MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures.

All organisms usually isolated in our laboratory are now routinely identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using the Andromas software. The aim of this study was to describe the use of this strategy in a routine clinical microbiology laboratory. The microorganisms identified included bacteria, mycobacteria, yeasts and Aspergillus spp. isolated on solid media or extracted directly from blood cultures. MALDI-TOF MS was performed on 2665 bacteria isolated on solid media, corresponding to all bacteria isolated during this period except Escherichia coli grown on chromogenic media. All acquisitions were performed without extraction. After a single acquisition, 93.1% of bacteria grown on solid media were correctly identified. When the first acquisition was not contributory, a second acquisition was performed either the same day or the next day. After two acquisitions, the rate of bacteria identified increased to 99.2%. The failures reported on 21 strains were due to an unknown profile attributed to new species (9) or an insufficient quality of the spectrum (12). MALDI-TOF MS has been applied to 162 positive blood cultures. The identification rate was 91.4%. All mycobacteria isolated during this period (22) were correctly identified by MALDI-TOF MS without any extraction. For 96.3% and 92.2% of yeasts and Aspergillus spp., respectively, the identification was obtained with a single acquisition. After a second acquisition, the overall identification rate was 98.8% for yeasts (160/162) and 98.4% (63/64) for Aspergillus spp. In conclusion, the MALDI-TOF MS strategy used in this work allows a rapid and efficient identification of all microorganisms isolated routinely.

Progress towards the eradication of Tsetse from the Loos islands, Guinea.

BACKGROUND: The tsetse fly Glossina palpalis gambiensis is the main vector of sleeping sickness (Human African Trypanosomiasis - HAT) in West Africa, in particular in littoral Guinea where this disease is currently very active. The Loos islands constitute a small archipelago some 5 km from mainland Guinea, where G. p. gambiensis is well known as a nuisance and potential disease vector by inhabitants of the three main islands, Fotoba, Room, and Kassa. The National Control Program against HAT of Guinea has decided to eradicate tsetse in Loos islands in order to sustainably protect humans and economic activities. After baseline data collection, tsetse control began on the islands in 2006. On each of the three islands a specific combination of control methods was implemented according to the entomological situation found. RESULTS: Starting densities before control operations were 10, 3 and 1 tsetse/trap/day in Kassa, Room and Fotoba respectively, but by July 2010, tsetse were no longer caught in any of the sentinel traps used for monitoring. The reduction rate was faster where several control methods were implemented as a combination (impregnated traps and targets ITT, selective groundspraying, epicutaneous insecticide treatment of pigs, and impregnated fences around pig pens), whereas it was slower when ITT were used as the only control method. CONCLUSIONS: This 100% suppression is a promising step in the eradication process, but G. p. gambiensis may still occur at very low, undetectable, densities on the archipelago. Next step will consist in assessing a 0.05 probability of tsetse absence to ascertain a provisional eradication status. Throughout these operations, a key factor has been the involvement of local teams and local communities without whom such results would be impossible to obtain. Work will continue thanks to the partners involved until total eradication of the tsetse on Loos islands can be declared.

Metronidazole resistance in Prevotella spp. and description of a new nim gene in Prevotella baroniae.

Nonduplicate clinical isolates of Prevotella spp. recovered from patients hospitalized between 2003 and 2006 in two French tertiary-care teaching hospitals were investigated for their susceptibility to metronidazole and the presence of nim genes. Of the 188 strains tested, 3 isolates displayed reduced susceptibility to metronidazole after 48 h of incubation, while 27 additional isolates exhibited heterogeneous resistance after prolonged incubation; all 30 of the isolates were nim negative. Among the remaining 158 isolates, 7 nim-positive isolates were detected. All of these strains were identified as Prevotella baroniae by 16S rRNA gene sequence analysis and contained a new nim gene, named nimI, as determined by DNA sequence analysis. Chromosomal localization of this single-copy gene was demonstrated in all clinical isolates as well as in type strain P. baroniae DSM 16972 by using Southern hybridization. No known associated insertion sequence elements were detected upstream of the nimI gene in any of the nim-positive strains by PCR mapping. After prolonged exposure to metronidazole, stable resistant subpopulations could be selected in nimI-positive Prevotella isolates (n = 6) as well as in nim-negative Prevotella isolates (n = 6), irrespective of their initial susceptibility to this antibiotic. This study is the first description of a new nitroimidazole resistance gene in P. baroniae which seems to be silent and which might be intrinsic in this species. Moreover, our findings highlight the fact that high-level resistance to metronidazole may be easily induced in both nim-positive and nim-negative Prevotella sp. strains.

[Monitoring of antibiotic resistance of gram negative anaerobes]. / Surveillance de la résistance aux antibiotiques des anaérobies stricts à Gram négatif.

MATERIAL AND METHOD: Using an agar reference method (Norma M11-A5, National Committee for Clinical and Laboratory Standards) the minimal inhibitory concentrations of nine antibiotics were determined for 376 anaerobic strains. The following strains were investigated: 254 Bacteroides fragilis group (including 143 B. fragilis), 122 other gram-negative anaerobes (Bacteroides spp., Prevotella, Fusobacterium, Porphyromonas, Suterella, Desulfomonas, Veillonella). RESULTS: In the B. fragilis group resistance rates were: coamoxyclav 2.8%, ticarcillin 27.5%, ticarcillin-clavulanic acid 1.9%, piperacillin-tazobactam 1.9%, cefoxitin 6.2%, imipenem 0.8%, clindamycin 28.3%, respectively. Based on previous studies, resistance to imipenem remained low in 2003 and was only observed for B. fragilis. Resistance to clindamycin was maintained around 25%. No metronidazole resistance was observed, but decreased susceptibility was found for B. fragilis, B. merdae and Prevotella, as in 4.3% of gram-negative anaerobes. DISCUSSION: This study confirms the high resistance rate of gram-negative anaerobes to clindamycin, the efficient activity of imipenem, beta-lactam/beta-lactamase inhibitor combinations and metronidazole. However, reduced metronidazole susceptibility seems to be increasing.

Prevotella nanceiensis sp. nov., isolated from human clinical samples.

Three strains of anaerobic, non-pigmented, Gram-negative bacilli isolated from various human clinical samples were characterized in terms of phenotypic and genotypic tests, including sequence analysis of 16S rRNA and rpoB genes. The strains were most closely related to the type strains of Prevotella marshii and Prevotella shahii on the basis of both 16S rRNA (89.8 and 89.0 % identity, respectively) and rpoB gene sequences (83.1 and 82.8 % identity, respectively). Phylogenetic analysis showed that the isolates constituted a robust homogeneous group distinct from known species in the genus Prevotella. The rrn skeleton (as determined by PFGE) and the DNA G+C content, determined to be 39.4 mol% for strain LBN 293(T), distinguished the novel isolates from the type strains of P. marshii and P. shahii. The three strains were saccharolytic and produced acetic, lactic and succinic acids as major metabolic end products. Polyphasic investigations supported the proposal of a novel species, Prevotella nanceiensis sp. nov., with LBN 293(T) (=AIP 261.03(T) =CIP 108993(T) =CCUG 54409(T)) as the type strain.

Beta-lactamase production in Prevotella and in vitro susceptibilities to selected beta-lactam antibiotics [corrected].

This study looked for beta-lactamase production in 100 Prevotella isolates. MICs were determined for amoxycillin, ticarcillin, amoxycillin+clavulanate, cephalothin, cefuroxime, cefixime, cefpodoxime and cefotaxime using the reference agar dilution method (standard M11 A4, NCCLS). Beta-lactamase activity was detected in 58 of the 100 isolates, 24 of 46 black-pigmented Provotella and 34 of 54 non-pigmented Prevotella. All beta-lactamase-negative strains were susceptible to all beta-lactam antibiotics with the exception of cefuroxime and cefixime. Overall, resistance rates of Prevotella strains were lower for ticarcillin (8%) and celefotaxime (12%) than for the other cephalosporins. All Prevotella isolates were susceptible to amoxycillin and were all inhibited by 2 mg/l or less amoxycillin [corrected].

Antibiotic resistance among anaerobic Gram-negative bacilli: lessons from a French multicentric survey.

Temporal changes of antibiotic susceptibilities among anaerobes in France are followed in our laboratory since 1992. For Bacteroides strains, resistance increased from 1992 to 1998 for amoxicillin-clavulanic acid, cefotetan and clindamycin. The present study evaluates the situation in 2000 for 434 Gram-negative anaerobic clinical isolates (obtained from 9 large university hospitals) by testing amoxicillin and ticarcillin alone or combined with clavulanic acid, cefoxitin, cefotetan, imipenem, clindamycin and metronidazole (using the NCCLS-approved method for MIC determination. The main genera tested included Bacteroides (359 strains of the fragilis group), Prevotella (40 strains), Fusobacterium (23 strains) and miscellaneous species (8 strains). Resistance rates within the B. fragilis group were: amoxicillin-clavulanic acid 5.6%, ticarcillin 33%, ticarcillin-clavulanic acid 2%, cefoxitin 13%, cefotetan 44%, clindamycin 33%, imipenem 1% and metronidazole <1%, respectively. Only one strain of B. fragilis was resistant to metronidazole (MIC=64 mg/L); due to the presence of the nimA gene on the chromosome. Resistance to imipenem or metronidazole was only found among the B. fragilis species. These two former drugs excepted, B. fragilis was less resistant to antibiotics than the other species. beta-lactamase production was detected for 357/359 strains of the fragilis group, 26/40 stains of Prevotella and 3/23 strains of Fusobacterium. Dynamic changes of antibacterial resistance are occurring within the B. fragilis group: decreased resistance to amoxicillin-clavulanic acid, ticarcillin-clavulanic acid, imipenem while resistance for cefoxitin, cefotetan, clindamycin continues to increase. Regular antibiotic surveys are needed as a source of information to guide the empirical therapy of anaerobic infections.

Antimicrobial susceptibilities of clinical Desulfovibrio isolates.

The antimicrobial susceptibilities of 16 clinical isolates of Desulfovibrio spp. were determined. All or most isolates were susceptible to imipenem (MIC(90) [MIC at which 90% of the isolates tested were inhibited], 0.5 microg/ml), metronidazole (MIC(90), 0.25 microg/ml), clindamycin (MIC(90), 4 microg/ml), and chloramphenicol (MIC(90), 16 microg/ml) but were resistant or intermediate to penicillin G (MIC(90), 64 microg/ml), piperacillin (MIC(90), 256 microg/ml), piperacillin-tazobactam (MIC(90), 256 microg/ml), cefoxitin (MIC(90), >256 microg/ml), and cefotetan (MIC(90), 64 microg/ml). Among isolates with decreased susceptibility to beta-lactams (n = 15), only six were beta-lactamase positive and susceptible to amoxicillin-clavulanate and ticarcillin-clavulanate.

Laboratory diagnosis of Clostridium difficile-associated diarrhea and colitis: usefulness of Premier Cytoclone A+B enzyme immunoassay for combined detection of stool toxins and toxigenic C. difficile strains.

Detection of Clostridium difficile toxins A and B in stools by Premier Cytoclone A+B enzyme immunoassay (EIA) was compared with detection by stool culture for C. difficile followed by detection of toxigenic isolates using the same EIA. Chart reviews were performed to evaluate the likelihood of C. difficile-associated diarrhea and colitis (CADC) for all patients with at least one positive toxin assay. While the toxins were detected in 58 of 85 consecutive CADC patients by both assays, CADC in 5 patients was detected only by stool toxin assay, and in 22 patients CADC was detected only by toxigenic culture. Our results suggest that for laboratories using a rapid toxin A+B EIA, direct toxin detection in stools should be combined with toxigenic culture in cases in which there is a negative stool toxin assay.

Bactericidal properties of the chloroform fraction from rhizomes of Aristolochia paucinervis Pomel.

The deffated chloroform fraction (APRC) obtained from the rhizomes of Aristolochia paucinervis Pomel (Aristolochiaceae) has a high bacteriostatic activity against bacterial strains like Clostridium perfringens ATCC 13124 and Enterococcus faecalis ATCC 29212. Here, we report the bactericidal activity of APRC against both strains which was evaluated by using time-to kill assays. The results showed that APRC produced an intense time-dependent bactericidal effect against C. perfringens, achieving over a 24 h-period a 5log10-unit decrease in CFU/ml at a concentration > or =1.25 x MIC. In contrast, when tested against E. faecalis, APRC exhibited a concentration-dependent killing activity at concentrations of 1.25 x MIC and 2.5 x MIC, yielding to a decrease of 1.5 and 2.5log10-unit in CFU/ml at 4 h, respectively. However, substantial regrowth of E. faecalis occurred within 24 h. Ultrastructural alterations were observed for both exposed microorganisms by scanning and transmission electron microscopy.

In vitro synergy between cefepime and vancomycin against methicillin-susceptible and -resistant Staphylococcus aureus and Staphylococcus epidermidis.

The in vitro activity of cefepime combined with vancomycin was assessed by the chequerboard method against 35 clinical isolates of methicillin-susceptible (MSSA, n = 8) or -resistant (MRSA, n = 10) Staphylococcus aureus and methicillin-susceptible (MSSE, n = 9) or -resistant (MRSE, n = 8) Staphylococcus epidermidis and S. aureus ATCC 25923 (MSSA). The combination was synergic against 16 isolates and additive/indifferent against 20. For 10 of the clinical isolates (two MSSA, three MRSA, two MSSE, three MRSE) and the reference strain, the interaction of cefepime and vancomycin was also determined by the time-kill method. Except for one MRSA isolate, synergic killing was demonstrated with clinically achievable concentrations of vancomycin (0.5-1 mg/L) and cefepime (methicillin-susceptible isolates: 0.5-1 mg/L; methicillin-resistant isolates: 2-64 mg/L).

Single or double mutational alterations of gyrA associated with fluoroquinolone resistance in Campylobacter jejuni and Campylobacter coli.

We looked for the presence of gyrA mutations in seven fluoroquinolone-resistant French clinical isolates of Campylobacter jejuni and Campylobacter coli. Three of the five isolates of C. jejuni and the two isolates of C. coli had high-level resistance to nalidixic acid (MICs 128-256 microg/ml) and ciprofloxacin (MICs 32 microg/ml). A gyrA mutation was found in all these isolates leading to the following substitutions: Thr86-Ile in four cases and Asp90-Tyr for one C. coli strain. One isolate had high-level resistance to nalidixic acid (MIC 64 microg/ml) but low-level resistance to ciprofloxacin (MIC 2 microg/ml) and also carried a gyrA mutation leading to a Thr86-Ala substitution. The last isolate of C. jejuni studied displayed an atypical resistance phenotype: It was resistant to high levels of ciprofloxacin (MIC 64 microg/ml) but remained fully susceptible to nalidixic acid (MIC 2 microg/ml). This phenotype was not explained by the presence of peculiar mutations in gyrA or gyrB. It carried a gyrA mutation leading to a Thr86-Ile substitution and was devoid of gyrB mutation. Despite numerous attempts with various degenerate oligonucleotide primers deduced from conserved regions of known parC genes, we were unable to amplify a corresponding sequence in C. jejuni or C. coli. First-step and second-step in vitro mutants, derived from reference strain C. coli ATCC 33559 with ciprofloxacin or moxifloxacin as selecting agents, were found to carry one and two mutations in gyrA, respectively. In contrast with the results obtained with clinical isolates, a variety of gyrA mutations were obtained in vitro.

Comparison of the in vitro activity of pristinamycin and quinupristin/dalfopristin against Streptococcus pneumoniae.

The in vitro activity of quinupristin/dalfopristin, a new injectable streptogramin, and pristinamycin was evaluated against 200 recently isolated clinical Streptococcus pneumoniae strains expressing various degrees of susceptibility to penicillin G and erythromycin. MICs were determined by the agar dilution method. All strains were susceptible to pristinamycin irrespective of their susceptibility to penicillin G or erythromycin (MIC90: 0.25 mg/L for each phenotype). The activity of quinupristin/dalfopristin was slightly lower than that of pristinamycin against 42 penicillin G-susceptible/erythromycin-susceptible strains (MIC90: 0.5 mg/L), 13 penicillin G-susceptible/erythromycin-resistant strains (MIC90: 1 mg/L), 25 penicillin G-intermediate or -resistant/erythromycin-susceptible strains (MIC90: 0.5 mg/L) and 120 penicillin G-intermediate or -resistant/erythromycin-resistant strains (MIC90: 0.5 mg/L). The activity of both streptogramins was not significantly altered in case of erythromycin resistance. Thus, both streptogramins might be useful for the treatment of penumococcal infections, especially in cases of multiresistant strains.

Bacteremia caused by a strain of Desulfovibrio related to the provisionally named Desulfovibrio fairfieldensis.

Eight isolates of Desulfovibrio spp. have been obtained over 5 years from abdominal or brain abscesses or blood. Seven isolates were part of a mixed flora [corrected]. One strain was isolated in pure culture from the blood of a patient with peritonitis of appendicular origin. According to the 16S rRNA gene sequences, this strain was close to Desulfovibrio fairfieldensis. The present report describes the fourth isolate of this recently described species to be isolated in pure culture or as a predominant part of the flora and to be associated with infectious processes. Thus, D. fairfieldensis may possess a higher pathogenic potential than other Desulfovibrio species.

Antibacterial activity of Aristolochia paucinervis Pomel.

Several fractions of the methanolic extract of the rhizome or the leaves of Aristolochia paucinervis Pomel were screened for antibacterial activity using the agar dilution method against fourteen reference bacterial strains. Only three fractions (defatted chloroformic rhizome fraction: APRC, rhizome ethyl acetate fraction: APRE and leaf chloroform fraction: APLC) showed an activity against at least one of the microorganisms tested. The minimum inhibitory concentration (MIC) determination showed that APRC was the most active against Clostridium perfringens, Clostridium difficile, Enterococcus faecalis, Micrococcus luteus and Bacillus subtilis. The high bacteriostatic activity of APRC was confirmed by its MIC determination against clinical strains of C. perfringens (n = 32), C. difficile (n = 31), and E. faecalis (n = 22). Results of this study suggest the potential interest of this highly active fraction and support the use of A. paucinervis Pomel in Moroccan traditional medicine to treat skin and soft-tissue infections, especially gas gangrene and intestinal diseases.

Survey of anaerobic susceptibility patterns: a French multicentre study.

In 1996, the in vitro antibiotic susceptibility of 463 anaerobes was measured in five hospitals using the reference agar dilution method. None of the 209 B. fragilis group strains showed resistance to imipenem or ticarcillin-clavulanic acid. High resistance rates (29%) were observed for cefotetan and clindamycin. beta-Lactamase production was detected respectively in 64% of the Prevotella and 7% of the Fusobacterium strains. Because the same standardized methods were used for many years, the authors were able to evaluate the evolution of antibiotic resistance. Clindamycin resistance had increased within the B. fragilis group (from 14% in 1992 to 29% in 1996) and also among strains of clostridia (32%), P. acnes (18%) and Peptostreptococcus (28%). In the B. fragilis group multidrug resistance was unlikely to occur.

Low-level vancomycin resistance in Clostridium innocuum.

Low-level vancomycin resistance was observed for 28 clinical Clostridium innocuum isolates and C. innocuum NCIB 10674, whereas teicoplanin was active. DNA from three clinical isolates and the type strain could not be amplified by PCR with primers specific for the genes vanA, vanB, and vanC, suggesting that C. innocuum is intrinsically resistant to vancomycin.

[Actinomycosis and non-Hodgkin's malignant lymphoma: fortuitous association?]. / Actinomycose et lymphome malin non hodgkinien: association fortuite?

Two cases of actinomycosis associated with non Hodgkin's lymphoma (NHL) are reported. In one case, low grade NHL was diagnosed many years after actinomycosis because of the persistence of abdominal lymphadenopathy in spite of antibiotic therapy. In the second case, hepatic metastasis were initially suspected until actinomycosis diagnosis was made by percutaneous liver biopsy under scanography. High grade NHL was diagnosed by laparotomy and liver biopsy performed 6 weeks after the onset of antibiotic therapy as no improvement in hepatic lesions was obtained. These two case reports outline the difficulties encountered in the diagnosis of actinomycosis and the indication of a repeat biopsy when actinomycosis does not respond to antimicrobial therapy because of the possibility of concomitant malignancy.