Editorial for the Special Issue, 'Secondary Metabolites from Microorganisms or Microorganism-Host Interaction?'

In this Special Issue, there are 13 published papers from over 10 countries [...].

Diel variations in planktonic ciliate community structure in the northern South China Sea and tropical Western Pacific.

Though diel variations are geographically widespread phenomena among phytoplankton and zooplankton, knowledge is limited regarding diel variations in planktonic ciliate (microzooplankton) community structure. In this study, we analyzed diel variations in community structure of planktonic ciliates in the northern South China Sea (nSCS) and tropical Western Pacific (tWP). Hydrological characteristics during day and night were slightly different over both the nSCS and tWP, while ciliate average abundance at night was clearly higher than in the day in the upper 200 m. In both the nSCS and tWP, abundance proportions of large size-fraction (> 30 µm) aloricate ciliates at night were higher than in the day. While for tintinnids, abundance proportion of large lorica oral diameter at night were lower than in the day. The relationship between environmental factors and ciliate abundance pointed out that depth and temperature were main factors influencing aloricate ciliate and tintinnid in both day and night. For some dominant tintinnid species, chlorophyll a was another important factor influencing their diel vertical distribution. Our results provide fundamental data for better understanding the mechanisms of planktonic ciliate community diel variation in the tropical Western Pacific Ocean.

Investigation of healthcare-associated COVID-19 in a large French hospital group by whole-genome sequencing.

OBJECTIVES: Despite the quick implementation of infection prevention and control procedures and the use of personal protective equipment within healthcare facilities, many cases of nosocomial COVID-19 transmission have been reported. We aimed to estimate the frequency and impact of healthcare-associated COVID-19 (HA-COVID-19) and evaluate the contribution of whole-genome sequencing (WGS) in cluster investigation. METHODS: We estimated the frequency and mortality of HA-COVID-19 infections from September 1 to November 30, 2020, with a focus on the evolution of hospitalized community-associated COVID-19 (CA-COVID-19) cases and cases detected among healthcare workers (HCWs) within the Sorbonne University Hospital Group (Paris, France). We thoroughly examined 12 clusters through epidemiological investigations and WGS. RESULTS: Overall, 209 cases of HA-COVID-19 were reported. Evolution of HA-COVID-19 incidence closely correlated with the incidence of CA-COVID-19 and COVID-19 among HCWs. During the study period, 13.9 % of hospitalized patients with COVID-19 were infected in the hospital and the 30-day mortality rate of HA-COVID-19 was 31.5 %. Nosocomial transmission of SARS-CoV-2 led to clusters involving both patients and HCWs. WGS allowed the exclusion of one-third of cases initially assigned to a cluster. CONCLUSIONS: WGS analysis combined with comprehensive epidemiological investigations is essential to understand transmission routes and adapt the IPC response to protect both patients and HCWs.

Subcutaneous pantoprazole in an elderly, palliative care patient.

Proton pump inhibitors (PPIs) have become the agents of choice for acid-related diseases. In some clinical situations, PPI therapy by oral or intravenous route may be difficult especially among elderly and patients in palliative care. Off-label PPI subcutaneous injection could be the last alternative to improve patient relief, despite limited published data. We report a case of linitis plastica, peritoneal carcinomatosis and occlusive syndrome who suffered from painful regurgitations which rapidly improved after subcutaneous pantoprazole. No related adverse effects were observed during PPI therapy. Despite some limitations, this report suggests that off-label subcutaneous pantoprazole could be an interesting alternative route when intravenous infusion may be difficult or harmful for elderly and patients in palliative care. Nevertheless, clinical safety and efficiency data on larger populations are needed to validate this use in such population.

Pyogenic lung abscess in an infectious disease unit: a 20-year retrospective study.

BACKGROUND: Pyogenic lung abscesses are rare and poorly described infections. This study aimed to describe their prognostic factors. METHODS: We retrospectively included all patients hospitalized between 1 January 1998 and 1 June 2018, with an International Classification of Diseases, version 10 (IDC-10) diagnosis of pyogenic lung abscess, from the Diamm based medical records (Micro6, Nancy, France). Parasitic, fungal, or mycobacterial lung abscesses were excluded. RESULTS: A total of 64 patients were included. Abscesses were associated with immunosuppression in 28 patients, including HIV infection and immunosuppressive therapy for eight and 12 patients, respectively. Bacterial identification was obtained for 36 patients. Nine patients (14%) developed lung abscesses after hematogenous dissemination. They differed from bronchogenic abscesses by their younger age (p = 0.03), the absence of smoking or emphysema (p = 0.05), Staphylococcus aureus (p = 0.001) or Streptococcus spp. (p = 0.05) isolation, and the smaller size of their abscess (p = 0.02). Overall, evolution was marked by radiological sequelae (46.9%), relapse (12.5%), and death (4.8%). Radiological sequelae occurred more frequently during the course of bronchogenic abscesses (p = 0.02), particularly when they spontaneously discharged (p = 0.04). Relapses were more frequent in patients with emphysema (p = 0.04) and when Haemophilus influenzae was isolated (p = 0.04). In multivariate analysis, poor outcomes, including death, sequelae, and relapse occurred more frequently in patients who had bronchogenic abscess (p = 0.02), and in those who received antibiotics during less than 6 weeks (p = 0.05). CONCLUSION: A duration of antibiotic treatment of less than 6 weeks and bronchogenic presentation were globally associated with poor outcome of pyogenic lung abscesses. These data should be considered when proposing guidelines for the care of pyogenic lung abscesses.The reviews of this paper are available via the supplemental material section.

Broad-based SARS-CoV-2 testing program for healthcare workers in a primary care hospital in France.

A broad-based SARS-CoV-2 testing program for all symptomatic healthcare workers (HCWs) was implemented in Tenon hospital, Paris, France. From February 26 to April 22, 2020, 701 symptomatic HCWs were screened, of whom 247 (35.2%) tested positive for SARS-Cov-2. Myalgia, fever, anosmia and ageusia were associated with RT-PCR positivity. Testing of HCWs is an essential step toward control of the epidemic. Further studies could establish clinical algorithms for SARS-CoV-2 diagnosis to compensate for RT-PCR test and chest CT limits or unavailability.

Resolution of Viable and Membrane-Compromised Free Bacteria in Aquatic Environments by Flow Cytometry.

In aquatic environments, free heterotrophic bacteria play an extremely important role due to their high biomass, wide panel of metabolisms, and ubiquity, as well as the toxicity of certain species. This unit presents a nucleic-acid double-staining protocol (NADS) for flow cytometry that can distinguish fractions of viable, damaged, or membrane-compromised cells within the free-bacterial community. The NADS protocol is based on the simultaneous utilization of two nucleic acid stains-membrane-permeant SYBR Green and membrane-impermeant propidium iodide (PI). The efficiency of the double staining on fresh samples is magnified by the FRET from SYBR Green to PI when both are bound to the nucleic acids. Full quenching of SYBR Green fluorescence by PI identifies cells with a compromised membrane, partial quenching indicates cells with a slightly damaged membrane, and lack of quenching characterizes cells with an intact membrane. Samples do not require any pretreatment and this protocol can be performed almost anywhere. © 2018 by John Wiley & Sons, Inc.

Modelling Tetraselmis sp. growth-kinetics and optimizing bioactive-compound production through environmental conditions.

The aim of this study is to predict Tetraselmis cells growth-kinetic and to induce the synthesis of bioactive compounds (chlorophylls, carotenoids and starch) with high potential for biotechnological applications. Using the statistical criteria, the Baranyi-Roberts model has been selected to estimate the microalgae growth-kinetic values. The simultaneous effects of salinity, light intensity and pH of culture medium were investigated to maximize the production of total chlorophylls, carotenoids and starch. The optimal culture conditions for the production of these compounds were found using Box-Behnken Design. Results have shown that total chlorophyll and carotenoids were attained 21.6mg·g-1DW and 0.042mg·g-1DW, respectively. In addition, the highest starch content of 0.624g·g-1DW has been obtained at neutral pH with high irradiance (182µmolphotonsm-2 s-1) and low salinity (20). A highly correlation (R2 = 0.884) has been found between the gravimetric and flow cytometric measurements of chlorophyll content.

Clostridium difficile bacteremia: Report of two cases in French hospitals and comprehensive review of the literature.

We report two cases of bacteremia due to Clostridium difficile from two French hospitals. The first patient with previously diagnosed rectal carcinoma underwent courses of chemotherapy, and antimicrobial treatment, and survived the C. difficile bacteremia. The second patient with colon perforation and newly diagnosed lung cancer underwent antimicrobial treatment in an ICU but died shortly after the episode of C. difficile bacteremia. A review of the literature allowed the identification of 137 cases of bacteremia between July 1962 and November 2016. Advanced age, gastro-intestinal disruption, severe underlying diseases and antimicrobial exposure were the major risk factors for C. difficile bacteremia. Antimicrobial therapy was primarily based on metronidazole and/or vancomycin. The crude mortality rate was 35% (21/60).

Assessing ultraphytoplankton and heterotrophic prokaryote composition by flow cytometry in a Mediterranean lagoon.

In the eutrophic Ghar El Melh Lagoon (GML, Tunisia), the distribution of heterotrophic prokaryotes, pico- and nanophytoplankton was studied at five stations in November 2012 at the single cell level, along with environmental factors. Flow cytometry analysis of ultraplankton (<10 µm) resolved (i) two heterotrophic prokaryote groups, low and high nucleic acid contents (LNA and HNA, respectively), and (ii) eight to nine ultraphytoplankton groups (cryptophyte-like cells, two nanoeukaryote subgroups, two picoeukaryote subgroups and three Synechococcus-like cells subgroups). Prochlorococcus was not detected. According to redundancy analysis (RDA), a significant difference was found in the distribution of the ultraplankton between stations (F = 2.61, p < 0.05); maximum proliferations of heterotrophic prokaryotes were observed in the inner parts of the lagoon at stations 3, 4 and 5 affected by urban, agricultural and industrial discharges. Ultraphytoplankton concentrations were the highest near the outlet of the lagoon at stations 1 and 2 influenced by freshwater outflow and oligotrophic Mediterranean water inflow, respectively. At station 1, the large ultraphytoplankton concentration derives from the high abundance of cryptophyte-like cells favoured by the freshwater outflow whereas at station 2, the input of oligotrophic Mediterranean water enhanced the abundance of Synechococcus and picoeukaryotes at the expense of nanoeukaryotes. Two trophic regimes were thus differentiated in GML.

Universal versus targeted additional contact precautions for multidrug-resistant organism carriage for patients admitted to an intensive care unit.

BACKGROUND: Although additional contact precautions (ACPs) are routinely used to reduce cross-transmission of multidrug-resistant organisms (MDROs), the relevance of isolation precautions remains debated. We hypothesized that the collection of recognized risk factors for MDRO carriage on intensive care unit (ICU) admission might be helpful to target ACPs without increasing MDRO acquisition during ICU stays, compared with universal ACPs. MATERIALS AND METHODS: This is a sequential single-center observational study performed in consecutive patients admitted to a French medical and surgical ICU. During the first 6-month period, screening for MDRO carriage and ACPs were performed in all patients. During the second 6-month period, screening was maintained, but ACP use was guided by the presence of at least 1 defined risk factor for MDRO. RESULTS: During both periods, 33 (10%) and 30 (10%) among 327 and 297 admissions were, respectively, associated with a positive admission MDRO carriage. During both periods, a second screening was performed in 147 (45%) and 127 (43%) patients. Altogether, the rate of acquired MDRO (positive screening or clinical specimen) was similar during both periods (10% [n = 15] and 11.8% [n = 15], respectively; P = .66). CONCLUSIONS: The results of our study contribute to support the safety of an isolation-targeted screening policy on ICU admission compared with universal screening and isolation regarding the rate of ICU-acquired MDRO colonization or infection.

Enhanced lipid and biomass production by a newly isolated and identified marine microalga.

BACKGROUND: The increasing demand for microalgae lipids as an alternative to fish has encouraged researchers to explore oleaginous microalgae for food uses. In this context, optimization of growth and lipid production by the marine oleaginous V2-strain-microalgae is of great interest as it contains large amounts of mono-unsaturated (MUFAs) and poly-unsaturated fatty acids (PUFAs). METHODS: In this study, the isolated V2 strain was identified based on 23S rRNA gene. Growth and lipid production conditions were optimized by using the response surface methodology in order to maximize its cell growth and lipid content that was quantified by both flow cytometry and the gravimetric method. The intracellular lipid bodies were detected after staining with Nile red by epifluorescence microscopy. The fatty acid profile of optimal culture conditions was determined by gas chromatography coupled to a flame ionization detector. RESULTS: The phenotypic and phylogenetic analyses showed that the strain V2 was affiliated to Tetraselmis genus. The marine microalga is known as an interesting oleaginous species according to its high lipid production and its fatty acid composition. The optimization process showed that maximum cell abundance was achieved under the following conditions: pH: 7, salinity: 30 and photosynthetic light intensity (PAR): 133 µmol photons.m-2.s-1. In addition, the highest lipid content (49 ± 2.1% dry weight) was obtained at pH: 7, salinity: 37.23 and photosynthetic light intensity (PAR): 188 µmol photons.m-2.s-1. The fatty acid profile revealed the presence of 39.2% and 16.1% of total fatty acids of mono-unsaturated fatty acids (MUFAs) and poly-unsaturated fatty acids (PUFAs), respectively. Omega 3 (ω3), omega 6 (ω6) and omega 9 (ω9) represented 5.28%, 8.12% and 32.8% of total fatty acids, respectively. CONCLUSIONS: This study showed the successful optimization of salinity, light intensity and pH for highest growth, lipid production and a good fatty acid composition, making strain V2 highly suitable for food and nutraceutical applications.

Microbial composition and ecological features of phototrophic biofilms proliferating in the Moidons Caves (France): investigation at the single-cell level.

The authors investigated the microbial composition of phototrophic biofilms proliferating in a show cave using flow cytometry for the first time in such a context. Results are based on several biofilms sampled in the Moidons Caves (France) and concern both heterotrophic prokaryotes and autotrophic microorganisms. Heterotrophic microorganisms with low nucleic acid content were dominant in biofilms, as can be expected from the oligotrophic conditions prevailing within the cave. Analysis of the biofilm autotrophic components revealed the presence of several taxa, particularly the unicellular green algae Chlorella minutissima, specifically well adapted to this cave. Relationships between flow cytometry results and environmental variables determined in the cave were established and discussed so as to better understand biofilm proliferation processes in caves.

The Challenging Diagnosis of Non-Community-Acquired Pneumonia in Non-Mechanically Ventilated Subjects: Value of Microbiological Investigation.

BACKGROUND: Early recognition and an attempt at obtaining microbiological documentation are recommended in patients with non-community-acquired pneumonia (NCAP), whether hospital-acquired (HAP) or health care-associated (HCAP). We aimed to characterize the clinical features and microbial etiologies of NCAP to assess the impact of microbiological investigation on their management. METHODS: This was a prospective 1-y study in a university hospital with 141 non-mechanically ventilated subjects suspected of having HAP (n = 110) or HCAP (n = 31). RESULTS: Clinical criteria alone poorly identified pneumonia (misdiagnosis in 50% of cases). Microbiological confirmation was achievable in 80 subjects (57%). Among 79 microorganisms isolated, 28 were multidrug-resistant aerobic Gram-negative bacilli and group III Enterobacteriaceae and 6 were methicillin-resistant Staphylococcus aureus. Multidrug-resistant aerobic Gram-negative bacilli accounted for one third of the microorganisms in early-onset HAP and for 50% in late-onset HAP. Methicillin-resistant S. aureus was most often recovered from subjects with HCAP. Inappropriate empirical antibiotics were administered to 36% of subjects with confirmed pneumonia. Forty subjects were admitted to the ICU, 13 (33%) of whom died. Overall, 39 subjects (28%) died in the hospital. CONCLUSIONS: Integrating the microbiological investigation in the complex clinical diagnostic workup of patients suspected of having NCAP is mandatory. Respiratory tract specimens should be obtained whenever possible for appropriate management.

Spatial and seasonal variability of pico-, nano- and microphytoplankton at the bottom seawater in the north coast of Sfax, Eastern Mediterranean Sea.

In the frame of the Taparura Project, we studied the distribution of pico-, nano- and microphytoplankton communities in relation to environmental variables at 18 stations sampled during four coastal cruises conducted between October 2009 and July 2010 at the bottom, on the north coast of Sfax (Tunisia, Eastern Mediterranean Sea). The restoration effect on coastal ultraphytoplankton (<10 µm) and microphytoplankton (<200 µm) was investigated using conventional flow cytometry and inverted microscopy. Flow cytometry analysis of ultraphytoplankton resolved six groups (Prochlorococcus, Synechococcus, nanoeukaryotes and three distinct subgroups within picoeukaryotes). In addition to these autotrophic groups, two unknown groups were characterised on the north coast. Picophytoplankton abundance shifted from a summer dominance of Synechococcus to a dominance of picoeukaryotes and Prochlorococcus during spring. Nanoeukaryotes were the most abundant in spring. Microphytoplankton was resolved into five groups, labelled Bacillariophyceae, Dinophyceae, Cyanobacteriae, Euglenophyceae and Chlorophyceae. A total of 90 microphytoplankton species were identified in all stations, with an overwhelming abundance of large diatoms, a typical trait of benthic communities (Coscinodiscus sp., Grammatophora sp., Navicula sp., Pleurosigma sp., Striatella unipunctata …). Results collected in this study are favouring a beneficial impact on the ecosystem of the Sfax north coast restoration achieved by the Taparura Project.

Onset of the spring bloom in the northwestern Mediterranean Sea: influence of environmental pulse events on the in situ hourly-scale dynamics of the phytoplankton community structure.

Most of phytoplankton influence is barely understood at the sub meso scale and daily scale because of the lack of means to simultaneously assess phytoplankton functionality, dynamics and community structure. For a few years now, it has been possible to address this objective with an automated in situ high frequency sampling strategy. In order to study the influence of environmental short-term events (nutrients, wind speed, precipitation, solar radiation, temperature, and salinity) on the onset of the phytoplankton bloom in the oligotrophic Bay of Villefranche-sur-Mer (NW Mediterranean Sea), a fully remotely controlled automated flow cytometer (CytoSense) was deployed on a solar-powered platform (EOL buoy, CNRS-Mobilis). The CytoSense carried out single-cell analyses on particles (1-800 µm in width, up to several mm in length), recording optical pulse shapes when analyzing several cm(3). Samples were taken every 2 h in the surface waters during 2 months. Up to 6 phytoplankton clusters were resolved based on their optical properties (PicoFLO, Picoeukaryotes, Nanophytoplankton, Microphytoplankton, HighSWS, HighFLO). Three main abundance pulses involving the 6 phytoplankton groups monitored indicated that the spring bloom not only depends on light and water column stability, but also on short-term events such as wind events and precipitation followed by nutrient pulses. Wind and precipitation were also determinant in the collapse of the clusters' abundances. These events occurred within a couple of days, and phytoplankton abundance reacted within days. The third abundance pulse could be considered as the spring bloom commonly observed in the area. The high frequency data-set made it possible to study the phytoplankton cell cycle based on daily cycles of forward scatter and abundance. The combination of daily cell cycle, abundance trends and environmental pulses will open the way to the study of phytoplankton short-term reactivity to environmental conditions.

Seasonal distribution of ultraphytoplankton and heterotrophic prokaryotes in relation to abiotic variables on the north coast of Sfax after restoration.

The Taparura project was set up to restore the north Sfax coast (Tunisia) by shutting down the northern phosphate plant responsible for chronic pollution and uncontrolled phosphogypsum dumping. The restoration effect on coastal ultraphytoplankton (<10 µm) and heterotrophic prokaryotes was investigated using conventional flow cytometry over four successive seasons during 2009-2010. Cell concentrations were generally higher than values reported for the open sea, both in the western and eastern Mediterranean basins. One striking point was that chl a concentration on the north Sfax coast was unchanged after restoration but was still one order of magnitude higher than in the Gulf of Gabès. Restoration of pH, following the shutdown of the phosphate processing plants on the north coast, appeared to reach normal levels for seawater during the study, whereas seawater acidification persisted on the south coast where plants are still in operation. The largest ultraphytoplankton biomass was from an unknown cell group, whose identity and role needs to be established.

[A sheet for deciphering the cries of hospitalized elderly patients]. / La fiche Déclic de décryptage des cris chez le sujet âgé hospitalisé.

Crying out is not an insignificant act and it is important to fight against this misconception. Any caregiver can be confronted with this phenomenon with elderly hospitalised patients. Their cries must be understood, analysed and taken into account as they correspond to a particular situation experienced by the elderly patient. There are tools to help caregivers diagnose and reflect on this clinical context. This article presents the example of an interpretation sheet which can help caregivers decipher patients' cries.