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Microbacterium sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42 Mb and one plasmid of 34.22 kb., (Copyright © 2020 Chéraiti et al.)

Currently, few techniques are available for the evaluation of bacterial biofilm adhesion. These detection tools generally require time for culture and/or arduous handling steps. In this work, the BioFilm Ring Test (BRT), a new technology, was used to estimate the biofilm formation kinetics of 25 strains of Pseudomonas aeruginosa, isolated from the sputum of cystic fibrosis (CF) patients. The principle of the new assay is based on the mobility measurement of magnetic microbeads mixed with a bacterial suspension in a polystyrene microplate. If free to move under the magnetic action, particles gather to a visible central spot in the well bottom. Therefore, the absence of spot formation in the plate reflects the bead immobilization by a biofilm in formation. The BRT device allowed us to classify the bacterial strains into three general adhesion profiles. Group 1 consists of bacteria, which are able to form a solid biofilm in <2 h. Group 2 comprises the strains that progressively set up a biofilm during 24 h. Lastly, group 3 includes the strains that stay in a planktonic form. The grouping of our strains did not differ according to culture conditions, i.e., the use of different sets of beads or culture media. The BRT is shown to be an informative tool for the characterization of biofilm-forming bacteria. Various application perspectives may be investigated for this device, such as the addition of antibiotics to the bacterial suspension to select which would have the ability to inhibit the biofilm formation., (Copyright © 2016 Olivares et al.)

The use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for staphylococcal identification is now considered routine in laboratories compared with the conventional phenotypical methods previously used. We verified its microbiological relevance for identifying the main species of coagulase-negative staphylococci (CoNS) by randomly selecting 50 isolates. From 1 January 2007 to 31 August 2008, 12,479 staphylococci were isolated with phenotypic methods, of which 4,594 were identified as Staphylococcus aureus and 7,885 were coagulase negative staphylococci. Using MALDI-TOF MS from 1 January 2011 to 31 August 2012, 14,913 staphylococci were identified, with 5,066 as S. aureus and 9,847 as CoNS. MALDI-TOF MS allowed the identification of approximately 85% of the CoNS strains, whereas only 14% of the CoNS strains were identified to the species level with phenotypic methods because they were often considered contaminants. Furthermore, the use of MALDI-TOF MS revealed the occurrence of recently characterized Staphylococcus species, such as S. pettenkoferi, S. condimenti, and S. piscifermentans. Microbiological relevance analysis further revealed that some species displayed a high rate of microbiological significance, i.e., 40% of the S. lugdunensis strains included in the analysis were associated with infection risk. This retrospective microbiological study confirms the role of MALDI-TOF MS in clinical settings for the identification of staphylococci with clinical consequences. The species distribution reveals the occurrence of the recently identified species S. pettenkoferi and putative virulent species, including S. lugdunensis., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)

The major goal of the present study was to investigate the potential use of a novel single nucleotide polymorphism (SNP) genotyping technology, called iPLEX Gold (Sequenom), for the simultaneous analysis of 16 SNPs that have been previously validated as useful for identification of Mycobacterium tuberculosis complex (MTBC) species and classification of MTBC isolates into distinct genetic lineages, known as principal genetic groups (PGGs) and SNP cluster groups (SCGs). In this context, we developed a 16-plex iPLEX assay based on an allele-specific-primer single-base-extension reaction using the iPLEX Gold kit (Sequenom), followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis on the commercially available Sequenom MassARRAY platform. This assay was tested on a panel of 55 well-characterized MTBC strains that were also genotyped for the same loci using the previously reported SNaPshot assay, as well as 10 non-MTBC mycobacteria and 4 bacteria not belonging to the genus Mycobacterium. All MTBC samples were successfully analyzed with the iPLEX assay, which yielded clear allelic data for 99.9% of the SNPs (879 out of 880). No false-positive results were obtained with the negative controls. Compared to the SNaPshot assay, the newly developed 16-plex iPLEX assay produced fully concordant results that allowed reliable differentiation of MTBC species and recognition of lineages, thus demonstrating its potential value in diagnostic, epidemiological, and evolutionary applications. Compared to the SNaPshot approach, the implementation of the iPLEX technology could offer a higher throughput and could be a more flexible and cost-effective option for microbiology laboratories.

Tick saliva has potent immunomodulatory properties. In arthropod-borne diseases, this effect is largely used by microorganisms to increase their pathogenicity and to evade host immune responses. We show that in Lyme borreliosis, tick salivary gland extract and a tick saliva protein, Salp15, inhibit in vitro keratinocyte inflammation induced by Borrelia burgdorferi sensu stricto or by the major outer surface lipoprotein of Borrelia, OspC. Chemokines (interleukin-8 [IL-8] and monocyte chemoattractant protein 1 [MCP-1]) and several antimicrobial peptides (defensins, cathelicidin, psoriasin, and RNase 7) were downregulated. Interestingly, antimicrobial peptides (AMPs) transiently inhibited bacterial motility but did not kill the organisms when tested in vitro. We conclude that tick saliva affects the chemotactic properties of chemokines and AMPs on immune cells and has an antialarmin effect on human primary keratinocytes. Alarmins are mediators that mobilize and activate antigen-presenting cells. Inhibition of cutaneous innate immunity and of the migration of immune cells to the site of the tick bite ensures a favorable environment for Borrelia. The bacterium can then multiply locally and, subsequently, disseminate to the target organs, including joints, heart, and the central nervous system.

A large body of evidence has convincingly shown that Toll-like receptors are necessary sensors for infections with pathogens, but their activation was also suggested to generate autoimmunity. During experimental infections, the lack of these sensors or of their signaling molecules should lead to a deficient immune response. We found out that MyD88, the major adaptor of the Toll/interleukin-1 (Toll/IL-1) receptor signaling pathway, can actually act as a negative regulator of B-cell function in some settings. MyD88-deficient mice infected by Borrelia burgdorferi developed extreme hypergammaglobulinemia compared to wild-type animals, with high levels of immunoglobulin M (IgM) autoantibodies. In vivo, cell transfer experiments and cell blocking assays showed that this phenotype was not linked to the absence of MyD88 in B cells but rather to CD4 T-cell and likely dendritic cell dysfunctions leading to a Th1-to-Th2 cytokine switch. In addition, our results suggest a relative defect in the Ig class switch recombination process, since MyD88 knockout mice developed mostly IgM antibodies. Collectively, these data emphasize the complex role of the Toll/IL-1 receptor pathway in tuning the immune response against infection and avoiding autoimmunity.

Cat scratch disease (CSD) is mostly due to Bartonella henselae after inoculation of the organism through a skin injury. Since the causative bacteria cannot be easily cultured from human lymph node samples, the diagnosis usually relies on epidemiological, clinical, histological, and serological criteria (classical criteria). A study was performed to determine the diagnostic value of PCR analysis for the detection of B. henselae for the diagnosis of CSD and its place in the diagnostic strategy alongside the classical criteria. Over a 7-year period, lymph node biopsy specimens or cytopunctures from 70 patients were systematically tested by PCR for the presence of B. henselae DNA (htrA gene) in the Bacteriology Laboratory of the Hôpitaux Universitaires de Strasbourg. Serological testing by an immunofluorescence assay for B. henselae antibodies was also performed for each patient, and clinical, epidemiological, and histological data were collected. The patients were then divided into two groups according to the number of positive diagnostic criteria for CSD: 29 patients with definite CSD (two or more classical criteria) and 15 patients with possible CSD (less than two classical criteria). The remaining 26 patients for whom another diagnosis was retained were used as a control group. Among all criteria, PCR analysis had the best specificity (100%). The PCR assay for B. henselae was positive for 22 (76%; 95% confidence interval [CI95], 56.5 to 89.7%) of the 29 definite CSD patients and 3 (20%; CI95, 4.3 to 48.1%) of the 15 possible CSD patients. We then studied combinations of diagnostic criteria, including B. henselae PCR analysis. The best diagnostic performance was observed if at least two criteria were present among serologic, epidemiologic, histological, and molecular criteria.

Fungemia is associated with a high mortality rate. We compared the performance of the Mycosis IC/F selective fungal medium and the Plus Aerobic/F standard bacteriological medium for the diagnosis of fungemia on the Bactec 9240 automatic system. We retrospectively analyzed 550 blood culture pairs composed of one Mycosis IC/F vial and one Plus Aerobic/F vial, drawn in 187 patients with fungemia. The positivity rate by vial was significantly higher on Mycosis IC/F medium than on Plus Aerobic/F medium (88.0% versus 74.9%, P < 0.0001). The positivity rate for fungus detection on Plus Aerobic/F medium fell to 26.9% when bacteria were present in the same vial. The positivity rate by patient was also significantly higher on Mycosis IC/F medium than on Plus Aerobic/F medium (92.5% versus 75.9%, P < 0.0001). A marked superiority of Mycosis IC/F medium was demonstrated for diagnosis of Candida glabrata fungemia (31 of 31, 100%, versus 18 of 31, 58.1%, P < 0.0001). The mean detection time was significantly shorter on Mycosis IC/F medium than on Plus Aerobic/F medium (28.9 +/- 22.2 h versus 36.5 +/- 24.6 h, P < 0.0001). The mean time saving was 8.8 h for Candida albicans and 43.7 h for C. glabrata. Mycosis IC/F medium enabled more sensitive and earlier diagnosis, particularly for the two strains most frequently responsible for fungemia, C. albicans and C. glabrata, and also in the event of the concomitant presence of both yeasts and bacteria. In patients with risk factors, it would thus appear to be sensible to draw a Mycosis IC/F vial in addition to the standard bacteriological vials.

To evaluate the prevalence of sulfate-reducing bacteria in septic processes, we searched for these bacteria by culture in 100 consecutive abdominal and pleural pus specimens. Twelve isolates were obtained from abdominal samples and were identified by a multiplex PCR as Desulfovibrio piger (formerly Desulfomonas pigra) (seven strains), Desulfovibrio fairfieldensis (four strains), and Desulfovibrio desulfuricans (one strain).

In this report, we review two cases of brain infection due to Dialister pneumosintes in previously healthy patients. The bacterium was isolated from the first patient by blood culture and directly from a brain abscess in the second patient. In both cases, the infection was suspected to be of nasopharyngeal or dental origin. The patients had favorable outcomes following surgical debridement and antibiotic treatment. After in vitro amplification and partial sequencing of the 16S rRNA gene, two strains were classified as D. pneumosintes. However, traditional biochemical tests were not sufficient to identify the bacteria. In addition to causing periodontal and opportunistic infections, D. pneumosintes, contained in mixed flora, may behave as a clinically important pathogen, especially in the brain. In addition to phenotypic characterization, 16S rRNA partial sequencing was used to identify D. pneumosintes definitively.

Since Lyme arthritis was first described in the United States, it has now been reported in many countries of Europe. However, very few strains of the causative bacterium, Borrelia burgdorferi, have been isolated from synovial samples. For this reason, different molecular direct typing methods were developed recently to assess which species could be involved in Lyme arthritis in Europe. We developed a simple oligonucleotide typing method with PCR fragments from the flagellin gene of B. burgdorferi sensu lato, which is able to differentiate seven different Borrelia species. Among 10 consecutive PCR-positive patients with Lyme arthritis from the northeastern France, two species were identified in synovial samples: B. burgdorferi sensu stricto in 9 cases and B. garinii in 1 case. Conversely, all B. burgdorferi sensu lato species detected in 10 consecutive PCR-positive biopsies from a second set of patients with erythema migrans from the same geographical area were identified as either B. afzelii or B. garinii (P < 0.001). These results indicate that B. burgdorferi sensu stricto is the principal but not the only Borrelia species involved in Lyme arthritis in northeastern France.

A one-step reverse transcriptase PCR (RT-PCR) method for detection of Borrelia burgdorferi mRNA in infected C3H mice is described. This simple procedure, less prone to nucleic acid cross-contamination than the standard method, was found to be 10-fold more sensitive than a classical two-step RT-PCR assay. By using one-step RT-PCR, flagellin mRNAs were detected in synovial and heart tissues from all seven infected mice tested.

The BBL Crystal MRSA ID test (Becton Dickinson) was applied directly to blood culture vials containing clusters of gram-positive cocci. The sensitivity and specificity of the test were 84 and 100% and 54 and 100% for vials containing Staphylococcus aureus and coagulase-negative staphylococci, respectively. This test is a reliable method for direct detection of methicillin resistance in positive blood culture vials when S. aureus is identified in parallel by rapid identification procedures.

A prospective study was conducted on 25 Legionella pneumophila culture-positive and 98 culture-negative bronchoalveolar lavage fluid samples to compare two DNA preparation methods: a rapid modified Chelex-based protocol and a proteinase K method. PCR was found to be more sensitive with the Chelex-based method (P = 0.03). N difference was found concerning the inhibition rate.

The aim of the present work was to determine by blood culture the prevalence of blood infection with Bartonella species in a well-defined, European, urban stray cat population. Therefore, 94 stray cats were trapped from 10 cat colonies. Blood samples of these cats were cultured on both blood agar and liquid medium in order to raise the likelihood of bacterial detection. Fifty blood samples (53%) gave a positive culture result for Bartonella species. Isolate identification was performed by sequencing the first 430 bases of the 16S ribosomal DNA. Three types of sequences were thus obtained. The first type (17 isolates; 34%) was identical to that of B. henselae Houston-1 and the corresponding strains were referred as B. henselae type I. The second sequence type (18 isolates; 36%) was identical to that initially described as "BA-TF," and the corresponding strains were referred to as B. henselae type II. The third sequence type (15 isolates; 30%) was identical to that of the Bartonella clarridgeiae type strain (ATCC 51734). Our study points out the major role of stray cats as a reservoir of Bartonella spp. which can be transmitted to pet cats and, consequently, to humans. The study also highlights the high prevalence of B. clarridgeiae (16%) in the blood of stray cats.

Serum samples from 35 cat scratch disease (CSD) patients, 180 control patients (123 without lymph node enlargement and 57 with lymph node enlargement not evoking CSD), and 102 nonpatient subjects (35 with cat contact and 67 without cat contact) were tested by semiquantitative indirect immunofluorescence assay for the presence of antibodies directed to Afipia felis (ATCC 53690T) or Bartonella henselae (ATCC 49882T). The CSD group had statistically higher antibody titers against B. henselae than the control groups (P < 10(-5)), whereas no difference in A. felis antibody titers was evidenced among all groups tested. Among the 317 serum samples studied, the three with high A. felis antibody titers ( > or = 64) also had high antibody titers against other alpha-2 proteobacteria. The value of the indirect immunofluorescence assay with B. henselae antigen for the diagnosis of CSD was as follows: for a cutoff of 32, sensitivity was 0.80, specificity was 0.85, and the likelihood ratio was 5.1; for a cutoff of 64, the likelihood ratio was 12.1. In summary, in France, CSD is associated with high antibody titers against B. henselae, as previously described in the United States. However, the causes for B. henselae seronegativity in CSD patients and those for high antibody titers outside the typical nosological frame of CSD still have to be identified.

By using Taq polymerase, DNA amplification of a specific fragment of the macrophage infectivity potentiator (mip) gene from Legionella pneumophila was used to detect Legionella spp. in bronchoalveolar lavage (BAL) fluid specimens. We were able to detect DNAs from all 30 L. pneumophila strains tested (serogroups 1 to 14), L. micdadei, and L. bozemanii serogroup 1. DNA from bacteria of other species tested and DNA from human leukocytes were not amplified by this procedure. After optimization of the conditions for DNA extraction from BAL fluid, a 2-ml sample of BAL fluid seeded with 25 CFU/ml tested positive after DNA amplification. A total of 68 frozen BAL fluid specimens sent to the laboratory because of suspected legionellosis were tested in a retrospective study. The eight culture-positive samples were all positive after specific DNA amplification. Among 60 culture-negative samples, 7 were positive after amplification. Of these seven samples, four were from patients who had presented a typical clinical history of legionellosis; the samples had antibody titer increases of 2 dilutions. For the three remaining samples, serological diagnosis of legionellosis in the patients from whom the samples were obtained could not be documented, and although the causative agent of these pulmonary infections was not determined, the clinical features of the patients were in accordance with legionellosis.

Pulsed-field gel electrophoresis (PFGE) after SmaI restriction of DNA from 239 methicillin-resistant Staphylococcus aureus isolates (from 142 patients) produced 26 different fingerprints. The deduced chromosome sizes ranged from 2,200 to 3,100 kb (+/- 100 kb). A total of 81 isolates taken from 65 patients were then typed by PFGE and ribotyping with ClaI, EcoRI, and HindIII. Ribotypes were less discriminating than PFGE. Ribotyping did not discriminate isolates from a given PFGE fingerprint into different subsets. PFGE may be a more effective epidemiological tool than ribotyping for the typing of methicillin-resistant S. aureus strains.