordonae (25%) and Mycobacterium xenopi (12%) among the slowly growing mycobacteria (SGM), while the Mycobacterium chelonae/abscessus group (11%) were the most frequently identified rapidly growing mycobacteria (RGM). Only 19% of all patients were treated, mostly for pulmonary infections: the MAC was the most frequently treated NTM (n = 19, 43% of cases in patients treated) followed by RGM (n = 15, 34%) and M. xenopi (n = 6, 14%). Among those treated, 23% were immunosuppressed, 12% had pulmonary comorbidities, and 5% systemic comorbidities. Cultures became positive after a median of 41 days (IQR: 23; 68) for SGM and 28 days (14; 35) for RGM.

CONCLUSIONS

In Western Switzerland, M. avium and M. gordonae were the most prevalent NTM identified. Positive cultures for NTM led to a specific treatment in 19% of subjects. Patients with a positive culture for NTM were mostly female, with a median age of 62 years, a low BMI, and a low prevalence of immunosuppression or associated severe comorbidities.

Gut barrier and microbiota changes with glycine and branched-chain amino acid supplementation in chronic haemodialysis patients

BACKGROUND

We have previously shown that glycine increases fat-free mass in chronic haemodialysis patients with features of malnutrition as compared with branched-chain amino acids (BCAAs). This multicentre randomized double-blind crossover study evaluates the impact of these amino acids on the gut barrier and microbiota.

METHODS

Haemodialysis patients were included if they had plasma albumin <38 g/L or weight loss >5% of dry body weight, and daily dietary intakes <30 kcal/kg and <1 g protein/kg. They consumed glycine or BCAA (7 g twice daily) for 4 months and underwent a 1 month washout period, before crossover of supplementations. Faecal microbiota (16S rRNA gene sequencing) and immunoglobulin A (IgA), serum levels of cytokines, surrogate markers of intestinal permeability, appetite mediators, and endocannabinoids were obtained at the start and end of each supplementation. Supplementations were compared by multiple mixed linear regression models, adjusted for age, sex, month of supplementation (0 and 4 in each period), and period (Period 1: first 4 months; Period 2: last 4 months). Microbiota comparisons were performed using principal coordinate analysis and permutational multivariate analysis of variance, Shannon diversity index estimate and analysis of composition of microbiomes analysis, and Wilcoxon tests.

RESULTS

We analysed 27 patients compliant to the supplementations. Multiple mixed linear regression models were significant only for interleukin-6 (P = 0.002), glucagon-like peptide 1 (P = 0.028), cholecystokinin (P = 0.021), and peptide YY (P = 0.002), but not for the other outcomes. The significant models did not show any impact of the type of supplementation (P < 0.05 in all models). Principal coordinate analysis and permutational multivariate analysis of variance (P = 0.0001) showed strong microbiota clustering by subject, but no effect of the amino acids. Bacterial alpha diversity and zero-radius operational taxonomic unit richness remained stable, whatever the supplementation. Lacticaseibacillus paracasei (0.030; Q1-Q3 0.008-0.078 vs. 0.004; Q1-Q3 0.001-0.070) and Bifidobacterium dentium (0.0247; Q1-Q3 0.002-0.191 vs. 0.003; Q1-Q3 0.001-0.086) significantly decreased with the BCAA supplementation.

CONCLUSIONS

The BCAA and glycine supplementations had no impact on the serum levels of cytokines, appetite mediators, intestinal permeability, endocannabinoids, or faecal IgA. Overall faecal microbiota composition and microbial diversity did not change with the glycine or BCAA supplementation but decreased the abundance of L. paracasei and B. dentium.

Glycine increases fat-free mass in malnourished haemodialysis patients: a randomized double-blind crossover trial

BACKGROUND

Protein energy wasting is associated with negative outcome in patients under chronic haemodialysis (HD). Branched-chain amino acids (BCAAs) may increase the muscle mass. This post hoc analysis of a controlled double-blind randomized crossover study assessed the impact of BCAAs on nutritional status, physical function, and quality of life.

METHODS

We included 36 chronic HD patient features of protein energy wasting as plasma albumin <38 g/L, and dietary intakes <30 kcal/kg/day and <1 g protein/kg/day. Patients received either oral BCAA (2 × 7 g/day) or glycine (2 × 7 g/day) for 4 months (Period 1), followed by a washout period of 1 month, and then received the opposite supplement (Period 2). The outcomes were lean body mass measured by dual-energy X-ray absorptiometry, fat-free mass index measured by bioelectrical impedance, resting energy expenditure, dietary intake and appetite rating, physical activity and function, quality of life, and blood parameters. Analyses were performed by multiple mixed linear regressions including type of supplementation, months, period, sex, and age as fixed effects and subjects as random intercepts.

RESULTS

Twenty-seven patients (61.2 ± 13.7 years, 41% women) were compliant to the supplementations (consumption >80% of packs) and completed the study. BCAA did not affect lean body mass index and body weight, but significantly decreased fat-free mass index, as compared with glycine (coeff -0.27, 95% confidence interval -0.43 to -0.10, P = 0.002, respectively). BCAA and glycine intake had no effect on the other clinical parameters, blood chemistry tests, or plasma amino acids.

CONCLUSIONS

Branched-chain amino acid did not improve lean body mass as compared with glycine. Unexpectedly, glycine improved fat-free mass index in HD patients, as compared with BCAA. Whether long-term supplementation with glycine improves the clinical outcome remains to be demonstrated.

Metataxonomic and Metabolic Impact of Fecal Microbiota Transplantation From Patients With Pancreatic Cancer Into Germ-Free Mice: A Pilot Study

Background

Body weight (BW) loss is prevalent in patients with pancreatic cancer (PC). Gut microbiota affects BW and is known to directly shape the host immune responses and antitumor immunity. This pilot study evaluated the link between gut microbiota, metabolic parameters and inflammatory/immune parameters, through the fecal material transplantation (FMT) of PC patients and healthy volunteers into germ-free (GF) mice.

Methods

We transplanted the feces from five PC patients and five age- and gender-matched healthy volunteers into two GF mice each. Mouse BW and energy intake were measured every 1-5 days, oral glucose on day 21, insulin tolerance on day 26, fecal bacterial taxonomic profile by 16S rRNA gene sequencing on day 5, 10, 15 and 30, and gut-associated lymphoid tissue T cells, plasma cytokines and weights of fat and muscle mass at sacrifice (day 34). Results are presented as mean ± SD. The continuous parameters of mice groups were compared by linear univariate regressions, and their bacterial communities by Principal Coordinates Analysis (PCoA), Bray-Curtis similarity and ANCOM test.

Results

Recipients of feces from PC patients and healthy volunteers had similar BW gain and food intake. Visceral fat was lower in recipients of feces from PC patients than from healthy individuals (0.72 ± 0.17 vs. 0.92 ± 0.14 g; coeff -0.19, 95% CI -0.38, -0.02, p=0.035). The other non-metataxonomic parameters did not differ between groups. In PCoA, microbiota from PC patients clustered apart from those of healthy volunteers and the same pattern was observed in transplanted mice. The proportions of Clostridium bolteae, Clostridium scindens, Clostridium_g24_unclassified and Phascolarctobacterium faecium were higher, while those of Alistipes obesi, Lachnospiraceae PAC000196_s and Coriobacteriaceae_unclassified species were lower in PC patients and in mice transplanted with the feces from these patients.

Conclusion

In this pilot study, FMT from PC patients was associated with a decrease in visceral fat as compared to FMT from healthy individuals. Some of the differences in fecal microbiota between PC and control samples are common to humans and mice. Further research is required to confirm that feces contain elements involved in metabolic and immune alterations.

Staphylococcusaureus Transcriptome Data and Metabolic Modelling Investigate the Interplay of Ser/Thr Kinase PknB, Its Phosphatase Stp, the glmR/yvcK Regulon and the cdaA Operon for Metabolic Adaptation

Serine/threonine kinase PknB and its corresponding phosphatase Stp are important regulators of many cell functions in the pathogen S. aureus. Genome-scale gene expression data of S. aureus strain NewHG (sigB⁺) elucidated their effect on physiological functions. Moreover, metabolic modelling from these data inferred metabolic adaptations. We compared wild-type to deletion strains lacking pknB, stp or both. Ser/Thr phosphorylation of target proteins by PknB switched amino acid catabolism off and gluconeogenesis on to provide the cell with sufficient components. We revealed a significant impact of PknB and Stp on peptidoglycan, nucleotide and aromatic amino acid synthesis, as well as catabolism involving aspartate transaminase. Moreover, pyrimidine synthesis was dramatically impaired by stp deletion but only slightly by functional loss of PknB. In double knockouts, higher activity concerned genes involved in peptidoglycan, purine and aromatic amino acid synthesis from glucose but lower activity of pyrimidine synthesis from glucose compared to the wild type. A second transcriptome dataset from S. aureus NCTC 8325 (sigB⁻) validated the predictions. For this metabolic adaptation, PknB was found to interact with CdaA and the yvcK/glmR regulon. The involved GlmR structure and the GlmS riboswitch were modelled. Furthermore, PknB phosphorylation lowered the expression of many virulence factors, and the study shed light on S. aureus infection processes.

Hydrogen Peroxide Affects Growth of S. aureus Through Downregulation of Genes Involved in Pyrimidine Biosynthesis

Reactive oxygen species (ROS) play a crucial role in the cellular defense against S. aureus, as evidenced by the importance of this pathogen in patients lacking the ROS-generating phagocyte NADPH oxidase NOX2. ROS concentrations required to kill S. aureus in vitro are much higher than those found in the phagosome. We therefore hypothesized that sublethal ROS concentrations may play a role in S. aureus gene dysregulation and investigated the in vitro transcriptomic response of S. aureus to sublethal concentrations of hydrogen peroxide (H₂O₂). A striking observation of these experiments was a coordinated and massive downregulation of genes involved in pyrimidine metabolism. Using transposon insertion mutants, we demonstrated that deletion of carA, a gene involved in pyrimidine synthesis, led to a significant growth defect and to an increased sensitivity of S. aureus to added H₂O₂. The phenotype of the carA mutant could be reversed through supplementation with the pyrimidine precursor uracil, or with a multicopy vector encoding carA. As opposed to the impact of ROS on extracellular survival, carA deletion did not affect the intracellular survival in neutrophils. Our results raise the possibility that ROS-dependent downregulation of pyrimidine metabolism might be a survival strategy of S. aureus, allowing colonization through intracellular survival, while decreasing the risk of killing the host through dampened extracellular growth.

Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial

Background

Shortening antibiotic-treatment durations is a key recommendation of antibiotic-stewardship programmes, yet it is based on weak evidence. We investigated whether halving antibiotic courses would reduce antibiotic-resistance genes (ARG) in the intestinal microbiomes of patients treated for gram-negative bacteraemia.

Methods

This nested prospective cohort study included adult patients hospitalized at Geneva University Hospitals (Switzerland) participating in the PIRATE randomized trial assessing non-inferiority of shorter antibiotic courses (7 versus 14 days) for gram-negative bacteraemia (‘cases’) and, simultaneously, hospitalized patients with similar demography and comorbidity yet no antibiotic therapy (‘controls’). Stool was collected from case and control patients on days 7, 14, 30 and 90 after antibiotic initiation (day 1) and days 7 and 14 after admission, respectively, and analysed by whole-metagenome shotgun sequencing. The primary outcome was ARG abundance at day 30; secondary outcomes included microbiota-species composition and clustering over time.

Findings

Forty-five patients and 11 controls were included and evaluable; ARG analyses were conducted on the 29 per-protocol patients receiving 7 (±2) days or 14 (±3) days of antibiotic therapy. At day 30, ARGs were not detected at similar abundance in patients receiving 7 and 14 days (median counts/million [mCPM]: 96 versus [vs] 71; p=.38). By day 30, total ARG content between both groups was not significantly different from that of controls at D7 (362 and 370 mCPM vs 314 mCPM, p=.24 and 0.19). There were no significant differences amongst antibiotic-treated patients at any timepoint in bacterial diversity or clustering, but Shannon species diversity was significantly reduced compared to controls through day 14 (median 3.12 and 3.24 in the 7-day and 14-day groups vs 3.61 [controls]; p=.04 and 0.012). Patients treated for 14 days had reduced faecal phage content during and after therapy compared to other patient groups.

Interpretation

Reducing antibiotic durations by half did not result in decreased abundance of ARGs in patients treated for gram-negative bacteraemia, nor did it improve microbiota species diversity.

Funding

The study was funded by the University of Geneva's Louis-Jeantet Foundation (grant no. S04_12) and the Swiss National Science Foundation (NRP Smarter Healthcare, grant no. 407,440_167359).

Outbreak of Pseudomonas aeruginosa producing VIM carbapenemase in an intensive care unit and its termination by implementation of waterless patient care

BACKGROUND

Long-term outbreaks of multidrug-resistant Gram-negative bacilli related to hospital-building water systems have been described. However, successful mitigation strategies have rarely been reported. In particular, environmental disinfection or replacement of contaminated equipment usually failed to eradicate environmental sources of Pseudomonas aeruginosa.

METHODS

We report the investigation and termination of an outbreak of P. aeruginosa producing VIM carbapenemase (PA-VIM) in the adult intensive care unit (ICU) of a Swiss tertiary care hospital with active case finding, environmental sampling and whole genome sequencing (WGS) of patient and environmental strains. We also describe the implemented control strategies and their effectiveness on eradication of the environmental reservoir.

RESULTS

Between April 2018 and September 2020, 21 patients became either infected or colonized with a PA-VIM strain. For 16 of them, an acquisition in the ICU was suspected. Among 131 environmental samples collected in the ICU, 13 grew PA-VIM in sink traps and drains. WGS confirmed the epidemiological link between clinical and environmental strains and the monoclonal pattern of the outbreak. After removing sinks from patient rooms and implementation of waterless patient care, no new acquisition was detected in the ICU within 8 months after the intervention.

DISCUSSION

Implementation of waterless patient care with removal of the sinks in patient rooms was successful for termination of a PA-VIM ICU outbreak linked to multiple environmental water sources. WGS provides highly discriminatory accuracy to investigate environment-related outbreaks.

Time to Detection of Growth for Mycobacterium tuberculosis in a Low Incidence Area

Background

Diagnosis of Mycobacterium tuberculosis (MTB) infection can be confirmed by Xpert assays within hours. However, when sample size does not allow performing both culture and Xpert, or if Xpert is negative, then formal diagnosis of MTB relies on culture and time to detection of growth (TDG) becomes critical for clinical management.

Objectives

To determine TDG in Xpert negative samples, or in samples in which Xpert could not be performed, in a low-incidence area for MTB.

Methods

Retrospective analysis (2015-2020) of a database including all cultures for mycobacteria in a University Hospital covering approximately 500'000 inhabitants. Analysis was restricted to culture positive (C+) samples for MTB for which 1/Xpert was negative or could not be performed because of limited sample volume, and 2/collected from subjects treated less than 24 hours. TDG was analyzed according to microscopy, origin of sample (pulmonary or not) and presence of cavitation.

Results

Among 837 C+ samples for MTB, 236 samples (80% of respiratory origin) from 147 patients fulfilled study criteria; 78 samples (49 patients, 33%) were acid-fast bacilli (AFB) positive. Median (IQR) TDG was 25 (17; 40) days for all samples. TDG exceeded 28 days in 43% of samples and was significantly shorter in AFB+ vs AFB- samples, and samples from cavitary vs non cavitary or extra-thoracic disease.

Conclusions

In Xpert negative samples, or samples for which Xpert could not be performed, TDG exceeded 4 weeks in 43% of samples. AFB+ and samples from cavitary lung disease had a significantly shorter TDG.

The human gut mycobiome and the specific role of Candida albicans: where do we stand, as clinicians?

BACKGROUND

The so-called 'mycobiome' has progressively acquired interest and increased the complexity of our understanding of the human gut microbiota. Several questions are arising concerning the role of fungi (and in particular of Candida albicans), the so-called 'mycobiome', that has been neglected for a long time and only recently gained interest within the scientific community. There is no consensus on mycobiome normobiosis because of its instability and variability. This review aims to raise awareness about this interesting topic and provide a framework to guide physicians faced with such questions.

OBJECTIVES

To summarize current knowledge and discuss current and potential implications of the mycobiome in clinical practice.

SOURCES

We performed a review of the existing literature in Medline Pubmed.

CONTENT

This review identifies several studies showing associations between specific mycobiome profiles and health. Fungi represent a significant biomass within the microbiota and several factors, such as diet, sex, age, co-morbidities, medications, immune status and inter-kingdom interactions, can influence its structure and population. The human gut mycobiota is indeed a key factor for several physiological processes (e.g. training of the immune system against infections) and pathological processes (e.g. immunological/inflammatory disorders, inflammatory bowel diseases, metabolic syndromes). Moreover, the mycobiome (and C. albicans in particular) could influence an even broader spectrum of conditions such as psychiatric diseases (depression, schizophrenia, bipolar disorder) or chronic viral infections (human immunodeficiency virus, hepatitis B virus); moreover, it could be implicated in tumorigenesis.

IMPLICATIONS

Candida albicans is a well-known opportunistic pathogen and a major component of the mycobiome but its role in the gastrointestinal tract is still poorly understood. From a potential screening biomarker to a key factor for several pathological processes, its presence could influence or even modify our clinical practice.

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.

Case Report: About a Case of Hyperammonemia Syndrome Following Lung Transplantation: Could Metagenomic Next-Generation Sequencing Improve the Clinical Management?

Background: Mycoplasma hominis and Ureaplasma spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients. Results: A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of M. hominis and Ureaplasma spp. and specific PCRs were positive for M. hominis and Ureaplasma parvum. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The Mycoplasma/Ureaplasma culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of Staphylococcus aureus and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to Corynebacterium propinquum (34.7%), S. aureus (24.1%) and Staphylococcus epidermidis (17.1%). Reads assigned to M. hominis, Ureaplasma urealyticum and parvum represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 10³, 9.7 × 10², and 3.7 × 10² genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection. Conclusions: mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.

Temporal and regional incidence of carbapenemase-producing Enterobacterales, Switzerland, 2013 to 2018

IntroductionIn contrast to countries where carbapenemase-producing Enterobacterales (CPE) are endemic, only sporadic cases were reported in Switzerland until 2013. An aggravation of the epidemiological situation in neighbouring European countries indicated the need for a surveillance study in Switzerland.AimWe aimed to describe CPE distributions in Switzerland and identify epidemiological factors associated with changes in incidence.MethodsData on all human CPE isolates from 2013 to 2018 were collected by the Swiss Centre for Antibiotic Resistance (ANRESIS) and analysed for temporal and regional trends by Generalised Poisson regression. Isolates associated with infection or colonisation were included in a primary analysis; a secondary analysis included invasive isolates only. Statistical detection of regional clusters was performed with WHONET/SaTScan.ResultsWe analysed 731 CPE isolates, of which 325 (44.5%) were associated with screenings and 173 (23.7%) with infections. Yearly detection of CPE isolates increased considerably during the study period from 65 to 212. The most frequently isolated species were Klebsiella pneumoniae (54%) and Escherichia coli (28%). The most frequent genotypes were OXA-48 (43%), KPC (21%) and NDM (14%). In contrast to the French-speaking parts of Switzerland (West, Geneva) where OXA-48 were the predominant genotypes (around 60%), KPC was the most frequently detected genotype in the Italian-speaking region (63%). WHONET/SaTScan outbreak detection analysis identified seven clusters in five regions of Switzerland.ConclusionsIn a first continuous surveillance of CPE in Switzerland, we found that the epidemiological situation aggravated nationwide and that regional patterns of CPE genotypes mirrored the situation in neighbouring European countries.

Dynamic assessment of the impact of gut microbiota transfer in a mouse model of chronic intestinal dysbiosis

Objective

There is growing evidence supporting that the gut microbiota is a major driver of human health and disease. While gut microbiota transfer (GMT) is commonly used as an approach to restore "eubiosis", there is a surprising lack of data on whether the transferred microbiota efficiently and durably repopulate the gut of the transplanted subject. Moreover, little is known on the effects of GMT on non-alcoholic fatty liver disease (NAFLD).

Methods

Chronic dysbiosis and NAFLD-like liver injury were induced by feeding C57Bl/6j mice for 16 weeks with a high-fat diet. For GMT, dysbiotic mice underwent preliminary gut cleansing, followed by oral gavage with a suspension of fresh fecal matter procured from a pool of lean mice (1 dose, or 10 doses). We next characterized microbiota composition and we measured the relative abundance of specific pathobionts in recipient mice, using high-throughput shotgun analysis in a dynamic manner, over time. All experiments took place in a specific germ-free environment.

Results

After 4 months on a high-fat diet, mice displayed fatty liver infiltration with moderate parenchymal inflammatory changes. Dysbiosis was evidenced by a reduced bacterial diversity, as well as a dramatically increased abundance of Firmicutes, and lower Verrucomicrobia and Actinobacteria. Gut microbiota transfer was associated with a transitory reduction in NAFLD-induced hepatocellular injury. While dysbiotic mice displayed a shift in their microbiota composition towards that of lean donors after GMT, this effect rapidly faded after one week, and mice recovered their initial, dysbiotic microbiota.

Conclusion

The current study indicates that, when used in mice with chronically established dysbiosis, GMT is merely associated with transitory changes in gut microbiota composition, as well as significant but moderate reduction in hepatocellular injury.

Mapping of aetiologies and clinical presentation of acute colitis: Results from a prospective cohort study in a tertiary centre

Objective

Our objective was to describe the aetiologies of acute colitis and to identify patients who require diagnostic endoscopy.

Methods

Patients with symptoms of gastrointestinal infection and colonic inflammation on computed tomography were prospectively included. Those immunosuppressed, with history of colorectal cancer or inflammatory bowel disease (IBD) were excluded. Stools were screened with BD-Max and BioFire FilmArray GI panel. Faecal calprotectin was determined. Patients with negative BD-Max underwent colonoscopy. The study was registered into clinicaltrials.gov (NCT02709213).

Results

One hundred and seventy-nine patients were included. BD-Max was positive in 93 patients (52%) and FilmArray in 108 patients (60.3%). Patients with infectious colitis (n = 103, 57.5%) were positive for Campylobacter spp (n = 57, 55.3%), Escherichia coli spp (n = 8, 7.8%), Clostridium difficile (n = 23, 22.3%), Salmonella spp (n = 9, 8.7%), viruses (n = 7, 6.8%), Shigella spp (n = 6, 5.8%), Entamoeba histolytica (n = 2, 1.9%) and others (n = 4, 3.9%). Eighty-six patients underwent colonoscopy, which was compatible with ischemic colitis in 18 patients (10.1%) and IBD in 4 patients (2.2%). Among patients with negative FilmArray, a faecal calprotectin &gt;625μg/g allowed identifying patients with IBD with an area under ROC curve of 85.1%. Introduction of a diagnostic management algorithm including FilmArray and faecal calprotectin could allow decreasing unnecessary colonoscopies from 82 to 29 (corresponding to a decrease of 64.6%).

Conclusion

Computed tomography-proven colitis was mostly of infectious aetiology. Diagnostic management of patients with acute colitis should include broad molecular testing of the stools and, in patients with a calprotectin concentration &gt;625μg/g, colonoscopy to exclude IBD.

Performances of automated digital imaging of Gram-stained slides with on-screen reading against manual microscopy

The objective of this study was to evaluate the performances of the automated digital imaging of Gram-stained slides against manual microscopy. Four hundred forty-three identified Gram-stained slides were included in this study. When both methods agreed, we considered the results as correct, and no further examination was carried out. Whenever the methods gave discrepant results, we reviewed the digital images and the glass slides by manual microscopy to avoid incorrectly read smears. The final result was a consensus of multiple independent reader interpretations. Among the 443 slides analyzed in this study, 101 (22.8%) showed discrepant results between the compared methods. The rates of discrepant results according to the specimen types were 5.7% (9/157) for positive blood cultures, 42% (60/142) for respiratory tract specimens, and 22% (32/144) for sterile site specimens. After a subsequent review of the discrepant slides, the final rate of discrepancies dropped to 7.0% (31/443). The overall agreement between the compared methods and the culture results reached 78% (345/443) and 79% (349/443) for manual microscopy and automated digital imaging, respectively. According to culture results, the specificity for automated digital imaging and manual microscopy were 90.8% and 87.7% respectively. In contrast, sensitivity was 84.1% for the two compared methods. The discrepant results were mostly encountered with microorganism morphologies of rare occurrence. The results reported in this study emphasize that on-screen reading is challenging, since the recognition of morphologies on-screen can appear different as compared to routine manual microscopy. Monitoring of Gram stain errors, which is facilitated by automated digital imaging, remains crucial for the quality control of reported Gram stain results.