In vitro susceptibility of ceftaroline against clinically important Gram-positive cocci, Haemophilus species and Klebsiella pneumoniae in Taiwan: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) in 2012-2018

BACKGROUND/PURPOSE

Ceftaroline, with a unique activity against methicillin-resistant Staphylococcus aureus (MRSA), was not launched in Taiwan before 2019. The in vitro susceptibility data of ceftaroline against important Taiwanese pathogens are lacking.

METHODS

The in vitro susceptibility of ceftaroline against important pathogens collected from 2012 through 2018 were extracted from the Antimicrobial Testing Leadership and Surveillance program. Broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) to ceftaroline against all isolates.

RESULTS

During the study period, the in vitro data regarding isolates of S. aureus (n = 2049), Staphylococcus epidermidis (n = 185), Streptococcus pneumoniae (n = 334), Streptococcus pyogenes (n = 170), Haemophilus influenzae (n = 75), Haemophilus parainfluenzae (n = 10) and Klebsiella pneumoniae (n = 680) regardless of hospital sites of collection were analyzed. Among the S. aureus isolates studied, 19.4% showed MICs of 1 mg/L to ceftaroline, and 4.4% showed in vitro susceptible-dose dependent to ceftaroline (all MICs, 2 mg/L). Most of other Gram-positive cocci, all H. influenzae and H. parainfluenzae isolates were susceptible to ceftaroline. By contrast, about one-third (35.9%) of K. pneumoniae isolates, irrespective of infection sources, exhibited non-susceptibility to ceftaroline (MIC range, 0.015-256 mg/L; MIC50 and MIC90 values, 0.12 and 256 mg/L, respectively).

CONCLUSIONS

From the pharmacodynamic perspectives, the ceftaroline dosage of 600 mg as a 2-h intravenous infusion every 8 h is effective against all S. aureus and other Gram-positive isolates regardless of acquisition sites in Taiwan. Before ceftaroline is prescribed in treatment of the patient with Gram-negative infection, a cautious evaluation about patient's healthcare-associated factor is warranted.

Surgical site infection after hip replacement due to a novel Peptoniphilus species, provisionally named 'Peptoniphilus nemausus' sp. nov

We report a case of surgical site infection after total hip prosthesis replacement due to an ofloxacin-resistant Peptoniphilus isolate belonging to an unknown species for which the name 'Peptoniphilus nemausus' sp. nov. is proposed. Follow-up was favourable under clindamycin and rifampin for 3 months in this patient whom had a Proteus mirabilis infection treated by fluoroquinolone.

[Evaluation of rapid genotype assay for the identification of gram-positive cocci from blood cultures and detection of mecA and van genes]

Rapid and accurate identification of bacterial pathogens grown in blood cultures of patients with sepsis is crucial for prompt initiation of appropriate therapy in order to decrease related morbidity and mortality rates. Although current automated blood culture systems led to a significant improvement in bacterial detection time, more rapid identification systems are still needed to optimise the establishment of treatment. Novel genotype technology which is developed for the rapid diagnosis of sepsis, is a molecular genetic assay based on DNA multiplex amplification with biotinylated primers followed by hybridization to membrane bound probes. The aim of this study was to evaluate the performance of "Genotype® BC gram-positive” test for the identification of gram-positive cocci grown in blood cultures and rapid detection of mecA and van genes. This test uses DNA.STRIP® technology which includes a panel of probes for identification of 17 gram-positive bacterial species and is able to determinate the methicillin and vancomycin resistance mediating genes (mecA and vanA, vanB, vanC1, vanC2/C3) simultaneously, in a single test run. A total of 55 positive blood cultures from BACTECTM Plus/F (Becton Dickinson, USA) aerobic and pediatric blood culture vials were included in the study. The isolates which exhibit gram-positive coccus morphology by Gram staining were identified by Genotype ® BC gram-positive test (Hain Life Science, Germany). All of the samples were also identified with the use of Phoenix PMIC/ID Panel (Becton Dickinson, USA) and antibiotic susceptibilities were determined. Of the 55 blood culture isolates, 17 were identified as Staphylococcus epidermidis [all were methicillin-resistant (MR)], 9 were S.aureus (one was MR), 18 were S.hominis (10 were MR), 4 were E.faecalis, 3 were E. faecium (one was vanconycin-resistant), 2 were S.saprophyticus (one was MR), 1 was S.warneri and 1 was S.haemolyticus, by Phoenix automated system. Genotype® BC gram-positive test results revealed consistency with Phoenix system regarding bacterial identification in 46 (83.6%) of the samples. The two bacteria identified as S.saprophyticus by the Phoenix system could not be identified by the Genotype® BC test since this species were not included in the identification panel of the system, however, mecA gene were detected in these two samples by Genotype® BC test. Genotype® BC test detected mecA gene in five samples which were not detected as methicillin resistant by the Phoenix system. Besides polymicrobial growth was determined in five samples by Genotype ® BC test, but not by the automated system. One E.faecium isolate with vanA gene was correctly identified by Genotype® BC test. In conclusion, Genotype® BC gram-positive test is a fast and reliable test for the identification of the most important gram-positive pathogens and mecA and van genes directly from positive blood culture bottles. This test was also found superior than the automated Phoenix system regarding the detection of polymicrobial growth. These data indicated that, routine use of DNA strip technology-based assay would be useful for clinical diagnosis in patients with sepsis.

Central line-associated bloodstream infection in hospitalized children with peripherally inserted central venous catheters: extending risk analyses outside the intensive care unit

BACKGROUND

Increasingly, peripherally inserted central venous catheters (PICCs) are placed for prolonged intravenous access. Few data exist regarding risk factors for central line-associated bloodstream infection (CLABSI) complicating PICCs in hospitalized children, especially children hospitalized outside the intensive care unit (ICU).

METHODS

We identified all children with a PICC inserted at The Johns Hopkins Hospital (Baltimore, MD) from 1 January 2003 through 31 December 2009 and used Poisson regression models to identify risk factors for PICC-associated CLABSIs.

RESULTS

A total of 2592 PICCs were placed in 1819 children. One hundred sixteen CLABSIs occurred over 44,972 catheter-days (incidence rate [IR], 2.58 cases per 1000 catheter-days; 95% confidence interval [CI], 2.07-3.00 cases per 1000 catheter-days). Independent predictors of CLABSI in the entire cohort included PICC dwell time of > 21 days (IR ratio [IRR], 1.53; 95% CI, 1.05-2.26), parenteral nutrition as indication for insertion (IRR, 2.24; 95% CI, 1.31-3.84), prior PICC-associated CLABSI (IRR, 2.48; 95% CI, 1.18-5.25), underlying metabolic condition (IRR, 2.07; 95% CI, 1.14-3.74), and pediatric ICU exposure during hospitalization (IRR, 1.80; 95% CI, 1.18-2.75). Risk factors for CLABSI in children without PICU exposure included younger age, underlying malignancy and metabolic conditions, PICCs inserted in the lower extremity, and a prior PICC-associated CLABSI.

CONCLUSIONS

Prolonged catheter dwell time, pediatric ICU exposure, and administration of parenteral nutrition as the indication for PICC insertion are important predictors of PICC-associated CLABSI in hospitalized children. A careful assessment of these risk factors may be important for future success in preventing CLABSIs in hospitalized children with PICCs.

Gram stain microbiological pattern of upper extremities suppuration at Baptist Medical Centre, Ogbomoso Nigeria: a fifteen month review

Sixty-eight (68) patients with serious upper extremity suppurative infections, presenting within a period of fifteen (15) months, were prospectively studied clinically, Gram stain of aspirates/pus were performed, specimen cultured, planted, and where indicated glucose levels and haemoglobin genotype determined. Half of the patients had hand infections. Staphylococcus aureus was isolated from thirty-nine (39) patients. Gram Negative bacilli, including Salmonella were more isolated from patients with diabetes mellitus or Hgb SS or SC. The Gram stain results correlated with the culture result 90%. When Gram Positive cocci were demonstrated in the primary microscopic examination, cultures were not mandatory. When no organism was demonstrated on primary Gram stain or the patient was diabetic or a sickler, cultures of the specimens were done. The Gram stain, well performed, remains a useful, inexpensive, technologically appropriate laboratory test for abetting decision making in patients with upper extremity suppurative infections. Organisms encountered in this study included: Staphylococcus aureus, Streptococcus pyogenes, Salmonella typhi, Proteus mirabilis, Pseudomonas aeruginosa, and Coliforms.

[An antimicrobial resistance surveillance of gram-positive cocci isolated from 12 teaching hospitals in China in 2009]

OBJECTIVE

To investigate antimicrobial resistance among gram-positive cocci in China in 2009.

METHODS

From June to December 2009, 1169 consecutive and non-repetitive gram-positive cocci were collected from 12 teaching hospitals at 9 cities. The minimal inhibitory concentration (MIC) of antibacterial agents was determined by agar dilution method.

RESULTS

The prevalences of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococci (MRCoNS) were 45.3% (211/466) and 89.5% (214/239), respectively. The isolation rate of MRSA was 33.3% - 68.1% from different samples. All Staphylococci isolates were susceptible to vancomycin, teicoplanin and linezolid. Five point five percent (7/128) E.faecium strains were resistant to vancomycin. All E. faecalis strains were susceptible to vancomycin. About 99.1% (108/109) of E.faecalis and E.faecium were susceptible to linezolid. The prevalence of penicillin-intermediate Streptococcus pneumoniae (PISP) was 21.6% (48/222). Only 1 (0.5%, 1/222) Streptococcus pneumoniae strain was resistant to penicillin. Teicoplanin, vancomycin, linezolid and tigecycline were the most active agents against Streptococcus pneumoniae (susceptible rate 100%).

CONCLUSIONS

The high prevalence of methicillin-resistance is among Staphylococcus strains. Different samples show a different MRSA prevalence. Teicoplanin, vancomycin and linezolid show very high activity to Staphylococci, E. faecalis, E. faecium and Streptococcus pneumoniae.

Mediastinitis after cardiac surgery in Madani Heart Center, Tabriz, Iran

Post-sternotomy infections are a kind of nosocomial infection involving the mediastinum space and the sternum, with a high morbidity and mortality rate. The present study was carried out to identify the incidence of mediastinitis following cardiac surgery and the most common risk factors. Cardic patients undergoing surgery were studied for suspicious mediastinitis infection at the Madani Heart Center, Tabriz, Iran from 2004 to 2006. The most common isolated agents included the coagulase-negative staphylococci, Staphylococcus aureus, Pseudomonas aeruginosa and Enterobacter spp. Incidence of postoperative mediastinitis after cardiac surgery was 1.2%. The mortality rate of postoperative mediastinitis was high (34.3%). Wound infection, especially mediastinitis following cardiac surgery, is rare but could be life-threatening. The most important step in the management of wound infections is prevention, and preventive measures could be strengthened by identifying the risk factors.

Accuracy and potential usefulness of triplex real-time PCR for improving antibiotic treatment of patients with blood cultures showing clustered gram-positive cocci on direct smears

Bacterial identification and antibiotic susceptibility testing currently require 48 h when a first blood culture (BC) is positive for clustered gram-positive cocci on direct smear examination (DSE). Meanwhile, antibiotic treatment is often inadequate, reducing the chances of effective treatment or creating unnecessary selective pressure. A new real-time PCR (RT-PCR) technique that differentiates Staphylococcus aureus from coagulase-negative staphylococci (CoNS) and detects methicillin resistance in 90 min in BC bottles could help solve these problems. BC bottles from 410 patients with gram-positive cocci on DSE were processed by current methods, and patients' treatments were prospectively recorded. The RT-PCR assay was performed on aliquots of these BCs, which had been kept frozen. For the 121 patients who had true bacteremia, we established whether the faster availability of RT-PCR results could have led to the initiation of treatments different from those actually given. RT-PCR sensitivity and specificity were 100% for differentiating between S. aureus and CoNS and detecting methicillin resistance with two manufacturers' BC bottles. For 31/86 (36%) of the S. aureus-infected patients and for 8/35 (23%) of the CoNS-infected patients who either had suboptimal or nonoptimal treatment or were untreated 48 h after positivity was detected, the early availability of RT-PCR results could have allowed more effective treatment. Unnecessary glycopeptide treatments could have been avoided for 28 additional patients. The use of RT-PCR would increase treatment effectiveness in patients with staphylococcal bacteremia and reduce the selective pressure created by glycopeptides.

High frequency of histamine-producing bacteria in the enological environment and instability of the histidine decarboxylase production phenotype

Lactic acid bacteria contribute to wine transformation during malolactic fermentation. They generally improve the sensorial properties of wine, but some strains produce histamine, a toxic substance that causes health issues. Histamine-producing strains belong to species of the genera Oenococcus, Lactobacillus, and Pediococcus. All carry an hdcA gene coding for a histidine decarboxylase that converts histidine into histamine. For this study, a method based on quantitative PCR and targeting hdcA was developed to enumerate these bacteria in wine. This method was efficient for determining populations of 1 to 10(7) CFU per ml. An analysis of 264 samples collected from 116 wineries of the same region during malolactic fermentation revealed that these bacteria were present in almost all wines and at important levels, exceeding 10(3) CFU per ml in 70% of the samples. Histamine occurred at an often important level in wines containing populations of the above-mentioned bacteria. Fifty-four colonies of histamine producers isolated from four wines were characterized at the genetic level. All were strains of Oenococcus oeni that grouped into eight strain types by randomly amplified polymorphic DNA analysis. Some strains were isolated from wines collected in distant wineries. Moreover, hdcA was detected on a large and possibly unstable plasmid in these strains of O. oeni. Taken together, the results suggest that the risk of histamine production exists in almost all wines and is important when the population of histamine-producing bacteria exceeds 10(3) per ml. Strains of O. oeni producing histamine are frequent in wine during malolactic fermentation, but they may lose this capacity during subcultures in the laboratory.

Development of 16S rRNA-based probes for the identification of Gram-positive anaerobic cocci isolated from human clinical specimens

Fluorescent probes targeted at 16S rRNA were designed for Peptostreptococcus anaerobius and Peptostreptococcus stomatis (Pana134), Parvimonas micra (Pamic1435), Finegoldia magna (Fmag1250), Peptoniphilus asaccharolyticus (Pnasa1254), Peptoniphilus ivorii (Pnivo731), Peptoniphilus harei (Pnhar1466), Anaerococcus vaginalis (Avag1280) and Anaerococcus lactolyticus (Alac1438), based on the 16S rRNA sequences of reference strains and 88 randomly chosen clinical isolates. These strains were also used for validation of the probes. Application of the probes to an additional group of 100 clinical isolates revealed that 87% of Gram-positive anaerobic cocci (GPAC) could be identified with this set of probes. The 16S rRNAs of 13 clinical isolates that could not be identified were sequenced. Most of these isolates were GPAC that were not targeted by the probes. No clinical isolates of Pn. asaccharolyticus were encountered. Near full-length sequences were obtained from 71 of 101 (n = 88 + 13) sequenced clinical isolates. Of these, 25 showed <98% similarity with the homologues of the closest established species. The Fmag1250, Pamic1435, Pnhar1466, Pana134, Pnasa1254 and Pnivo731 probes allowed reliable identification and hybridised with all corresponding isolates. The Avag1280 and Alac1438 probes failed to hybridise with two isolates and one isolate, respectively, because of intra-species variation. However, overall, the set of probes yielded fast and reliable identification for the majority of clinical isolates.

Development of a base stacking hybridization-based microarray method for rapid identification of clinical isolates

A base stacking hybridization-based microarray method was developed for rapid identification of clinical isolates within 2 h. The oligonucleotide probe sequences for species or genus-level identification were targeted against ribosomal RNA. Isolates were lysed and directly hybridized to the microarray-bound capture probes without conventional DNA or RNA isolation and prior polymerase chain reaction amplification. Five bacterial species encountered frequently in the clinical setting, Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae, and one genus Enterococcus, could be discriminated by the microarray-based assay. Identification by this method matched biochemical identification for 150 of 152 clinical strains. This base-stacking hybridization microarray offers a simple, fast (</=2 h), and accurate identification of bacterial cultures and is a potential tool for routine clinical diagnosis.

Population dynamics and metabolite target analysis of lactic acid bacteria during laboratory fermentations of wheat and spelt sourdoughs

Four laboratory sourdough fermentations, initiated with wheat or spelt flour and without the addition of a starter culture, were prepared over a period of 10 days with daily back-slopping. Samples taken at all refreshment steps were used for determination of the present microbiota. Furthermore, an extensive metabolite target analysis of more than 100 different compounds was performed through a combination of various chromatographic methods including liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. The establishment of a stable microbial ecosystem occurred through a three-phase evolution within a week, as revealed by both microbiological and metabolite analyses. Strains of Lactobacillus plantarum, Lactobacillus fermentum, Lactobacillus rossiae, Lactobacillus brevis, and Lactobacillus paraplantarum were dominating some of the sourdough ecosystems. Although the heterofermentative L. fermentum was dominating one of the wheat sourdoughs, all other sourdoughs were dominated by a combination of obligate and facultative heterofermentative taxa. Strains of homofermentative species were not retrieved in the stable sourdough ecosystems. Concentrations of sugar and amino acid metabolites hardly changed during the last days of fermentation. Besides lactic acid, ethanol, and mannitol, the production of succinic acid, erythritol, and various amino acid metabolites, such as phenyllactic acid, hydroxyphenyllactic acid, and indolelactic acid, was shown during fermentation. Physiologically, they contributed to the equilibration of the redox balance. The biphasic approach of the present study allowed us to map some of the interactions taking place during sourdough fermentation and helped us to understand the fine-tuned metabolism of lactic acid bacteria, which allows them to dominate a food ecosystem.

Planococcus columbae sp. nov., isolated from pigeon faeces

An orange-pigmented, Gram-positive bacterial strain, designated PgEx11T, was isolated from pigeon faeces. Analysis of the 16S rRNA gene sequence of the isolate indicated that it had 94.2–98.2 % sequence identity with respect to those of seven recognized species of the genus Planococcus. The strain PgEx11T contained anteiso-C15 : 0 as a major cellular fatty acid and MK-7 and MK-8 as the major menaquinones. The DNA G+C content of strain PgEx11T was 50.5 mol%. Furthermore, analysis of the 16S rRNA gene sequence indicated high levels of similarity with Planococcus rifietoensis (98.2 %), Planococcus maitriensis (97.6 %), Planococcus citreus (97.5 %) and Planococcus maritimus (97.1 %). However, the mean value for DNA–DNA relatedness between PgEx11T and these four closely related species was in the range 45.4–16.8 %, respectively. Moreover, strain PgEx11T also differs from its close relatives with regard to biochemical and chemotaxonomic characteristics. On the basis of phenotypic, chemotaxonomic and genotypic differences, strain PgEx11T represents a novel species of the genus Planococcus, for which the name Planococcus columbae sp. nov. is proposed. The type strain is PgEx11T (=MTCC 7251T=DSM 17517T).

Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin

Three groups of previously unknown gram-positive, anaerobic, coccus-shaped bacteria were characterized using phenotypic and molecular taxonomic methods. Phenotypic and genotypic data demonstrate that these organisms are distinct, and each group represents a previously unknown subline within Clostridium cluster XIII. Two groups are most closely related to Peptoniphilus harei in the genus Peptoniphilus, and the other group is most closely related to Anaerococcus lactolyticus in the genus Anaerococcus. Based on the findings, three novel species, Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov., are proposed. The type strains of Peptoniphilus gorbachii sp. nov., Peptoniphilus olsenii sp. nov., and Anaerococcus murdochii sp. nov. are WAL 10418(T) (= CCUG 53341(T) = ATCC BAA-1383(T)), WAL 12922(T) (= CCUG 53342(T) = ATCC BAA-1384(T)), and WAL 17230(T) (= CCUG 53340(T) = ATCC BAA-1385(T)), respectively.

Granulicatella elegans native valve infective endocarditis: case report and review

Granulicatella elegans is a fastidious organism that is rarely implicated as a cause of infective endocarditis. Here, we describe a patient with mitral valve prolapse who developed G. elegans endocarditis. The organism was isolated from blood cultures and the patient had mitral valvuloplasty and repair, and completed a course of 6 weeks of intravenous antibiotics with no sequela.

Antipropionibacterial activity of BAL19403, a novel macrolide antibiotic

BAL19403 exemplifies a new family of macrolide antibiotics with excellent in vitro activity against propionibacteria. MICs indicated that BAL19403 was very active against erythromycin-resistant and clindamycin-resistant propionibacteria with mutations in the region from positions 2057 to 2059 (Escherichia coli numbering) of the 23S rRNA, although it is less active against those rare clinical isolates in which a methyltransferase, ErmX, confers macrolide and lincosamide resistance by dimethylation of the adenine moiety at position 2058. BAL19403 was predominantly bacteriostatic toward the propionibacteria, and population analyses indicated resistance selection frequencies for BAL19403 and the comparator drugs (erythromycin, clindamycin) in the range 10(-8) to 10(-9) for cutaneous propionibacteria with diverse antibiotic resistance profiles. On the basis of its antipropionibacterial activity and its high anti-inflammatory activity, BAL19403 represents a promising topical treatment for mild to moderate inflammatory acne vulgaris.

Laboratory-based evaluation of the colorimetric VITEK-2 Compact system for species identification and of the Advanced Expert System for detection of antimicrobial resistances: VITEK-2 Compact system identification and antimicrobial susceptibility testing

The newly redesigned colorimetric VITEK-2 Compact system with updated Advanced Expert System (AES) (bioMerieux, Marcy l'Etoile, France) was evaluated for its accuracy and rapidity to identify clinical isolates and to detect several antimicrobial resistances. Overall, the VITEK-2 gave 95.8% of compatibility with the reference API strips (bioMerieux) in the identifications (IDs) of Gram-positive cocci (GPC), Gram-negative rods (GNR), and yeasts. The accuracy was finally estimated to 98.3% through additional confirmatory tests. Also, >90% of IDs of GPC and GNR were obtained within 7 h of incubations. The VITEK AES correctly detected 97.7% of antimicrobial resistances, including extended-spectrum beta-lactamases, oxacillin and inducible clindamycin resistances in staphylococci, vancomycin resistance in enterococci, and penicillin and erythromycin resistances in Streptococcus pneumoniae. The most resistant isolates were identified within 12 h of incubations. In conclusion, the new colorimetric VITEK-2 Compact system with AES greatly improved its accuracy in species ID and detection of antimicrobial resistances, and it will be highly acceptable to clinical microbiology laboratory function.

Evaluation of the in vitro activity of daptomycin against 19615 clinical isolates of Gram-positive cocci collected in North American hospitals (2002-2005)

We evaluated the antimicrobial activity of daptomycin against 19,615 clinical strains consecutively collected by numerous centers located across the United States and Canada (2002-2005). Daptomycin was very active against all indicated species (>99% susceptible), with the highest MIC results being 2, 8, 0.5, and 1 microg/mL for staphylococci, enterococci, beta-hemolytic streptococci, and viridans group streptococci, respectively, and no significant loss in potency was observed over the period studied.

Evaluation of the Merlin MICRONAUT system for rapid direct susceptibility testing of gram-positive cocci and gram-negative bacilli from positive blood cultures

Bloodstream infections are life-threatening conditions which require the timely initiation of appropriate antimicrobial therapy. We evaluated the automated Merlin MICRONAUT system for rapid direct microtiter broth antimicrobial susceptibility testing (AST) of gram-positive cocci and gram-negative bacilli from BACTEC 9240 bottles with positive blood cultures in comparison to the standard method for the Merlin MICRONAUT system. This prospective study was conducted under routine working conditions during a 9-month period. Altogether, 504 isolates from 409 patients and 11,819 organism-antibiotic combinations were evaluated for comparison of direct and standard AST methods. For gram-negative bacilli, direct and standard AST of 110 isolates was evaluated and MIC agreement was found for 98.1% of 2,637 organism-antibiotic combinations. Category (susceptible, intermediate susceptible, resistant [SIR]) agreement was found for 99.0%, with results for 0.04% of combinations showing very major errors, those for 0.2% showing major errors, and those for 0.8% showing minor errors. For gram-positive cocci, 373 isolates were evaluated and MIC agreement was found for 95.6% of 8,951 organism-antibiotic combinations. SIR agreement was found for 98.8%, with results for 0.3% of combinations showing very major errors, those for 0.4% showing major errors, and those for 0.5% showing minor errors. Although the number of tested isolates was limited (n = 33), direct AST of streptococci was performed for the first time, yielding promising results with SIR agreement for 98.6% of 363 organism-antibiotic combinations. In conclusion, direct AST of gram-negative bacilli and gram-positive cocci from positive blood cultures with the MICRONAUT system is a reliable technique that allows for the omission of repeat testing of subcultured isolates. Thereby, it reduces the time to results of blood culture testing and may have a positive impact on patient care.

In vitro activities of the lipopeptides palmitoyl (Pal)-Lys-Lys-NH(2) and Pal-Lys-Lys alone and in combination with antimicrobial agents against multiresistant gram-positive cocci

The in vitro activities of the lipopeptides palmitoyl (Pal)-Lys-Lys-NH(2) and Pal-Lys-Lys against gram-positive cocci were investigated. Enterococci and streptococci demonstrated higher susceptibilities than staphylococci and Rhodococcus equi. A positive interaction was shown when the lipopeptides were combined with beta-lactams and vancomycin. These results suggest that lipopeptides are promising candidates for antimicrobial therapy for infections caused by gram-positive organisms.

Contemporary causes of skin and soft tissue infections in North America, Latin America, and Europe: Report from the SENTRY Antimicrobial Surveillance Program (1998–2004)

The morbidity and cost for cure associated with skin and soft tissue infections (SSTIs) have recently become more complicated because of the increasing prevalence of multidrug-resistant pathogens associated with this healthcare problem. The SENTRY Antimicrobial Surveillance Program has been monitoring SSTI since 1997, and now presents data from 3 continents over a 7-year period (1998-2004). Isolates were tested by reference broth microdilution methods at a central laboratory using the Clinical and Laboratory Standards Institute (formerly the National Committee for Clinical Laboratory Standards) methods and interpretative criteria. The predominant pathogens included Staphylococcus aureus (ranked 1st in all geographic regions), Pseudomonas aeruginosa, Escherichia coli, and Enterococcus spp. A considerable variation in the methicillin (oxacillin)-resistant S. aureus rate was noted between countries and continents, with the overall rate highest in North America (35.9%) compared with Latin America (29.4%) and Europe (22.8%). Vancomycin-resistant Enterococcus spp. increased in Europe (4.1%) and North America (6.2%) during the period, but remained low and relatively unchanged in Latin America. Among the P. aeruginosa isolates tested, susceptibility to imipenem was much lower in Latin America (65.3%) compared with the other regions (80.7-88.7%), and resistance being associated with an increase in metallo-beta-lactamase-producing strains in Latin America and in some European countries. Multidrug-resistant strains of P. aeruginosa were also more of a concern in Latin America (24.7%) compared with Europe (10.8%) or North America (3.2%). Latin America also had the highest occurrence of extended-spectrum beta-lactamase-producing isolates among E. coli (15.1%) and Klebsiella spp. (48.0%) when compared with other regions. Continued surveillance of pathogen prevalence and antimicrobial resistance patterns should provide information that is important to improve empiric care particularly in the hospital environment.

Humicoccus flavidus gen. nov., sp. nov., isolated from soil

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

Multiple-Stress Tolerance of Ionizing Radiation-Resistant Bacterial Isolates Obtained from Various Habitats: Correlation Between Stresses

Isolation of five ionizing radiation (IR)-resistant bacteria by screening of isolates from various habitats classified as common and stressed is reported. IR-resistant isolates exhibited varying degrees of resistance to gamma-radiation and were classified as highly and moderately radiation resistant. Resistance to ultraviolet (UV) radiation correlated well with gamma-radiation resistance, whereas a comparable desiccation resistance for all the highly and moderately radiation-resistant isolates was observed. However, salt tolerance failed to correlate with IR resistance, indicating a divergent evolution of the salt tolerance and radiation resistance. Characterization of isolates by the amplified rDNA restriction analysis profiling attested to the clustering of these isolates with their stress phenotype. 16S rRNA gene-based analysis of the isolates showed that the bacteria with similar-resistance physiologies clustered together and belonged to related genera. Hydrogen peroxide resistance and mitomycin survival patterns of the isolates indicated the roles of oxidative-stress tolerance in desiccation survival and recombination repair in higher radiation resistance, respectively.

Development of a flow chart for identification of gram-positive anaerobic cocci in the clinical laboratory

Gram-positive anaerobic cocci (GPAC) are a heterogeneous group of organisms that are isolated from clinical specimens more often than any group of anaerobic bacteria except Bacteroides species, yet many strains are still difficult or impossible to identify in the diagnostic laboratory. In this study, a total of 124 strains, including 13 reference strains of GPAC species and 111 isolates that had been recovered from clinical specimens previously and identified by 16S rRNA gene sequencing, were subjected to biochemical characterization. Based on the results, a short biochemical scheme that involves the minimum essential biochemical tests for accurate identification of clinically important GPAC was developed.

Globicatella sanguinis is an etiological agent of ventriculoperitoneal shunt-associated meningitis

Globicatella sanguinis is a very rare isolate in clinical samples. We present a case of meningitis in a 69-year-old female patient after implantation of an external left ventricular drainage due to a hydrocephalus. She recovered after antibiotic treatment with ceftriaxone.

Clinical and microbiological profiles of ear infections in Osogbo, Nigeria

Despite the fact that discharging ears (DE) are one of the most common presentations to ear, nose and throat (ENT) clinics in the tropics, few reports have documented the aetiologic agents involved. The pathogenesis is therefore not fully understood and treatment remains controversial. We present in this report the microbiological characteristics of DE over a 3-year-period at the ENT clinic of Ladoke Akintola University Teaching Hospital, Osogbo, Southwest Nigeria.

Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue

Six strains of lactic acid bacteria were isolated in Japan from a composting distilled shochu residue. The six isolates grew poorly on MRS agar and slowly in MRS broth. The 16S rRNA gene sequences did not show high levels of similarity to those of the recognized species of lactic acid bacteria, and formed a subcluster within the cluster comprising obligately heterofermentative lactic acid bacteria closely related to Oenococcus oeni. The levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon and were genetically separate from O. oeni. Furthermore, various phenotypic characteristics such as the optimum pH for growth, malolactic fermentation and resistance to 10 % ethanol revealed that the isolates are distinguishable from O. oeni. On the basis of their phylogenetic and phenotypic characteristics, the isolates represent a novel species, for which the name Oenococcus kitaharae sp. nov. is proposed. The type strain is NRIC 0645T (=JCM 13282T=DSM 17330T).

Bacteremia after diagnostic conventional laparoscopy and minilaparoscopy: a prospective study in 100 patients

BACKGROUND/GOALS

Diagnostic laparoscopy under sedoanalgesia is a valuable tool in the work-up of liver diseases and is helpful as a staging procedure. The rate of bacteremia caused by this procedure is unknown, in particular when performed as minilaparoscopy.

STUDY

A 100 consecutive patients having undergone diagnostic laparoscopy carried out either conventionally (group I, n=50) or as minilaparoscopy (group II, n=50) were prospectively enrolled in this study. Blood cultures were drawn before and within 5 minutes after the procedure. Risk factors for bacteremia were evaluated.

RESULTS

Bacterial growth occurred in 4 blood cultures drawn immediately after laparoscopy. No patient developed fever or other signs of infection in the follow-up. Risk factors predisposing to bacteremia could not be identified.

CONCLUSIONS

Conventional diagnostic laparoscopy under sedoanalgesia and minilaparoscopy are associated with a low rate of bacteremia as in diagnostic upper endoscopy.

Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22

The potential for biodegradation of aromatic hydrocarbons simultaneously at low temperatures and under saline and alkaline conditions is not well understood, but such biodegradation would be useful for remediation of polluted sites. A psychrotolerant, moderately haloalkaliphilic pure culture using benzene as a sole source of carbon and energy was isolated by selective enrichment from alkaline and saline soils in the vicinity of the Daqing oil field in China. An analysis of the 16S rDNA gene sequence and morphological and physiological characteristics showed that this strain is a member of the genus Planococcus, and it was designated as strain ZD22. Strain ZD22 could grow at temperatures between 2 and 36 degrees C (pH 7.5-11) and salt concentrations from 0.5 to 25%. Its optimal conditions for biodegradation of benzene were 20 degrees C (pH 9.5) and 10% salt concentration. Strain ZD22 not only utilized benzene, toluene, ethylbenzene and o-xylene, but also degraded chlorobenzene, bromobenzene, iodobenzene and fluorobenzene. The kinetic model of strain ZD22 for benzene was solved to obtain mumax=0.34 h-1, Ks=0.041 mM, n=1.21, Sm=10.2 mM. To our knowledge, this is the first report of biodegradation of benzene and its derivatives simultaneously under multiple extreme conditions.

Acute cholecystitis accompanied by acute pancreatitis potentially caused by Dolosigranulum pigrum

We report a case of acute cholecystitis accompanied by acute pancreatitis and caused by Dolosigranulum pigrum in a 76-year-old male with gallstones. D. pigrum was isolated from a blood culture and confirmed by biochemistry tests and 16S rRNA sequencing. The isolate was susceptible to the beta-lactams ampicillin, penicillin, cephalothin, ceftriaxone, ceftazidime, chloramphenicol, and vancomycin but was intermediate to erythromycin and clindamycin. The patient recovered without sequelae after treatment with appropriate antibiotics for two weeks.

High frequency of Alloiococcus otitidis in the nasopharynx and in the middle ear cavity of otitis-prone children

OBJECTIVE

Colonization of middle ear pathogens is facilitated in the nasopharynx of otitis-prone children, and is associated with the development of otitis media. Recently, a new species of bacterium, Alloiococcus otitidis, is considered as one of the major middle ear pathogens. However, as far as we know, no study has been reported concerning the prevalence of A. otitidis in the nasopharynx of otitis-prone children. And, no study has been conducted on the association of A. otitidis in the nasopharynx with otitis media.

METHODS

The frequency of A. otitidis in 83 middle ear effusions (MEE) and 56 nasopharyngeal swab (NPS) specimens from 56 children with otitis media was investigated by culture and polymerase chain reaction (PCR).

RESULTS

A. otitidis was detected in 24 (28.9%) of MEE and in 6 (10.7%) of NPS specimens. When the frequency was investigated in relation to proneness to otitis media, A. otitidis was detected in 16 (64%) of 25 MEE and in 5 (29.4%) of 17 NPS specimens from otitis-prone children, whereas it was detected in 8 (13.8%) of 58 MEE and in 1 (2.6%) of 39 NPS specimens from non-otitis-prone children. The frequency of A. otitidis in both NPS and MEE specimens was significantly higher in otitis-prone than in non-otitis-prone children.

CONCLUSIONS

Our results suggest that colonization of A. otitidis is facilitated in the nasopharynx of otitis-prone children. And, nasopharyngeal colonization of A. otitidis may be associated with the frequency of otitis media.

Reduction of catheter-related colonisation by the use of a silver zeolite-impregnated central vascular catheter in adult critical care

Central vascular catheters (CVC) are used extensively in critical care for monitoring and therapy. They can become colonised with viable micro-organisms within 24 h of insertion, which can rapidly form biofilm. This colonisation is a precursor of catheter-related bloodstream infections (CR-BSI), which are associated with substantial morbidity, mortality, prolonged hospital stay and increased cost. Antimicrobials have been incorporated into the bulk material of CVC or applied to their surfaces as a coating in an attempt to reduce the incidence of CVC colonisation and infection. This study examines the effect of a silver zeolite-impregnated catheter on catheter-related colonisation and infection in adult critical care patients. The study was conducted in adult Intensive Care Units (ICU) at three acute hospitals over 14 months and involved 246 CVC insertions (122 silver-impregnated and 124 non-impregnated). CVC tip colonisation was detected by the Maki Roll culture and CR-BSI by differential time-to-positivity of blood cultures. Overall colonisation rate was significantly lower in the silver zeolite-impregnated CVC tips (58%) as compared with the control CVC tips (73%) (p<0.025). In addition, there was a lower rate (34%) of tip colonisation by coagulase negative staphylococci in the silver zeolite-impregnated CVC tips as compared with the control CVC tips (47%) (p<0.05). Four episodes of CR-BSI were detected in each arm by differential time-to-positivity in a subset of patients. This study indicates that the silver zeolite-impregnated catheter is superior to non-impregnated catheter in reducing the rate of CVC colonisation but it showed no difference in the rates of CR-BSI in the two arms. Larger prospective randomised control studies are required to evaluate its role in the prevention of CR-BSI.

Catellicoccus marimammalium gen. nov., sp. nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium from porpoise and grey seal

Two strains of an unknown Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped bacterium, originating from a porpoise and a grey seal, were characterized using phenotypic, biochemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type L-lys-gly-D-Asp) and a DNA G+C content of 38 mol%. Comparative 16S rRNA gene sequencing showed that this unidentified coccus-shaped organism formed a hitherto unknown subline closely related to, albeit distinct from, a number of other catalase-negative genera which included Enterococcus, Melissococcus, Tetragenococcus and Vagococcus. Other known Gram-positive, catalase-negative taxa were more distantly related. Tree-branching considerations and sequence divergence values of >6% with recognized taxa were indicative of this novel bacterium representing a separate genus. Based on phenotypic and phylogenetic evidence, it is proposed that this unknown bacterium, recovered from a porpoise and a grey seal, be classified as a novel genus and species, Catellicoccus marimammalium gen. nov., sp. nov. The type strain is M35/04/3T (=CCUG 49459T=CIP 108575T).

Evaluation of the LightCycler Staphylococcus M GRADE kits on positive blood cultures that contained gram-positive cocci in clusters

We evaluated the Roche LightCycler Staphylococcus M(GRADE) kits to differentiate between Staphylococcus aureus and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing S. aureus), the assay was 100% sensitive and 98.44% specific for S. aureus and 100% sensitive and specific for coagulase-negative staphylococci.

Sau-PCR, a novel amplification technique for genetic fingerprinting of microorganisms

The proposed technique is based on the digestion of genomic DNA with the restriction endonuclease Sau3AI and subsequent amplification with primers whose core sequence is based on the Sau3AI recognition site. The method was tested on strains of lactic acid bacteria but could be proposed for virtually any culturable organism from which DNA can be extracted.

Evaluation of intra-specific diversities in Oenococcus oeni through analysis of genomic and expressed DNA

In winemaking Oenococcus (O.) oeni is the most frequent species of lactic acid bacteria (LAB) associated with malolactic fermentation (MLF). Several studies have demonstrated that O. oeni is a quite homogeneous species and strains are difficult to differentiate especially when isolates from the same region are analyzed. In this study, the molecular biodiversity of O. oeni isolated from wines of the same region (Aglianico produced in Basilicata Region, Southern Italy) was evaluated with the aim of designing a molecular approach for discrimination and characterization of the isolates at the strain level. Three molecular techniques were applied: random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR), restriction endonucleases analysis-pulsed field gel electrophoresis (REA-PFGE) and differential display PCR (DD-PCR). The results obtained by RAPD-PCR confirmed the difficulty in differentiating isolates. By means of REA-PFGE a higher polymorphism, often related to the origin (winery) of strains, was revealed. However, on analyzing strains isolated from the same winery, only in some cases was more than one REA-PFGE pattern obtained. By analyzing dendrograms constructed on the basis of DD-PCR profiles differentiation of strains isolated from the same winery, in some cases, could be accomplished. The reliability of the DD-PCR in the differentiation of closely related strains suggests that this method could represent an alternative and/or additional tool to other molecular methods, such as REA-PFGE, for fine characterization of oenococcal strains.

Evaluation of a rapid direct assay for identification of bacteria and the mec A and van genes from positive-testing blood cultures

We performed the first evaluation of a DNA strip assay (GenoType blood culture; Hain Lifescience, Nehren, Germany) for the detection of the most relevant bacterial sepsis pathogens directly from positive BACTEC blood culture bottles (Becton Dickinson, Heidelberg, Germany). The test comprises two panels, one for the direct species identification of important gram-positive cocci and the other for gram-negative rods. Additionally, detection of the mec A and the van genes are implemented. The GenoType assay was validated regarding its analytical sensitivity with blood cultures spiked with reference strains. Approximately 10(4) CFU per ml were detected. Analytical specificity was calculated with a test panel of 212 reference strains. Of the strains tested, 99% were correctly identified. Additionally, 279 consecutive blood cultures signaled positive by BACTEC were processed directly, in comparison to conventional methods. The GenoType assays were performed according to Gram stain morphology. A total of 243 (87.1%) of the 279 organisms isolated were covered by specific probes. A total of 152 organisms were gram-positive cocci, of which 148 (97.4%) were correctly identified by the GenoType assay. Ninety-one organisms were gram-negative rods, of which 89 (97.8%) were correctly identified. Concerning mec A gene detection, GenoType assay correctly detected 12 of 13 methicillin-resistant Staphylococcus aureus isolates. One Enterococcus faecium isolate with a positive van A gene isolated was correctly differentiated by the assay. All results were available 4 h after the results of microscopic analysis. The evaluated GenoType blood culture assay showed fast and reliable results in detecting the most important sepsis pathogens and the mec A and van genes directly from positive blood culture bottles.

Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules

A Gram-positive bacterium, designated strain AG019T, was isolated by micromanipulation from aerobic granules obtained from a laboratory-scale sequencing batch reactor. This isolate grew axenically as cocci clustered predominantly in tetrads, and was morphologically similar to the dominant organisms observed in the biomass. The morphology also resembled that of the tetrad-forming organisms commonly seen in activated sludge samples. Strain AG019T was found to be an oxidase-negative, catalase-positive, non-motile aerobe that does not reduce nitrate and grows at temperatures between 15 and 40 °C, with an optimum at 37 °C. The pH range for growth was 5·0–9·0, with an optimum at pH 7·5. Strain AG019T contained a peptidoglycan with directly cross-linked meso-diaminopimelic acid (type A1γ) and lacked mycolic acids. The G+C content of the DNA was 75 mol%. Menaquinone MK-8(H2) was the major isoprenoid quinone. The bacterium stained positively for intracellular polyphosphate granules but not for poly-β-hydroxyalkanoates. It produced capsular material and showed autoaggregation ability. Phenotypic and 16S rRNA gene analyses showed that the bacterium differed sufficiently from its closest phylogenetic relatives, namely members of the suborder Frankineae, which includes the genera Geodermatophilus, Blastococcus, Frankia, Sporichthya, Acidothermus and Microsphaera, that it is proposed that it be placed in a novel genus, Quadrisphaera, as Quadrisphaera granulorum gen. nov., sp. nov. The type strain is AG019T (=ATCC BAA-1104T=DSM 44889T).

Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium

A Gram-positive, non-motile, non-spore-forming coccus (strain JST) was isolated from kimchi (a traditional Korean food) and investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between strain JST and its closest relative, Tetragenococcus halophilus IAM 1676T, was 98·1 %. The level of DNA–DNA relatedness between the two strains was 9·7 %. Strain JST had a DNA G+C content of 38·3 % and a cellular fatty acid profile containing 16 : 0, 18 : 1 and cyclo fatty acids. Phylogenetic data and genomic and phenotypic features demonstrated that strain JST represents a novel species, for which the name Tetragenococcus koreensis sp. nov. is proposed. The type strain is JST (=KCTC 3924T=DSM 16501T=LMG 22864T).

Atopococcus tabaci gen. nov., sp. nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega9, C(16:0) and C(18:1)omega9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allofustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (=CIP 108502(T)).

Population dynamics ofOenococcus oenistrains in a new winery and the effect of SO2and yeast strain

The effects of different yeast starters and SO(2) addition on malolactic fermentation in a new winery were evaluated by a molecular approach in three vintages. Alcoholic fermentations with 40 and 100mgl(-1) SO(2) were carried out, followed by uninoculated malolactic fermentations. Isolated colonies of Oenococcus oeni obtained from samples throughout the vinification were identified and typified by multiplex RAPD-PCR. This made it possible to monitor the population dynamics and follow the proportion of as many as 29 different indigenous strains. In one of the vintages, O. oeni strains were more inhibited when a specific yeast starter was used.

Blood culture Gram stain and clinical categorization based empirical antimicrobial therapy of bloodstream infection

Early antimicrobial treatment has a great influence on the outcome of patients with blood stream infections (BSI). The study was designed to see if the simple practice of patient categorization (community acquired, nosocomial or infection in haematological unit) combined with Gram stain data could be used to guide empirical treatment of BSI in 1901 consecutive positive blood culture findings. There were considerable differences in the occurrence of common pathogens and their antimicrobial susceptibilities between patient categories especially for Gram-positive cocci. For example, second generation cephalosporins covered more than 70% cocci in clusters and over 80% of cocci in chains in community acquired infections whereas in hospital acquired infections the corresponding figures were only 47 and 44%. We conclude that Gram stain results of positive blood cultures along with the knowledge of where the infection was acquired, would allow early accurate targeting of antimicrobial therapy for BSI.

Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov

Phylogenetic analysis of 16S rRNA gene sequences revealed thatEnterococcus solitariusis not a member of the genusEnterococcus, but is related to species of the genusTetragenococcus. On a phylogenetic tree,E. solitariusclustered withTetragenococcus halophilusandTetragenococcus muriaticus, with which it showed the highest 16S rRNA gene sequence similarity level (about 94 %). Phenotypic studies indicated thatE. solitariuswas also unable to produce acid from lactose, providing further evidence of its affiliation to the genusTetragenococcus. DNA hybridization studies indicated thatE. solitariuswas clearly a separate species, different fromT. halophilusandT. muriaticus(reassociation levels of about 23 and 54 %, respectively). As suggested in previous studies,E. solitariusis closely related to but clearly distinct fromT. halophilus. Based upon properties that taxonomically distinguish it from species of the genusEnterococcus, it is proposed thatE. solitariusbe transferred to the genusTetragenococcusand reclassified asTetragenococcus solitariuscomb. nov. (type strain, 885/78T=ATCC 49428T=CCUG 29293T=CIP 103330T=DSM 5634T=JCM 8736T=LMG 12890T=NCTC 12193T).

Fastidiosipila sanguinis gen. nov., sp. nov., a new Gram-positive, coccus-shaped organism from human blood

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6 % O(2). Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al., Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15 % or more were observed between the unidentified bacterium and all other recognized species within this and related rRNA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp. nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (=CIP 108292(T)).

Fast protocols for the 5S rDNA and ITS-2 based identification ofOenococcus oeni

To identify specific marker sequences for the rapid identification of Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-labeled specific oligonucleotides for fluorescence in situ hybridization (FISH). These probes are partial complementary to each other. This feature promotes the accessibility to the target sequence within the ribosome and enhances the fluorescence signal. For the rapid identification of Oenococci both the 5S rRNA gene and the ITS-2 region are useful targets.

Performance of the new VITEK 2 GP card for identification of medically relevant gram-positive cocci in a routine clinical laboratory

The VITEK 2 gram-positive (GP) identification card (bioMerieux, Marcy l'Etoile, France) has been redesigned to achieve greater accuracy in the identification of gram-positive cocci. A total of 43 biochemical tests, including 17 enzymatic tests, are present in the card and interpreted in a kinetic mode, for up to 8 h. The VITEK 2 database, used in conjunction with the GP identification card, allows the identification of 115 different taxa. A total of 364 strains of GP cocci (217 Streptococcaceae strains and 147 Micrococcaceae strains) belonging to 31 taxa were tested with the new VITEK 2 GP identification card. Of the 364 strains, 105 were taken from routine primary plating media. A total of 344 strains (94.5%) were correctly identified to the species level and 17 strains (4.7%) were identified with low discrimination, requiring additional tests, whereas 1 strain (0.3%) was incorrectly identified and 2 strains (0.5%) remained unidentified. Within 7 h of the start of incubation, more than 90% of all strains were identified. Of the 105 primary cultures, 97% were correctly identified to the species level, 2% were identified with low discrimination, and 1% remained unidentified. Identification performance data were independent of each of the three plating media used. It is concluded that the new VITEK 2 GP identification card provides reliable results for the identification of GP cocci under routine laboratory conditions.