Multiplex microarray PCR Unyvero BCU system to accelerate relevant antimicrobial treatment in polymicrobial bloodstream infection.

PURPOSE: To evaluate the performance of a rapid multiplex microarray-based method (Unyvero BCU system, BCU) to identify microorganisms and detect antimicrobial resistance directly from positive blood culture (BC) bottles with polymicrobial growth, and to assess relevance of information provided for timely guidance of polymicrobial bloodstream infection treatment. METHODS: Accuracy, time-to-actionable results and potential impact of BCU on antimicrobial treatment were compared with those of standard of care during a prospective study for the sample analysis (November 2017-November 2018) and a retrospective study for the clinical data analysis and the time-to-result analysis. The study was complemented with an experimental study, based on spiked blood cultures to assess the ability of the method to detect antimicrobial resistance genes. RESULTS: Sixty-five clinical polymicrobial BC samples (163 total microorganisms) and 30 simulated polymicrobial BC samples (60 strains) were included. BCU reported 84.6% samples as polymicrobial, correctly identified all the bacteria of the mix for 72.3% samples (47/65) and detected bacteria that were missed by the conventional culture for 13.8% samples. All identifications and antimicrobial resistances were accurately detected for 61.5% (40/65) samples. Limitations concerned the detection of anaerobes, enterococci and enterobacterial susceptibility to third generation cephalosporins. BCU results would have guided antimicrobial treatment for 50.8% of the cases (33/65) in a timely and relevant manner, had no impact for 27.7% (18/65) and been misleading for 18.5% (12/65). CONCLUSIONS: Despite some limitations, the Unyvero BCU system is a rapid and reliable method for polymicrobial BC sample analysis.

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.

Community-acquired pneumonia: impact of empirical antibiotic therapy without respiratory fluoroquinolones nor third-generation cephalosporins.

Guidelines for inpatients with community-acquired pneumonia (CAP) propose to use respiratory fluoroquinolone (RFQ) and/or third-generation cephalosporins (Ceph-3). However, broad-spectrum antibiotic therapy is associated with the emergence of drug-resistant bacteria. We established a guideline in which RFQ and Ceph-3 were excluded as a first course. Our aim was to evaluate the impact of our therapeutic choices for CAP on the length of hospital stay (LOS) and patient outcome. This was a cohort study of patients with CAP from July 2005 to June 2014. We compared patients benefiting from our guideline established in 2008 to those receiving non-consensual antibiotics. Disease severity was evaluated through the Pneumonia Severity Index (PSI). The empirical treatment for PSI III to V was a combination therapy of amoxicillin-clavulanic acid (AMX-C) + roxithromycin (RX) or AMX + ofloxacin. Adherence to guidelines was defined by the prescription of one of these antibiotic agents. Requirement for intensive care or death defined unfavorable outcome. Among 1,370 patients, 847 were treated according to our guideline (61.8 %, group 1) and 523 without concordant therapy (38.2 %, group 2). The mean PSI was similar: 82 vs. 83, p > 0.5. The mean LOS was lower in group 1: 7.6 days vs. 9.1 days, p < 0.001. An unfavorable outcome was less frequent in group 1: 5.4 % vs. 9.9 %, p = 0.001. In logistic regression models, concordant therapy was associated with a favorable outcome: adjusted odds ratio (AOR) [95 % confidence interval (CI)] 1.85 [1.20-2.88], p = 0.005. CAP therapy without RFQ and Ceph-3 use was associated with a shorter LOS and fewer unfavorable outcomes.

Fatal pulmonary infection related to Nocardiopsis dassonvillei in a patient with chronic obstructive pulmonary disease.

Nocardiopsis species are aerobic, gram-positive, non-acid fast rods isolated from soil, waters, and animals. They are opportunistic human pathogens, but very few cases have been published so far. We report the first case of fatal pulmonary infection related to Nocardiopsis dassonvillei in an immunocompetent patient with chronic obstructive pulmonary disease.

Tuberculosis trends in a hot-spot region in Paris, France.

SETTING: Tuberculosis (TB) incidence is declining overall in France, but not in Paris where some areas remain relative hot spots for TB.OBJECTIVES: To obtain a better knowledge of local TB epidemiology in order to facilitate control measures.DESIGN: Analysis of demographic data of TB patients diagnosed at the Bichat-Claude Bernard Hospital from 2007 to 2016, with spoligotyping of Mycobacterium tuberculosis complex isolates.RESULTS: During the study period, 1096 TB patients were analysed. The incidence of TB diagnosis was stable, averaging 115 patients per year, predominantly males (71%), foreign-born (81%), with pulmonary TB (77%) and negative HIV serology (88%). The mean age of foreign-born TB patients decreased over the study period, most significantly in recent arrivals in France, whose average age decreased by two years (P = 0.001). The time period between arrival in France and being diagnosed with active TB decreased annually significantly by 0.75 years (P = 0.02). The proportion of L4.6.2/Cameroon and L2/Beijing sub-lineages increased annually by 0.7% (P < 0.05). Multi-drug resistant strains, representing 4% of all strains, increased annually by 0.75% (P = 0.03)CONCLUSION: The number of TB patients remained high in northern Paris and the surrounding suburbs, suggesting the need for increased control measures.

Characterization of the immune response in the synovitis, acne, pustulosis, hyperostosis, osteitis (SAPHO) syndrome.

OBJECTIVE: The aetiology of SAPHO (synovitis, acne, palmoplantar pustulosis, hyperostosis, osteitis) syndrome seems to involve genetic, infectious and immunological components. We examined innate and adaptive immune responses in SAPHO syndrome, as compared with PsA and RA. We also studied the effect of etanercept on immunological parameters. METHODS: We studied 29 patients with SAPHO syndrome, as well as 22 patients with RA, 21 patients with PsA and 15 healthy controls. Adaptive immune responses were investigated by assaying total serum immunoglobulins and several autoantibodies. Innate immunity was studied by quantifying blood PMN functions and plasma cytokine levels. PMN responses to Propionibacterium acnes were tested ex vivo. Eight patients who received etanercept for refractory rheumatic disorders were tested before and after 28 days of treatment. RESULTS: SAPHO syndrome was associated with elevated IL-8 and IL-18 plasma levels. IL-8 and TNF-alpha production by purified PMN was higher in the three patient groups than in the healthy controls, but the oxidative burst and IL-18 production were normal. No autoantibodies were detected in SAPHO patients. Induction of PMN IL-8 and TNF-alpha production by P. acnes was impaired in the SAPHO group as compared with the RA and PsA groups. After 28 days of etanercept therapy, PMN IL-8 and TNF-alpha production was down-regulated and TNF-alpha plasma levels were increased. CONCLUSIONS: These results support the view that the SAPHO syndrome may be triggered by an infectious state involving P. acnes, contributing to the strong humoral and cellular pro-inflammatory responses. Etanercept modulation of PMN activation status emphasizes these new immunological findings.

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.

Rapid control of an outbreak of vancomycin-resistant enterococci in a French university hospital.

Vancomycin-resistant enterococci (VRE) are emerging in French hospitals. A VRE outbreak occurred in our hospital, prompting efforts to eradicate the organism. The following interventions were implemented simultaneously to control the outbreak: (1) creation of a VRE control committee; (2) cohorting of VRE carriers in a dedicated ward; (3) extensive screening of contact patients; (4) use of a sensitive technique for detecting VRE in rectal samples; (5) intervention of a dedicated team to reduce consumption of selected antibiotics; (6) information for, and education of, all hospital staff; and (7) electronic tracking of in-hospital transfer and readmission of VRE carriers and contact patients. Over a four-week period following admission of the index case, 37 carriers of a single strain of vanA vancomycin-resistant Enterococcus faecium were identified across seven units. A single additional readmitted contact patient was identified later. Of the 39 VRE-positive patients, two had urinary tract infections and 37 were colonised. Of the 32 patients with known VRE stool concentrations, 23 had low and nine high concentrations. One low-concentration patient precipitated transmission in another unit. This aggressive, co-ordinated, multifaceted strategy was successful in halting a widespread VRE outbreak in our hospital.

Multidrug-resistant tuberculous meningitis in an HIV-positive patient: a challenging disease.

We report two cases of disseminated multidrug-resistant tuberculosis with meningitis in HIV-positive patients, who were both recent emigrants from sub-Saharan Africa. Our two cases highlight new challenges in the care of HIV and tuberculosis coinfection including early diagnosis and treatment of multidrug-resistant tuberculosis that is spreading.

'Nissabacter archeti' gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France.

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

An update on bacterial brain abscess in immunocompetent patients.

BACKGROUND: A brain abscess is a focal infection of the brain that begins as a localized area of cerebritis. In immunocompetent patients, bacteria are responsible for >95% of brain abscesses, and enter the brain either through contiguous spread following otitis, sinusitis, neurosurgery, or cranial trauma, or through haematogenous dissemination. AIMS: To identify recent advances in the field. SOURCES: We searched Medline and Embase for articles published during years 2012-2016, with the keywords 'brain' and 'abscess'. CONTENT: The triad of headache, fever and focal neurological deficit is complete in ∼20% of patients on admission. Brain imaging with contrast-preferentially magnetic resonance imaging-is the reference standard for diagnosis, and should be followed by stereotactic aspiration of at least one lesion, before the start of any antimicrobials. Efforts should be made for optimal management of brain abscess samples, for reliable microbiological documentation. Empirical treatment should cover oral streptococci (including milleri group), methicillin-susceptible staphylococci, anaerobes and Enterobacteriaceae. As brain abscesses are frequently polymicrobial, de-escalation based on microbiological results is safe only when aspiration samples have been processed optimally, or when primary diagnosis is endocarditis. Otherwise, many experts advocate for anaerobes coverage even with no documentation, given the sub-optimal sensitivity of current techniques. A 6-week combination of third-generation cephalosporin and metronidazole will cure most cases of community-acquired brain abscess in immunocompetent patients. IMPLICATIONS: Significant advances in brain imaging, minimally invasive neurosurgery, molecular biology and antibacterial agents have dramatically improved the prognosis of brain abscess in immunocompetent patients over the last decades.

Actinotignum schaalii (formerly Actinobaculum schaalii): a newly recognized pathogen-review of the literature.

The genus Actinotignum contains three species, Actinotignum schaalii (formerly Actinobaculum schaalii), Actinotignum urinale and Actinotignum sanguinis. A. schaalii is the species most frequently involved in human infections, with 172 cases, mostly urinary tract infections (UTIs), reported so far. Invasive infections have also been described. This facultative anaerobic Gram-positive rod is part of the urinary microbiota of healthy patients. It is responsible for UTIs, particularly in elderly men and young children. A. schaalii is an underestimated cause of UTIs because of its fastidious growth on usual media and difficulties associated with its identification using phenotypic methods. Indeed, this slow-growth bacterium requires blood-enriched media and an incubation time of 48 hours under anaerobic or 5% CO2 atmosphere. Furthermore, only matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) or molecular-based methods allow the accurate identification of this bacteria. MALDI-TOF using Microflex LT with the Biotyper database (Bruker Daltonics, Bremen, Germany) is the most reliable technology for the routine identification of A. schaalii. The identification of this uropathogen is all the more important because it is resistant to trimethoprim/sulfamethoxazole and second-generation quinolones that are widely used in the treatment of UTIs. Antimicrobial therapy using ß-lactams prolonged for up to 2 weeks is the most efficient treatment and should be recommended. Microbiologists should assess the presence of A. schaalii in urine using appropriate culture and identification methods in the case of a direct examination that is positive for small coccoid rods, a negative nitrite urinary stick associated with leukocyturia, treatment failure with trimethoprim/sulfamethoxazole or fluoroquinolones, or undocumented, repeated UTIs.

A phylogeny of the genus Nocardia deduced from the analysis of small-subunit ribosomal DNA sequences, including transfer of Nocardia amarae to the genus Gordona as Gordona amarae comb. nov.

According to phylogenetic analyses of nearly complete small-subunit ribosomal DNA sequences, the genus Nocardia should not comprise the two species Nocardia petroleophila and Nocardia amarae. N. amarae should be reassigned to the genus Gordona as Gordona amarae. All of the other Nocardia species form a monophyletic unit, closely related to species of the genus Rhodococcus. It is proposed to revive the name 'CMN' to comprise the genera Corynebacterium, Tsukamurella, Mycobacterium, Gordona, Rhodococcus and Nocardia that form a well identified and monophyletic unit. They are all characterized by a cell wall chemotype IV with mycolic acids.

Taxonomy of Corynebacterium diphtheriae and related taxa, with recognition of Corynebacterium ulcerans sp. nov. nom. rev.

Levels of genomic DNA relatedness were determined using a S1 nuclease procedure for reference bacteria identified as biotypes of Corynebacterium diphtheriae, biovars of Corynebacterium pseudotuberculosis, and 'Corynebacterium ulcerans'. These results showed that the three species are separate taxa at the genomospecies level whereas biotypes and biovars are closely related genomically within each species. Phylogenetic analyses of small-subunit rDNA sequences revealed that 'Corynebacterium ulcerans' forms a tight cluster with Corynebacterium pseudotuberculosis within the robust branch that groups all Corynebacterium sequenced to date. Therefore, we propose that the species incertae sedis 'C. ulcerans' should be conclusively recognized as a distinct species within the genus Corynebacterium with strain CCUG 2708 = NCTC 7910 as type strain. This species is characterized by urease production and fermentation of glycogen.

Epidemiology of Pseudomonas aeruginosa and risk factors for carriage acquisition in an intensive care unit.

Because of a high prevalence of Pseudomonas aeruginosa infections, we conducted an epidemiological study to assess the need for systematic surveillance, as well as the value of applying barrier precautions toP. aeruginosa carriers. From July 1997 to February 1998, we conducted a prospective cohort study in an 18-bed medical intensive care unit (ICU), which is part of the infectious diseases department in a 1200-bed tertiary-care teaching hospital. Rectal and oropharyngeal swabs were obtained on admission and twice weekly. Acquired strains were genotypically characterized by pulsed-field gel electrophoresis (PFGE). A risk factor analysis for carriage, colonization and infection was performed. Among 269 eligible patients, 116 (43%) were P. aeruginosa carriers, with 46 (17%) detected on admission and 70 (26%) who acquired carriage during their stay in ICU. Among these 70 patients, 29 became colonized (N=13) or developed infection (N=16). Conversely, in the 121 patients who remained free of carriage, no colonization or infection were detected. Genotyping analysis using PFGE was performed for 81/85 (95%) acquired strains in 67 patients. The same genotype I was observed for 58/81 (70%) of these strains issued from 47 patients, and a distinct genotype II affected two other patients (three strains). The last 20 strains were not genetically related. In a multivariate model, mechanical ventilation was associated with the acquisition of P. aeruginosa carriage. Antibiotics ineffective against P. aeruginosa significantly increased the risk of colonization or infection in ICU. Although several recent studies concluded that endogenous sources account for the majority of P. aeruginosa colonizations or infections, we conclude that epidemiology may vary according to the ICU, and that cross-colonization (i.e., exogenous source) may occur and warrant reinforced barrier precautions.

The changing clinical aspects of infective endocarditis: descriptive review of 90 episodes in a French teaching hospital and risk factors for death.

OBJECTIVE: We wanted to describe the epidemiological aspects of infective endocarditis (IE) in a French hospital and identify the prognostic factors. METHODS: We reviewed the clinical, echocardiographic and microbiological features, and the outcome of 89 patients (90 episodes, median age 60 years) with IE over 18 months. Logistic regression analysis was used to identify prognostic factors for death. RESULTS: A native valve was involved in 68 cases (75.5%); in 7 of these the patient was an intravenous drug user. A prosthetic valve was involved in 22 cases (24.5%); 5 of these were of early onset. Diagnosis was definite in 87% of cases. Median time to diagnosis was 3 days. Twenty-five patients (28%) were immunocompromised. A portal of entry, usually cutaneous, was identified in 65% of cases. Sixty-two percent of patients had an underlying heart disorder, usually degenerative. The infection involved the left heart in more than 75% of cases. One or more vegetations were detected in 75% of cases. The median size of vegetation was 15 mm. Isolated agents were mainly staphylococci (n=40 (44%), including 12 coagulase-negative isolates), and streptococci (n=23 (25%), including 7 enterococci). In 11 cases (12%), cultures remained negative. Nineteen episodes were nosocomial and Staphylococcus aureus was implicated in 11 of them. Fifty percent of patients had at least one complication: heart failure (n=42), kidney failure (n=44), embolism (n=35), septic shock (n=19). Surgery was performed in 49 cases (54%) due to heart failure (n=19), cerebral embolism (n=12), and/or severe valve lesions (n=27). Eighteen patients died, 10 of whom were infected with S. aureus. Nosocomial IE (P=0.0008), heart failure (P=0.004) and prosthetic valve (P=0.01), but not S. aureus were independently associated with death. CONCLUSIONS: S. aureus was the main microorganism isolated in our patients. However, it was not independently predictive of fatal outcome.

Tuberculosis in the intensive care unit: a descriptive analysis in a low-burden country.

BACKGROUND: Although tuberculosis (TB) is not a major public health issue in low-burden countries, severe cases are still a matter of concern. OBJECTIVE: To assess the risk factors for mortality due to TB in a low-burden setting. DESIGN: A retrospective study of 97 patients hospitalised with active TB in the intensive care unit (ICU) of the Bichat-Claude Bernard Hospital, Paris, France, from 2000 to 2009. RESULTS: The mean age was 47.4 ± 14.7 years; 40 patients were human immunodeficiency virus (HIV) infected, with a median CD4 cell count of 74 cells/mm(3). The survival analysis showed that 21 patients died during their time in the ICU. The observed risk factors for ICU mortality were organ failure, high Simplified Acute Physiology Score II (SAPS II) and Sequential Organ Failure Assessment scores, and concomitant non-tuberculous infection. In multivariate analysis, only SAPS II score was significantly associated with mortality. CONCLUSION: Risk factors identified in this study are different from those in high-burden countries, and were not associated with the site of TB disease. There was no difference in TB presentation between HIV-infected and non-HIV-infected patients, and HIV was not a mortality risk factor. Low-burden countries still experience high death rates due to severe TB.