Using MALDI-TOF MS typing method to decipher outbreak: the case of Staphylococcus saprophyticus causing urinary tract infections (UTIs) in Marseille, France.

Staphylococcus saprophyticus is one of the leading causes of urinary tract infections (UTI). In December 2014, our surveillance system identified an abnormal increase in S. saprophyticus causing UTIs in four university hospitals in Marseille, indicating a suspected community S. saprophyticus UTI outbreak. This was detected by our surveillance system BALYSES (Bacterial real-time Laboratory-based Surveillance System). S. saprophyticus/ Escherichia coli UTI ratio increased three-fold from 0.0084 in 2002 to 0.025 in December 2015 in Marseille with an abnormal peak in December 2014, and with an annual estimated ratio trend of 5.10-6 (p-value < 10-3). Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS) spectral analysis of strains was used to analyse strains cluster expansion, comparing strains from Marseille to those from Nice during the same period. MALDI-TOF MS spectral analysis revealed a geographical restricted clonal expansion of the strains clusters in Marseille as compared to Nice. Our finding suggests (i) a geographically restricted expansion of a specific S. saprophyticus strain clusters circulating in Marseille, and (ii) MALDI-TOF MS can be used as a cost-effective tool to investigate an outbreak.

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases.

Molecular tools have shown an added value in the diagnosis of infectious diseases, in particular for those caused by fastidious intracellular microorganisms, or in patients receiving antibiotics before sampling. If 16S rDNA amplification had been gradually implemented in microbiology laboratories, specific real-time polymerase chain reaction (PCR) would have permitted an increase in the sensitivity of molecular methods and a reduction of contamination. Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad. Among these samples, 81,476 PCRs were performed, of which 1,192 were positive. Molecular techniques detected intracellular microorganisms in 31.3 % of respiratory samples, 27.8 % of endocarditis samples and 51.9 % of adenitis samples. Excluding intracellular bacteria, 25 % of the positive samples in this series were sterile in culture. Conventional broad-range PCR permitted the identification of fastidious and anaerobic microorganisms, but specific real-time PCR showed a significant superiority in the diagnosis of osteoarticular infections, in particular for those caused by Kingella kingae and Staphylococcus aureus, and for endocarditis diagnosis, specifically when Streptococcus gallolyticus and Staphylococcus aureus were involved. The sensitivity of conventional broad-range PCR was 62.9 % concerning overall diagnoses for which both techniques had been performed. These findings should lead microbiologists to focus on targeted specific real-time PCR regarding the clinical syndrome. Finally, syndrome-driven diagnosis, which consists of testing a panel of microorganisms commonly involved for each syndrome, permitted the establishment of 31 incidental diagnoses.

Scalp eschar and neck lymphadenopathy after tick bite: an emerging syndrome with multiple causes.

The clinical and epidemiological features of 56 patients with scalp eschar associated with neck lymphadenopathy after a tick bite (SENLAT) syndrome were evaluated at the National French Rickettsial Center. Eschar swabs, crusts, and biopsies as well as ticks and blood samples were acquired for molecular and serological assays. SENLAT predominantly affects children (p < 0.05), followed by 40- to 70-year-olds, and it is found mostly in women (p < 0.05). The seasonal distribution has two peaks: one in the spring (55%) and one in the autumn (30%). The etiological agent was identified in 18 cases, which include Rickettsia slovaca in 13 cases with incidences of two co-infections with Rickettsia raoultii and one case caused by Rickettsia sibirica mongolitimonae. Other possible agents that were found in attached ticks were Candidatus R. rioja, Coxiella burnetii, and Borrelia burgdorferi. The tick vector was Dermacentor marginatus in almost all cases, with the exception of one case, in which Ixodes ricinus was identified as the vector. Our findings show that SENLAT is a clinical entity characterized as a local infection controlled by the immune system and is neither pathogen- nor vector-specific.

The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics.

Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.

Real-life requests for Bordetella polymerase chain reaction testing in children presenting to hospital.

From 2015 to 2017, 3197 interpretable Bordetella polymerase chain reaction (PCR) tests were performed for 2760 children presenting to our tertiary university hospital. Requests mainly came from the emergency department (62%) and for children older than 1 year (68%). Only 32 PCR (1%) results were positive, mainly in children younger than 1 year (n = 29/32, 90.6%; p<0.001). When focusing on the PCR indications in 2017, we found the requests were mainly based on nonspecific respiratory symptoms and were clinically unjustified in 383 cases (39%). Pediatricians overused Bordetella PCR in clinical practice. They should reserve their requests for cases of young children with symptoms suggestive of respiratory illness and/or incomplete pertussis immunization.

Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota.

Pseudoruminococcus massiliensis strain Marseille-P3876T (= CSUR P3876) is a new genus from the family Ruminococcaceae that was isolated from the gut microbiota of a healthy Senegalese man.

Dialister massiliensis sp. nov., a new bacterium isolated from the human gut.

Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual.

Clinical efficacy of chloroquine derivatives in COVID-19 infection: comparative meta-analysis between the big data and the real world.

In the context of the current coronavirus disease 2019 (COVID-19) pandemic, we conducted a meta-analysis on the effects of chloroquine derivatives in patients, based on unpublished and published reports available publicly on the internet as of 27 May 2020. The keywords 'hydroxychloroquine', 'chloroquine', 'coronavirus', 'COVID-19' and 'SARS-Cov-2' were used in the PubMed, Google Scholar and Google search engines without any restrictions as to date or language. Twenty studies were identified involving 105 040 patients (19 270 treated patients) from nine countries (Brazil, China, France, Iran, Saudi Arabia, South Korea, Spain and the USA). Big data observational studies were associated with conflict of interest, lack of treatment dosage and duration, and absence of favourable outcome. Clinical studies were associated with favourable outcomes and details on therapy. Among clinical studies, three of four randomized controlled trials reported a significant favourable effect. Among clinical studies, a significant favourable summary effect was observed for duration of cough (OR 0.19, p 0.00003), duration of fever (OR 0.11, p 0.039), clinical cure (OR 0.21, p 0.0495), death (OR 0.32, p 4.1 × 10-6) and viral shedding (OR 0.43, p 0.031). A trend for a favourable effect was noted for the outcome 'death and/or intensive care unit transfer' (OR 0.29, p 0.069) with a point estimate remarkably similar to that observed for death (∼0.3). In conclusion, a meta-analysis of publicly available clinical reports demonstrates that chloroquine derivatives are effective to improve clinical and virological outcomes, but, more importantly, they reduce mortality by a factor of 3 in patients with COVID-19. Big data are lacking basic treatment definitions and are linked to conflict of interest. The retraction of the only big data study associated with a significantly deleterious effect the day after (June 5, 2020) the acceptance of the present work (June 4, 2020) confirms the relevance of this work.

Corrigendum to 'Phoenicibacter congonensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman.

[This corrects the article DOI: 10.1016/j.nmni.2017.04.003.].

Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery.

A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T.

Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum.

Enterococcus timonensis sp. nov., strain Marseille-P2817T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).

Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result.

BACKGROUND: Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection. AIMS: We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing. SOURCES: A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source. CONTENT: Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered. IMPLICATIONS: The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.

'Massilimalia timonensis' sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol.

We describe the main characteristics of a new bacterial species 'Massilimalia timonensis' sp. nov. The type strain Marseille-P3753T (=CSUR P3753) was isolated from the stool of a healthy Senegalese man.

Escherichia coli spontaneous community-acquired meningitis in adults: A case report and literature review.

Gram-negative bacillary meningitis occurring post-trauma and following neurosurgical procedures has been described widely. However, reports of spontaneous cases are sparse, particularly community-acquired cases. Spontaneous community-acquired Escherichia coli meningitis is a rare (although increasingly seen) and specific entity that is poorly reported in the literature. A review of the literature identified only 43 cases of community-acquired E. coli meningitis reported between 1946 and 2016. This article describes two new cases of spontaneous community-acquired E. coli meningitis encountered in Marseille, France, and presents the results of a literature review on spontaneous community-acquired E. coli meningitis.

'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome.

We report the main characteristics of 'Enterococcus timonensis' strain Marseille-P2817T (CSUR P2817), 'Leptotrichia massiliensis' sp. nov., strain Marseille-P3007T (CSUR P3007), 'Actinomyces marseillensis' sp. nov., strain Marseille-P2818T (CSUR P2818), 'Actinomyces pacaensis' sp. nov., strain Marseille-P2985T (CSUR P2985), 'Actinomyces oralis' sp. nov., strain Marseille-P3109T (CSUR P3109), 'Actinomyces culturomici' sp. nov., strain Marseille-P3561T (CSUR P3561) and 'Gemella massiliensis' sp. nov., strain Marseille-P3249T (CSUR P3249) which were isolated from human sputum samples.

Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.

We present the description of Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.

Genome sequence and description of Paenibacillus ihuae strain GD6 sp. nov., isolated from the stool of a 62-year-old Frenchman.

Paenibacillus ihuae strain GD6 (=CSUR P892 = DSMZ 45751T) is the new type strain collected from the stool of a 69-year-old Frenchman admitted to an intensive care unit and receiving a 10-day course of imipenem at the time of stool collection. This is a Gram-positive, facultative anaerobic, rod-shaped bacterium. We describe here the features of this organism, together with its complete genome sequence and annotation. The genome size is 6 719 043 bp with 49.6% G+C content and contains 6211 protein-coding and 65 sRNA genes, including four 5S rRNA genes, one 16S rRNA gene and one 23S rRNA gene.

Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces.

Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.

"Intestinimonas massiliensis" sp. nov, a new bacterium isolated from human gut.

Here we report the main features of the proposed new bacterial species "Intestinimonas massiliensis" sp. nov. The type strain GD2T (CSUR = P1930) was isolated from the gut microbiota of a healthy patient using a culturomics approach combined with taxonogenomics.