Complete genome and description of Corynebacterium incognita sp. nov.: a new bacterium within the Corynebacterium genus.

In 2020, as part of the diagnosis in IHU-Méditerranée Infection Institute in Marseille (France) we isolated the new bacterial strain Marseille-3630T from a 7-year-old girl blood specimen (= CSUR: Q3630). Matrix-assisted desorption ionisation time-of-flight mass spectrometry failed to identify this isolate. Analysis of the 16S rRNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family Corynebacteriaceae in the phylum Actinobacteria. We described here its main phenotypic characteristics, genome sequence and annotation of Corynebacterium incognitum strain Marseille-3630T, a new member of the Corynebacterium genus, that we propose as type strain.

Draft genome and description of Microvirga mediterraneensis strain Marseille-Q2068T sp. nov., a new bacterium isolated from human healthy skin.

In 2019, by culturing a skin swab from the forehead of a 70-year-old healthy woman via the culturomics method, we isolated the new bacterial strain Marseille-Q2068T (= CSUR-Q2068). Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family Methylobacteriaceae in the phylum Proteobacteria. We describe here its main phenotypic characteristics, genome sequence and annotation of Microvirga mediterraneensis strain Marseille-Q2068T, a new member of the Microvirga genus, which we propose as the type strain.

Draft genome and description of Mixta mediterraneensis strain Marseille-Q2057T sp.nov., a new bacterium isolated from human healthy skin.

In 2019, by culturing a skin swab from the hand of a 30-year-old healthy woman using the culturomic method, we isolated the new bacterial strain Marseille-Q2057T (= CSUR-Q2057). Matrix-assisted desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S rRNA gene and Genome-to-Genome comparison suggested that this taxon belongs to a novel bacterial species within the family Erwiniaceae, phylum Proteobacteria. We describe here its main phenotypic characteristics, genome sequence and annotation of Mixta mediterraneensis strain Marseille-Q2057T, a new member of the Mixta genus, that we propose as type strain.

Draft genome and description of Chryseobacterium manosquense strain Marseille-Q2069T sp. nov., a new bacterium isolated from human healthy skin.

In 2019, by culturing a skin swab from the hand of a 35-year-old healthy woman using culturomics methods, we isolated the new bacterial strain Marseille-Q2069T =CSUR-Q2069. Matrix-assisted desorption/ionization time-of-flight mass spectrometry failed to identify this isolate. Analysis of the 16S rRNA gene and Genome-to-Genome comparison suggested that this taxon belongs to a novel bacterial species within the family Flavobacteriaceae in the phylum Bacteroidetes. We described here the main phenotypic characteristics, genome sequence and annotation of Chryseobacterium manosquense strain Marseille-Q2069T, a new member of the Chryseobacterium genus, that we propose as type strain.

Draft genome and description of Aeromicrobium phoceense strain Marseille-Q0843T sp. nov., a new bacterium isolated from human healthy skin.

In 2019, by culturing a skin swab sample from the back of the hand of a 61-year-old healthy woman and assessing it via the culturomics method, we isolated the new bacterial strain Marseille-Q0843T (= CSUR-Q0843). Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-genome comparison suggested that this taxon belongs to a novel bacterial species within the family in Nocardioidaceae in the phylum Actinobacteria. We describe here the main phenotypic characteristics, genome sequence and annotation of Aeromicrobium phoceense strain Marseille-Q0843T, a new member of the Aeromicrobium genus, which we propose as the type strain.

Draft genome and description of Corynebacterium haemomassiliense strain Marseille-Q3615T sp. nov., a new bacterium isolated from a 59-year-old man with chronic obstructive pulmonary disease symptoms.

In 2020, as part of a diagnosis attempt at IHU Méditerranée Infection in Marseille (France), a blood specimen was obtained from a 59-year-old man with chronic obstructive pulmonary disease symptoms, from which we isolated the new bacterial Corynebacterium haemomassiliense strain Marseille-Q3615T. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S ribosomal RNA gene and genome-to-Genome comparison suggested that this taxon belongs to a novel bacterial species within the family Corynebacteriaceae in the phylum Actinobacteria. We describe the main phenotypic characteristics, genome sequence and annotation of Corynebacterium haemomassiliense strain Marseille-Q3615T, a new member of the Corynebacterium genus, which we propose as the type strain.

Aminoglycosides in critically ill patients: which dosing regimens for which pathogens?

Modifications of antibiotic pharmacokinetic parameters have been reported in critically ill patients, resulting in a risk of treatment failure. We aimed to determine optimised amikacin (AMK), gentamicin (GEN) and tobramycin (TOB) intravenous dosing regimens in this patient population. Patients admitted to the medical ICU and treated with AMK, GEN or TOB were included. Analyses were performed using a parametric population approach. Monte Carlo simulations were performed and the probability of target attainment (PTA) was calculated using Cmax/MIC ≥ 8 and trough concentrations as targets. A total of 117 critically ill hospitalised patients were studied. Median values (interindividual variability, É·2) of clearance were 3.51 (0.539), 3.53 (0.297), 2.70 (0.339) and 5.07 (0.339) L/h for AMK, GEN, TOB, and TOB in cystic fibrosis (CF), respectively. Median values (É·2) of central volume of distribution were 30.2 (0.215), 20.0 (0.109) and 25.6 (0.177) L for AMK, GEN and TOB, respectively. Simulations showed that doses should be adjusted to actual body weight and creatinine clearance (CLCR) for AMK and GEN, and according to CLCR and presence of CF for TOB. In conclusion, our recommendations for treating Pseudomonas aeruginosa infections in this population include using initial doses of 35 mg/kg for AMK or 10 mg/kg for TOB (CF and non-CF patients). GEN demonstrated the best rates of target attainment against Staphylococcus aureus infections with a dose of 5 mg/kg. As high aminoglycoside doses are required in this population, efficacy and safety targets are conflicting and therapeutic drug monitoring remains an important tool to manage this issue.

Peripherally inserted central catheters: a hidden emerging cause of infection outbreaks.

In our institution, between January 2010 and December 2017, 15 140 peripherally inserted central catheters (PICCs) were inserted in 12 314 patients. Using time-series analysis to evaluate the annual historical trend (AHT), we observed a significant increase in bloodstream infections (BSIs; AHT = 24; p < 0.001) and associated deaths (AHT = 3; p 0.02) in patient with PICCs. The risk of experiencing a BSI was significantly higher in patients with PICCs (odds ratio = 9.6; 95% confidence interval, 9.08-10.18; p < 0.001). To reduce PICC-related BSIs and their related mortality, it is important to limit the overuse of PICCs and to implement a 'no PICC' policy by limiting the insertion of PICCs to situations without other available options.

Mediastinitis in the intensive care unit patient: a narrative review.

BACKGROUND: Mediastinitis is a rare but severe infection, defined as an inflammation of the connective tissues and structures within the mediastinum. Due to its proximity to vital structures, mediastinitis represents a highly morbid pathological process associated with a high risk of mortality. In most cases mediastinitis requires treatment in the intensive care unit. OBJECTIVES: To highlight to the reader the clinical features of mediastinitis, to attempt to define each clinical scenario, to describe the responsible pathogens and finally to depict both the medical and surgical treatments. SOURCES: We performed a literature search of the PubMed and Cochrane libraries, limited for articles published between January 2003 and December 2018, reporting on acute mediastinitis. CONTENT: The term covers different entities of different aetiologies including deep sternal wound infection related to sternotomy; oesophageal perforation or anastomosis leakage; and finally descending necrotizing mediastinitis, often secondary to oropharyngeal abscess. The responsible pathogens and therefore subsequent management depends on the underlying aetiology. Empirical antimicrobial therapy should cover the suspected microorganisms while surgery and supportive measures should aim to reduce the inoculum of pathogens by providing adequate drainage and debridement. IMPLICATIONS: Literature concerning mediastinitis in the intensive care unit is relatively scarce. We have collated the evidence and reviewed the different causes and treatment options of acute mediastinitis with a particular focus on microbiological epidemiology. Future research in larger cohorts is needed to better understand the treatment of this difficult disease.

Genome sequence and description of Coprococcus phoceensis gen. nov., sp. nov., a new bacterial genus isolated from the human left colon.

We report here the main characteristics of Coprococcus phoceensis strain Marseille-P3062T (CSUR P3062). The 16S rDNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum analysis were used to identify and characterize this new anaerobic bacterial species, which was isolated from the left colon cleansing of a 25-year-old French man with Crohn's disease.

'Selenomonas massiliensis,' a new anaerobic bacterial species isolated from human oral microbiota.

We report the main characteristics of 'Selenomonas massiliensis' sp. nov., strain Marseille-P4036T (= CSUR P4036). The culturomic combined with taxonogenomic methods were used to identify and characterize this new anaerobic bacterial species, which was isolated from an oral sample of a 25-year-old healthy woman.

'Bacteroides cutis,' a new bacterial species isolated from human skin.

We report the main characteristics of 'Bacteroides cutis' sp. nov., strain Marseille-P4118T (= CSUR P4118), a new species within the genus Bacteroides. This strain was isolated from a skin sample of a 75-year-old man from Marseille.

Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.

Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: 'Clostridium amazonitimonense' strain LF2T, 'Clostridium massilidielmoense' strain MT26T, 'Clostridium nigeriense' strain Marseille-P2414T and 'Clostridium merdae' strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

'Clostridium mediterraneense,' a new bacterial species isolated from the human gut.

We report the main characteristics of 'Clostridium mediterraneense' sp. nov., strain Marseille-P2434T (CSUR P2434), a new species within the genus Clostridium. This strain was isolated from the gut microbiota of a 66-year-old diabetic patient in Marseille, France.

Emergence of Clostridium difficile tcdC variant 078 in Marseille, France.

The purpose of this investigation was to evaluate the epidemiology of hypervirulent Clostridium difficile ribotypes from January 2013 to February 2017 in the Marseille area of southern France. By using the Xpert Clostridium difficile Epi polymerase chain reaction (PCR) assay and sequencing the tcdC gene, we characterised C. difficile isolates from symptomatic patients diagnosed with C. difficile infection (CDI) in Marseille university hospitals. We first tested retrospectively 278 C. difficile samples isolated from January 2013 to December 2014 and observed a high prevalence of isolates with tcdC mutations and deletions previously described in both hypervirulent ribotypes RT027 and RT078 (16.4% and 10.7%, respectively). We highlighted the co-circulation of these two hypervirulent C. difficile tcdC variants (tV) with distinct epidemiological characteristics. While an RT027 outbreak occurred mainly as healthcare-associated infection in the elderly, CDI caused by tV078 occurred mainly in a younger population as community-associated infection. From January 2016, a systematic survey of these two hypervirulent C. difficile ribotypes revealed the emergence of CDI caused by tV078, currently being more prevalent than RT027 in the Marseille area. The present study is the first report of the emergence of CDI caused by tV078 in southern France. We showed the simultaneous circulation and sequential spread of hypervirulent ribotypes, such as RT027 and tV078. This emphasises the need for an efficient surveillance system for CDI with ribotyping and an optimised management of CDI caused by hypervirulent strains.

Multi-spacer typing as an effective method to distinguish the clonal lineage of Clostridium butyricum strains isolated from stool samples during a series of necrotizing enterocolitis cases.

BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC cases involving four neonatal intensive care units. A clonal lineage of these strains was observed by in-silico multi-locus sequence typing. AIM: To confirm the previous findings by sequencing a larger number of C. butyricum genomes and using other genotyping approaches. METHODS: The previously isolated 15 C. butyricum strains were characterized and compared with 17 other commensal and environmental C. butyricum strains using whole-genome sequencing (WGS). In addition, the clustering was analysed using multi-spacer sequence typing (MST). FINDINGS: The core genome of C. butyricum was composed of 1251 genes, and its pan-genome consisted of 12,628 genes with high variability between strains. It was possible to distinguish the clonal lineage of strains from a series of NEC cases, forming three clades with geographical clustering. The results obtained using WGS and MST approaches were congruent. CONCLUSION: MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.

Rapid diagnostic test and use of antibiotic against methicillin-resistant Staphylococcus aureus in adult intensive care unit.

Ventilator-associated pneumonia (VAP) due to methicillin-resistant Staphylococcus aureus (MRSA) is associated with excess mortality and costs. Molecular biology test allows rapid identification of MRSA in sputum with high negative predictive value. We hypothesized that use of a rapid diagnostic test in patients with suspected VAP was associated with reduced use of antibiotics directed against MRSA. This retrospective, observational study was conducted in a polyvalent intensive care unit (ICU) of a university hospital. We compared two periods: before (2007-2010) and after (2010-2015) the implementation of a rapid diagnostic test, which uses RT-PCR to detect pathogens in 60 minutes. The primary endpoint was the effect on the empirical use of anti-MRSA antibiotics. The second endpoint was the effect of this strategy on the cost regarding antibiotic treatment. The first group included 120 suspected VAP (88 patients) and the second group 121 suspected VAP (89 patients). Empirical use of vancomycin and linezolid decreased by 50 % between the two periods. Twenty-seven VAP (22 %) were treated with an anti-MRSA treatment between 2007 and 2010, and 13 (11 %) between 2010 and 2015 (p = 0.04). The mean cost of anti-MRSA treatment by patients in the first group was 63 ± 223 €, and 13 ± 52 € in the second group (p < 0.001). This study shows that a rapid diagnostic test was associated with reduced use and cost of anti-MRSA antibiotics in patients with suspected VAP. These results should be confirmed by further multicenter prospective studies.

Description of Clostridium phoceensis sp. nov., a new species within the genus Clostridium.

Clostridium phoceensis sp. nov., strain GD3T (= CSUR P1929 = DSM 100334) is the type strain of C. phoceensis sp. nov., a new species within the genus Clostridium. This strain was isolated from the gut microbiota of a 28-year-old healthy French man. C. phoceensis is a Gram-negative, spore-forming, nonmotile, strictly anaerobic bacterium. We describe its complete genome sequence and annotation, together with its phenotypic characteristics.

"Lachnoclostridium touaregense," a new bacterial species isolated from the human gut microbiota.

We report the main characteristics of "Lachnoclostridium touaregense" strain Marseille-P2415T (= CSUR P2415 = DSM 102219), a new bacterial species isolated from the gut microbiota of a healthy young girl from Niger.