The Occurrence of Vibrionaceae, Staphylococcaceae, and Enterobacteriaceae in Green Turtle Chelonia mydas Rearing Seawater

In this study, levels of Vibrionaceae, Staphylococcaceae, and Enterobacteriaceae were observed in seawater from juvenile green turtle Chelonia mydas rearing tanks and in the incoming coastal seawater (the water supply). Bacterial loads were compared between the incoming coastal seawater and two different rearing conditions: in cement tanks at a low stocking density and in fiberglass tanks at a high stocking density. The total bacterial counts in seawater from fiberglass tanks were statistically greater than those in cement tanks. The nonlactose and lactose fermenting enterobacteria, tellurite-reducing bacteria, and total plate counts in water from all rearing containers were greater than those in coastal seaweater by a logarithmic fold change of 2--3. Differences in bacterial population structure of the incoming coastal seawater and rearing water were also addressed. The results from biochemical identification of 344 isolates revealed that the bacteria that were commonly found in water samples were Citrobacter spp., Enterobacteria spp., Edwardsiella spp., Staphylococcus spp., Staphylococcus aureus, Photobacterium spp., Vibrio alginolyticus, and Vibrio spp. Conclusively, the microbiological monitoring of rearing water provides important and essential information on the management of aquatic animal health and husbandry.

Blood culture result profile and antimicrobial resistance pattern: a report from neonatal intensive care unit (NICU), Asella teaching and referral hospital, Asella, south East Ethiopia

Background

Antimicrobial resistance is one of the major public health emergencies worldwide, and this trend didn't spare developing countries like Ethiopia. The objective of this study was to evaluate patterns of bacterial isolates and local antimicrobial susceptibility patterns in neonatal sepsis.

Methods

A hospital based observational study was conducted from April 2016 to May 2017 in Asella teaching and referral hospital (ATRH). A total of 303 neonates with clinical sepsis were included. Collected data were entered into EPI-INFO version 3.5.1 for cleanup; and then exported to SPSS version 21 for further analysis. Frequencies and proportion were used to describe the study population in relation to relevant variables.

Results

Bacterial growth was detected in 88 (29.4%) of blood cultures. Predominantly isolated bacteria were coagulase negative staphylococci (CoNS) 22 (25%), Escherichia coli (E.Coli) 18 (20.5%) and Staphylococcus aureus 16 (18%). Resistance rates of S. aureus and CoNS against Ampicillin were 11 (69%) and 20 (91%) respectively. The resistance rate of E. coli against Ampicillin and Gentamycin were 12 (66.7%) and 10 (55.6%) while Klebsiella spp. resistance rate gets much higher against these two first line antibiotics [10 (91%) and 9 (82%) respectively]. Similarly, both Gram-positive and Gram-negative bacteria isolates were also highly resistant to third generation Cephalosporins, and 63 (72%) isolated bacteria showed multidrug-resistance. However; Gram-positive bacteria isolates had better susceptibility patterns to third line antibiotics like Clindamycin, Vancomycin and Ciprofloxacin while Gram-negative isolates had a higher susceptibility to Ciprofloxacin and Amikacin.

Conclusion

CoNS, S. aureus, E. coli and Klebsiella spp. were the leading bacterial causes of neonatal sepsis in our study. They were highly resistant to first- and second-line empiric antimicrobial treatment used at NICU (Neonatal intensive care unit), reducing the antimicrobial choices for management of neonatal sepsis. Fortunately, the mentioned isolated bacteria remained susceptible to third line antibiotics used to treat neonatal sepsis.

Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing

Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.

Culturable symbionts associated with the reproductive and digestive tissues of the Neotropical brown stinkbug Euschistus heros

Symbionts are widely distributed in eukaryotes, and potentially affect the physiology, ecology and evolution of their host. Most insects harbour free-living bacteria in their haemocoel and gut lumen, intracellular-living bacteria in a range of tissues or bacteria in host-derived specialized cells. Stinkbugs, as do many arthropods, harbour extracellular bacteria in the gut that may affect the fitness of their host. This study identified the culturable symbionts associated with the ovaries, spermatheca, seminal vesicle and posterior midgut region (V4) of males and females of Euschistus heros (F.) (Hemiptera: Pentatomidae). Several culture media were used to isolate the bacteria associated with these structures. The selected colonies (morphotypes) were cultured in liquid medium, subjected to genomic DNA extraction, 16S rRNA gene amplification, and restriction fragment length polymorphism (RFLP) analyses. Morphotypes with distinct RFLP patterns were purified and sequenced, and the sequences obtained were used for putative identification and phylogenetic analysis. Comparison of the sequences with those available in the EzTaxon-e database and the use of a matrix of paired distances grouped the isolates in phylotypes belonging to the Phylum Proteobacteria. Proteobacteria was represented by γ-Proteobacteria phylotypes belonging to Enterobacteriaceae, while Firmicutes had Bacilli phylotypes distributed in Enterococcaceae and Staphylococcaceae. Some of the phylotypes identified were associated exclusively with single structures, such as ovaries, spermatheca and the V4 midgut region of males and females. All culturable bacteria associated with the seminal vesicle were also associated with other tissues.

Concentration of facultative pathogenic bacteria and antibiotic resistance genes during sewage treatment and in receiving rivers

Whereas the hygienic condition of drinking and bathing water by law must be monitored by culture-based methods, for quantification of microbes and antibiotic resistance in soil or the aquatic environment, often molecular genetic assays are used. For comparison of both methods, knowledge of their correlation is necessary. Therefore the population of total bacteria, Escherichia coli, enterococci and staphylococci during sewage treatment and in receiving river water was compared by agar plating and quantitative polymerase chain reaction (qPCR) assays. In parallel, all samples were investigated for clinically relevant antibiotic resistance genes. Whereas plating and qPCR data for total bacteria correlated well in sewage after primary treatment, qPCR data of river water indicated higher cell numbers for E. coli. It is unknown if these cells are 'only' not growing under standard conditions or if they are dead. Corresponding to the amount of non-culturable cells, the 'breakpoints' for monitoring water quality should be adapted. The abundances of clinically relevant antibiotic resistance genes in river water were in the same order of magnitude or even higher than in treated sewage. For estimation of the health risk it is important to investigate which species carry respective genes and whether these genes are disseminated via gene transfer.

Salinicoccus amylolyticus sp. nov., isolated from a saltern

A Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA-DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTmwas >5 °C indicating that the strain represents a novel species of the genus Salinicoccus. Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccusamylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants

BACKGROUND

The microbiota plays an important role in insect development and fitness. Understanding the gut microbiota composition is essential for the development of pest management strategies. Midgut bacteria were isolated from nine wild B. cucurbitae populations collected from different agroecological zones of India. These isolates were further studied for attractant potential of fruit fly adults, and the chemical constituents in the supernatants of gut bacteria were analysed.

RESULTS

Twenty-six bacterial isolates belonging to the families Enterobacteriaceae, Bacillaceae, Micrococcaceae and Staphylococcaceae were isolated and identified on the basis of 16S rRNA gene sequence analysis. The dominant species in the midgut of melon fly were from the genera Enterobacter (34.6%), Klebsiella (19.2%), Citrobacter (7.7%), Bacillus (15.4%) and Providencia (7.7%), and 3.8% each of Micrococcus, Staphylococcus, Leclercia and Exiguobacterium. Bactrocera cucurbitae and B. dorsalis adults were significantly attracted to bacterial whole cell cultures and their supernatants in the fruit fly attraction bioassays. Bacillus cereus, Enterobacter, Klebsiella, Citrobacter and Providencia species attracted both male and females of Bactrocera species. The supernatants of Klebsiella, Citrobacter and Providencia species attracted a significantly greater number of females than males. The most abundant chemical constituents in supernatants of K. oxytoca and C. freundii were 3-methyl-1-butanol, 2-phenylethanol, butyl isocyanatoacetate, 2-methyl-1-propanol and 3-hydroxy-2-butanone, as identified by gas chromatography-mass spectrometry.

CONCLUSIONS

The bacterial endosymbionts associated with melon fly exhibited attractant potential which could facilitate eco-friendly insect control strategies. © 2015 Society of Chemical Industry.

The visualization of biofilms in chronic diabetic foot wounds using routine diagnostic microscopy methods

Diabetic foot wounds are commonly colonised by taxonomically diverse microbial communities and may additionally be infected with specific pathogens. Since biofilms are demonstrably less susceptible to antimicrobial agents than are planktonic bacteria, and may be present in chronic wounds, there is increasing interest in their aetiological role. In the current investigation, the presence of structured microbial assemblages in chronic diabetic foot wounds is demonstrated using several visualization methods. Debridement samples, collected from the foot wounds of diabetic patients, were histologically sectioned and examined using bright-field, fluorescence, and environmental scanning electron microscopy and assessed by quantitative differential viable counting. All samples (n = 26) harboured bioburdens in excess of 5 log₁₀ CFU/g. Microcolonies were identified in 4/4 samples by all three microscopy methods, although bright-field and fluorescence microscopy were more effective at highlighting putative biofilm morphology than ESEM. Results in this pilot study indicate that bacterial microcolonies and putative biofilm matrix can be visualized in chronic wounds using fluorescence microscopy and ESEM, but also using the simple Gram stain.

The routine use of atypical cultures in presumed aseptic revisions is unnecessary

BACKGROUND

In presumed aseptic hip and knee revisions, it is common practice to send intraoperative cultures to screen for occult infection. Currently no guidelines exist for the routine use of acid-fast bacillus (AFB) and fungal cultures in this setting.

QUESTIONS/PURPOSES

We established (1) the rate of positive fungal and AFB cultures in aseptic hip and knee revision arthroplasties, (2) factors associated with positive fungal and AFB cultures, (3) the likelihood that positive cultures represent true-positive results, and (4) the hospital charges of sending fungal and AFB cultures routinely.

METHODS

We retrospectively evaluated all 1717 presumed aseptic hip and knee revisions performed from January 2006 to November 2011: 1139 patients had at least one intraoperative fungal culture and 1133 patients had at least one intraoperative AFB culture, with 923 and 920, respectively, achieving 1-year followup. The Musculoskeletal Infection Society criteria were used to classify subsequent infections. We attempted to identify risk factors for positive cultures.

RESULTS

We observed six (0.5%) patients with positive AFB cultures and 19 (1.7%) with positive fungal cultures. Patients undergoing reimplantation procedures were more likely to have a positive fungal culture. The true-positive rate was 0% and 0.1% for AFB and fungal cultures, respectively. The total hospital charges for these cultures over the time frame of our study were USD 1,315,533.

CONCLUSIONS

Given the extremely low rate of true-positive AFB and fungal cultures in presumed aseptic revision joint arthroplasty and the charges associated with maintaining these cultures, we believe their routine use is unwarranted.

LEVEL OF EVIDENCE

Level III, prognostic study. See the Instructions for Authors for a complete description of evidence.

Appropriateness of Empiric Gentamicin and Vancomycin Therapy for Bacteremias in Chronic Dialysis Outpatient Units in the Era of Antibiotic Resistance

Bacteremias in inpatient chronic HD units have been described, but there is little information on bacteremias in ambulatory HD units. To determine the frequency of bacteremia and pathogen distribution in ambulatory chronic HD units, we retrospectively reviewed our experience with 107 bacteremias in 5 chronic ambulatory HD units over a 3 year period. The object of the study was twofold. The first objective was to determine if bacteremias in ambulatory HD setting were substantially different in frequency or type than in the inpatient HD setting. Secondly, febrile patients suspected of having bacteremia in chronic HD patients are often empirically treated with vancomycin and gentamicin. Chronic HD patients require repeated and frequent venous access for HD. Bacteremias are common in chronic HD patients and may be primary or secondary and are often related to venous access site infections. The distributions of bacteremia pathogens in chronic HD patients are predominantly reflective of skin flora, i.e., staphylococci and to lesser extent aerobic Gram-negative bacilli. After S. aureus (MSRA/MSSA) and coagulase-negative staphylococcus (CoNS), enterococci are the next most important Gram-positive pathogens in bacteremic HD patients. Most strains of E. faecalis are sensitive to vancomycin and for practical purposes should be considered as vancomycin sensitive enterococci (VSE). In contrast, most strains of E. faecium are resistant to vancomycin and should be considered as vancomycin resistant enterococci (VRE). We retrospectively reviewed 107 patients on chronic ambulatory HD to determine the adequacy of empiric vancomycin and gentamicin prophylaxis. We found amikacin is preferred to gentamicin and that meropenem is an effective alternate substitution for gentamicin and vancomycin combination therapy.

16S rRNA terminal restriction fragment length polymorphism for the characterization of the nasopharyngeal microbiota

A novel non-culture based 16S rRNA Terminal Restriction Fragment Length Polymorphism (T-RFLP) method using the restriction enzymes Tsp509I and Hpy166II was developed for the characterization of the nasopharyngeal microbiota and validated using recently published 454 pyrosequencing data. 16S rRNA gene T-RFLP for 153 clinical nasopharyngeal samples from infants with acute otitis media (AOM) revealed 5 Tsp509I and 6 Hpy166II terminal fragments (TFs) with a prevalence of >10%. Cloning and sequencing identified all TFs with a prevalence >6% allowing a sufficient description of bacterial community changes for the most important bacterial taxa. The conjugated 7-valent pneumococcal polysaccharide vaccine (PCV-7) and prior antibiotic exposure had significant effects on the bacterial composition in an additive main effects and multiplicative interaction model (AMMI) in concordance with the 16S rRNA 454 pyrosequencing data. In addition, the presented T-RFLP method is able to discriminate S. pneumoniae from other members of the Mitis group of streptococci, which therefore allows the identification of one of the most important human respiratory tract pathogens. This is usually not achieved by current high throughput sequencing protocols. In conclusion, the presented 16S rRNA gene T-RFLP method is a highly robust, easy to handle and a cheap alternative to the computationally demanding next-generation sequencing analysis. In case a lot of nasopharyngeal samples have to be characterized, it is suggested to first perform 16S rRNA T-RFLP and only use next generation sequencing if the T-RFLP nasopharyngeal patterns differ or show unknown TFs.

[Infectious endocarditis due to Gemella morbillorum found by splenic infarction--a case report]

A 64-year-old man with prostate cancer and bone metastasis admitted for nausea, left abdominal pain showed no abnormal, and fever, abdominal ultrasound or chest X-ray findings. Despite antibiotics, left abdominal pain persisted for several days. Abdominal computed tomography (CT), showed splenic infarction. Transesophageal echocardiography suggested infectious endocarditis (IE) as a possible infarction cause, and roth spots were found on the retina. Gemella morbillorum was detected from blood culture. IE commonly causes Fever of Unknown Origin found by infarction. G. morbillorum, an anaerobic gram-positive, viridans group streptococci, is indigenous to the oropharynx, upper respiratory, urogenital, and gastrointestinal tracts, and is thought to have weak toxicity and pathogenicity in the body.

Salinicoccus kekensis sp. nov., a novel alkaliphile and moderate halophile isolated from Keke Salt Lake in Qinghai, China

A novel alkaliphilic and moderate halophilic bacterium, designated strain K164(T), was isolated from Keke Salt Lake in Qinghai, China. The strain grew with 2.0-20.0% (w/v) NaCl, at 4-50 degrees C and pH 6.5-11.5, with an optimum of 8% (w/v) NaCl, 37degrees C and pH 10, respectively. The predominant respiratory quinone was menaquinone 6 (MK-6) and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were anteiso-C(15:0) and iso-C(15:0). The genomic DNA G+C content was 50.16 mol. Phylogenetic analysis based on the full-length 16S rRNA gene sequence revealed that strain K164(T) was a member of the genus Salinicoccus. Strain K164(T) showed the highest similarity (98.4%) with Salinicoccus alkaliphilus AS 1.2691(T) and below 97% similarity with other recognized members of the genus in 16S rRNA gene sequence. Level of DNA-DNA relatedness between strain K164(T) and Salinicoccus alkaliphilus AS 1.2691(T) was 20.1%. On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain K164(T) is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccus kekensis sp. nov. is proposed. The type strain is K164(T) (=CGMCC 1.10337(T) = DSM 23173(T)).

[Influence of immunodepressors on population level and adhesive characteristics of opportunistic bacteria in large intestine of white mice]

AIM

To assess the effects of cyclophosphamide (CP), methotrexate (MT), and prednisolone (PS) on the levels of staphylococci, enterococci, Escherichia coli (EC) and lactose-negative enterobacteria (LNEB) in feces of white mice as well as to determine adhesive properties of isolated microorganisms.

MATERIALS AND METHODS

Drugs were administered intragastrically during 6 weeks; CP in dose 35.4 mg/kg daily; MT - 2.5 mg/kg over week; PS - 2.5 mg/kg daily; sterile distilled water was administered to controls. Microflora was assessed by common methods; adhesion of microorganisms to group 0 (I) human erythrocytes was determined.

RESULTS

Administration of prednisolone leads to increase of isolation rate of staphylococci, CP increased levels of LNEB and EC with suppressed enzymatic activity (P < 0.05). MT decreased isolation rate of typical EC (P < 0.05). MT also decreased degree of adhesion of EC and LNEB, whereas PS enhanced adhesiveness of LNEB, and CP decreased adhesion of staphylococci (P < 0.05). Statistically significant correlation between number and adhesiveness of enterobacteria was established (r = 0.73, P < 0.01).

CONCLUSION

Immunodepressors from different groups have non-similar effects on quantitative characteristics of microflora and adhesiveness of isolated opportunistic microorganisms.

[Cutaneous abscess due to Gemella morbillorum]

We report a cutaneous abscess due to Gemella morbillorum, a Gram positive coccus found in oropharyngeal flora, that rarely causes disease in humans. Infections associated to this agent are similar to those related to viridans streptococci. There have been reports of endovascular infections (predominantly endocarditis) and also of acute invasive infections. Few previous reports are available of cutaneous infection.

Gemella morbillorum liver abscess

We report a case of liver abscess caused by Gemella morbillorum. G. morbillorum was isolated and confirmed from both pus and blood. The patient recovered uneventfully after catheter drainage and treatment with cefmetazole. This is the first case report of liver abscess caused by G. mobillorum in the English literature.

Jeotgalicoccus marinus sp. nov., a marine bacterium isolated from a sea urchin

A novel non-sporulating, non-motile, catalase- and oxidase-positive, facultatively anaerobic, moderately halophilic, Gram-positive coccus, designated JSM 076033(T), was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. Strain JSM 076033(T) was able to grow in the presence of 0.5-25.0 % (w/v) total salts and at pH 6.0-10.0 and 10-45 degrees C; optimum growth was observed with 5.0-10.0 % (w/v) total salts and at pH 7.0-8.0 and 25-30 degrees C. The major amino acid constituents of the cell wall were glycine, lysine and alanine. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The respiratory quinones were MK-7 (60.7 %) and MK-6 (39.3 %) and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 40.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 076033(T) should be assigned to the genus Jeotgalicoccus. The sequence similarities between the novel isolate and the type strains of recognized Jeotgalicoccus species were in the range 95.2-97.2 %. The results of the phylogenetic analysis, combined with DNA-DNA relatedness data, phenotypic characteristics and chemotaxonomic information, support the view that strain JSM 076033(T) represents a novel species of the genus Jeotgalicoccus, for which the name Jeotgalicoccus marinus sp. nov. is proposed. The type strain is JSM 076033(T) (=CCTCC AA 207028(T) =DSM 19772(T) =KCTC 13189(T)).

Peritoneal dialysis-related peritonitis caused by Gemella morbillorum in a patient with systemic lupus erythematosus receiving steroid therapy

Gemella morbillorum, a Gram-positive coccus, is a natural inhabitant of the human oropharyngeal, upper respiratory and gastrointestinal tracts. Human infections caused by this organism are rare. We describe a case of peritoneal dialysis-related peritonitis due to G. morbillorum in a patient with systemic lupus erythematosus receiving steroid therapy. The patient responded well to antibiotics, without removal of the peritoneal catheter.

Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China

A novel yellow-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, obligately aerobic, moderately halophilic, facultatively alkaliphilic Gram-positive coccus, strain YIM Y15(T), was isolated from a brine sample from a salt mine in Yunnan, south-west China. Strain YIM Y15(T) grew in the presence of 0.5-25 % (w/v) NaCl and at pH 6.0-10.0, with optimum growth at 8-10 % (w/v) NaCl and pH 8.0. It grew at 4-45 degrees C, with optimum growth at 37.0 degrees C. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Menaquinone 6 (MK-6) was the major respiratory quinone. The cell wall contained Lys and Gly. The DNA G+C content was 46.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15(T) was a member of the genus Salinicoccus, with low 16S rRNA gene sequence similarity to the type strains of the five described species of the genus, Salinicoccus alkaliphilus JCM 11311(T) (sequence similarity 96.0 %), Salinicoccus roseus DSM 5351(T) (94.9 %), Salinicoccus jeotgali KCTC 13030(T) (94.8 %), Salinicoccus salsiraiae LMG 22840(T) (94.8 %) and Salinicoccus hispanicus DSM 5352(T) (94.7 %). Together with the phenotypic differences, these results supported the proposal of a novel species of the genus Salinicoccus, Salinicoccus kunmingensis sp. nov., with YIM Y15(T) (=DSM 17847(T) =CGMCC 1.6302(T)) as the type strain.

Salinicoccus salitudinis sp. nov., a new moderately halophilic bacterium isolated from a saline soil sample

A novel pale-yellow-pigmented, moderately halophilic, facultatively alkaliphilic, non-motile, non-spore-forming, catalase- and oxidase-positive, obligately aerobic Gram-positive coccus, strain YIM-C678T was isolated from a saline soil sample collected from a hypersaline habitat in the Qaidam basin, northwest China. The organism grew at 4-37 degrees C and pH 6.0-11.0, with optimum growth at 25 degrees C and pH 8.0. Strain YIM-C678T grew optimally in the presence of 10-12% (w/v) NaCl and growth was observed in 1-25% (w/v) NaCl. The cell wall murein type was L: -Lys-Gly5. Major cellular fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C16:0. Menaquinone 6 (MK-6) was the major respiratory quinone. The DNA G + C content was 46.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM-C678T belonged to the family Staphylococcaceae and was most closely related to the eight described species of the genus Salinicoccus with sequence similarities from 92.2 (S. luteus YIM 70202T) to 97.5% (S. kunmingensis YIM Y15T). The DNA-DNA relatedness between strain YIM-C678T and S. kunmingensis YIM Y15T was 35.4%. Chemotaxonomic data and 16S rRNA gene sequence analysis supported the affiliation of strain YIM-C678T with the genus Salinicoccus. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that the bacterium represents a novel species of the genus Salinicoccus, for which the name Salinicoccus salitudinis sp. nov. is proposed, with YIM-C678T (=DSM 17846 = CGMCC 1.6299) as the type strain.

Salinicoccus siamensis sp. nov., isolated from fermented shrimp paste in Thailand

Fifteen strains of moderately halophilic, Gram-positive cocci were isolated from a traditional fermented shrimp paste ('ka-pi') produced in Thailand. These bacteria were strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. They produced orange pigment and grew in the presence of 1.5-25 % (w/v) NaCl. They grew optimally in 10 % (w/v) NaCl, at pH 8.5 and at 37 degrees C. The cell-wall peptidoglycan was of l-Lys type. Menaquinone with six isoprene units (MK-6) was a major component. The dominant cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). DNA G+C contents were in the range 44.5-47.5 mol%. Comparative 16S rRNA gene sequence analyses indicated that representative strain PN1-2(T) was related most closely to Salinicoccus roseus JCM 14630(T), with 97.3 % similarity. The other novel strains were included in the same species based on their levels of DNA-DNA relatedness to strain PN1-2(T) (> or =76.6 %) but showed low DNA-DNA relatedness to S. roseus JCM 14630(T) (21.7 %). On the basis of the phenotypic and molecular data presented, the 15 novel strains are suggested to represent a single novel species of the genus Salinicoccus, for which the name Salinicoccus siamensis sp. nov. is proposed. The type strain is PN1-2(T) (=JCM 12822(T) =PCU 242(T) =TISTR 1562(T)).

Salinicoccus luteus sp. nov., isolated from a desert soil

A moderately halophilic bacterium, strain YIM 70202(T), was isolated from a desert soil sample collected from Egypt and was subjected to a taxonomic investigation. In a phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70202(T) was affiliated to the Salinicoccus clade, showing 94.5-96.8 % 16S rRNA gene sequence similarity to the recognized species of the genus Salinicoccus, in which Salinicoccus roseus CCM 3516(T) was the nearest neighbour. The DNA-DNA relatedness value of the novel isolate with S. roseus CCM 3516(T) was 12.7 %. The novel isolate grew at temperatures between 4 and 45 degrees C and at pH values ranging from 7.0 to 11.0, with an optimum of 30 degrees C and pH 8.0-9.0, respectively. Strain YIM 70202(T) grew optimally in the presence of 10 % NaCl (w/v) and growth was observed at NaCl concentrations in the range 1-25 % (w/v). Chemotaxonomic data revealed that strain YIM 70202(T) contained MK-6 as the predominant respiratory quinone, possessed L-Lys-Gly(5) as the cell-wall peptidoglycan, had phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid as the polar lipids and contained i-C(15 : 0) and ai-C(15 : 0) as the predominant fatty acids. The DNA G+C content was 49.7 mol%. The biochemical and chemotaxonomic properties demonstrate that strain YIM 70202(T) represents a novel species of the genus Salinicoccus. The name Salinicoccus luteus sp. nov. is proposed with strain YIM 70202(T) (=CGMCC 1.6511(T)=KCTC 3941(T)) as the type strain.

Bacterial diversity in aphthous ulcers

INTRODUCTION

Recurrent aphthous ulcers are common lesions of the oral mucosa of which the etiology is unknown. This study aimed to estimate the bacterial diversity in the lesions and in control mucosa in pooled samples using a culture-independent molecular approach.

METHODS

Samples were collected from ten healthy individuals and ten individuals with a clinical history of recurrent aphthous ulcers. After DNA extraction, the 16S ribosomal RNA bacterial gene was amplified by polymerase chain reaction with universal primers; amplicons were cloned, sequenced and matched to the GenBank database.

RESULTS

A total of 535 clones were analyzed, defining 95 bacterial species. We identified 62 putative novel phylotypes. In recurrent aphthous ulcer lesions 57 phylotypes were detected, of which 11 were known species. Control samples had 38 phylotypes, five of which were already known. Only three species or phylotypes were abundant and common to both groups (Gemella haemolysans, Streptococcus mitis strain 209 and Streptococcus pneumoniae R6). One genus was found only in recurrent aphthous ulcer samples (Prevotella) corresponding to 16% of all lesion-derived clones.

CONCLUSION

The microbiota found in recurrent aphthous ulcers and in the control groups diverged markedly and the rich variety of genera found can provide a new starting point for individual qualitative and quantitative analyses of bacteria associated with this oral condition.

Infectious Crystalline Keratopathy Caused by Gemella haemolysans

PURPOSE

To report a novel case of infectious crystalline keratopathy after penetrating keratoplasty caused by Gemella haemolysans.

METHODS

Observational case report. Patient notes and literature review.

RESULTS

A 51-year-old woman presented with the clinical picture of infectious crystalline keratopathy 18 months after a second penetrating keratoplasty was performed for corneal decompensation secondary to recurrent herpes simplex infection. Corneal biopsy yielded a heavy growth of G. haemolysans. Initial treatment was made up of frequent topical vancomycin 0.5% and was later changed to topical cefuroxime 5% and ofloxacin 0.3%. Snellen visual acuity after complete resolution of the keratitis was 6/60 as a result of a residual corneal scar.

CONCLUSIONS

Gemella haemolysans may be an etiologic agent in infectious crystalline keratopathy. A corneal biopsy may be diagnostic but may also promote healing by allowing direct access of antibiotics to deep-seated infected tissue and by altering the growth environment of the organism.

Nosocomial meningitis caused by Staphylococcus other than S. aureus in children: multicentre study

Analysing 101 cases of nosocomial meningitis due to staphylococci other than S. aureus within last 15 years, coagulase negative staphylococci represented the commonest pathogen. Major risk factor for staphylococcal meningitis was prior neurosurgery, mainly ventriculoperitoneal shunt insertion. Ten of 101 cases were caused by glycopeptide intermediate resistant strains in patients pretreated with multiple combination of antibiotics including vancomycin and shunt exchanges: 76% of strains were also oxacillin resistant.

Salinicoccus jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

A novel, moderately halophilic, Gram-positive coccus, designated strain S2R53-5(T), was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. Strain S2R53-5(T) grew in the presence of 0.5-15 % (w/v) NaCl and at pH 6.5-11.0, with optimum growth at 5 % (w/v) NaCl and pH 7.0. The temperature range for growth was 20.0-30.0 degrees C, with an optimum temperature of 30 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2R53-5(T) belongs to the family Staphylococcaceae and was most closely related to Salinicoccus roseus DSM 5351(T) (96.8 % gene sequence similarity), Salinicoccus hispanicus DSM 5352(T) (96.1 %), Salinicoccus alkaliphilus T8(T) (95.2 %) and Jeotgalicoccus halotolerans YKJ-101(T) (95.1 %). The genomic DNA G+C content was 47.0 mol%, which is in the range of 46-51 mol% that is characteristic for the genus Salinicoccus. Levels of DNA-DNA relatedness between strain S2R53-5(T) and S. roseus DSM 5351(T), S. hispanicus DSM 5352(T) and S. alkaliphilus KCTC 13928(T) were 32.2, 15.4 and 4.6 %, respectively. Chemotaxonomic data (major menaquinone, MK-6; major fatty acids, iso-C(15 : 0) and anteiso-C(15 : 0); cell-wall murein type, Lys and Gly) and 16S rRNA gene sequence analysis supported the affiliation of strain S2R53-5(T) with the genus Salinicoccus. The combined evidence from the low DNA-DNA relatedness, physiological, biochemical and other genotypic data indicate that strain S2R53-5(T) clearly represents a novel species of the genus Salinicoccus, for which the name Salinicoccus jeotgali sp. nov. is proposed. The type strain is S2R53-5(T) (=KCTC 13030(T)=LMG 23640(T)).

Meningitis due to Gemella haemolysans in a pediatric case

Gemella haemolysans is a rare pathogen in cases of bacterial meningitis. We present a case of meningitis due to G. haemolysans in a 17-month-old boy. This is the first reported case of Gemella meningitis in a child. The patient completely recovered following intravenous therapy with linezolid and chloramphenicol.

Pulmonary Nodules Associated With Gemella Bacteremia

Gemella morbillorum and Gemella haemolysans are normal oral flora that can also be pathogenic. We report 2 cases of adolescents with osteosarcoma who developed multiple pulmonary nodules associated with Gemella bacteremia. These nodules mimicked metastatic disease. To our knowledge, this manifestation of Gemella infection has not been previously reported. In the setting of malignancy, infectious pulmonary nodules must be distinguished from metastatic nodules in order to treat appropriately.

[Search for lactate oxidase producer microorganisms]

Using the method of enrichment cultures, eight lactate oxidase producer strains of the fungus Geotrichum candidum were identified. The microorganisms were isolated from diverse specimens of fermented vegetables and manure. Variation in the content of glucose and lactate and the degree of aeration made it possible to attain lactate oxidase activities of up to 130-140 U per 11 grown medium containing microbial cells.

Gemella haemolysans infectious crystalline keratopathy

PURPOSE

To report a case of infectious crystalline keratopathy caused by Gemella haemolysans.

METHODS

Observational case report. A 65-year-old woman underwent penetrating keratoplasty for contact lens-related Acanthamoeba keratitis and developed a nonhealing epithelial defect. Despite continued prophylaxis with topical gatifloxacin, small superficial stromal opacities were noted and cultured 6 months after penetrating keratoplasty. The opacities coalesced into a fine, crystalline keratopathy in the superficial stroma with persistent overlying epithelial defect.

RESULTS

Culture results from corneal scraping showed more than 100 colonies of G. haemolysans. Topical vancomycin was instituted, with complete resolution of the crystalline keratopathy and epithelial defect over the next 2 months.

CONCLUSIONS

G. haemolysans can be a causative organism of infectious crystalline keratopathy. This infection can arise in a postkeratoplasty patient despite prophylaxis with a fourth-generation fluoroquinolone.

Molecular epidemiology of macrolide and tetracycline resistances in commensal Gemella sp. isolates

The epidemiologic relatedness of 29 erythromycin-resistant Gemella sp. strains from normal flora, characterized previously, were evaluated by pulsed-field gel electrophoresis (PFGE). Three isolates carried the tet(O) gene and the tet(M) gene. The msr(A) gene was found in two Gemella morbillorum strains in combination with the erm(B) or mef(E) gene. The sequences of the mef(A/E), erm(B), and msr(A) genes showed a high similarity to the corresponding sequences of other gram-positive cocci. All the strains harboring the mef(A/E) gene and the msr(D) gene possessed open reading frame 3 (ORF3)/ORF6. The 16 G. morbillorum isolates represented 15 distinct DNA profiles. Four clusters were identified (>or=80% genetic relatedness). The 12 Gemella haemolysans strains belonged to different PFGE types. The clonal diversity found suggests that horizontal transfer may be the main route through which erythromycin resistance is acquired.

Recurrent upper airway infections and bacterial biofilms

BACKGROUND

Bacterial biofilms identified in various medical devices used in otorhinolaryngology, including tympanostomy tubes, voice prostheses, and cochlear implants, can directly colonise mucosal tissues. The upper airways seem to be at high risk for this type of colonisation. Chronic and/or recurrent upper airway infections may be related to the complex structural and biochemical (quorum sensing) organisation of the biofilm which interferes with the activity of antibiotics (including those with proven in vitro efficacy), thus promoting the establishment of a chronic infection eradicable only by surgical treatment. Biofilm formation plays a role in upper respiratory infections: it not only explains the resistance of these infections to antibiotic therapy but it also represents an important element that contributes to the maintenance of a chronic inflammatory reaction.

OBJECTIVES

To document the presence of biofilms in surgical tissue specimens from patients with recurrent infection diseases, and identify their possible role in the chronicity of these infectious processes.

METHOD

We examined 32 surgical specimens from the upper respiratory tract (tonsils, adenoids, mucosa from the ethmoid and maxillary sinuses) of 28 patients (20 adults, eight children) with upper airway infections that had persisted despite repeated treatment with anti-inflammatory agents and antibiotics with demonstrated in vitro efficacy. Tissues were cultured using conventional methods and subjected to scanning electron microscopy for detection of biofilm formation.

RESULTS

Over 80 per cent (26/32; 81.3 per cent) of the tissue specimens were culture-positive. Bacterial biofilms (associated in most cases with coccoid bacteria) were observed in 65.6 per cent of the tissue samples.

Gemella endocarditis: consider the colon

Gemella species, including Gemella morbillorum, are part of the normal flora of the human oropharynx, upper respiratory tract and gastrointestinal tract. Differentiation of Gemella from viridans streptococci in the laboratory may be difficult. Although uncommonly pathogenic, they have been implicated in a variety of human infections, most notably infective endocarditis. Dental instrumentation appears to be the usual source of infection. The case is reported of Gemella morbillorum native valve endocarditis, which was associated with an underlying colonic carcinoma. An association with colonic neoplasm has been described in three previous cases of endocarditis attributed to Gemella. It is well documented that Streptococcus bovis endocarditis may occur in the setting of colonic neoplasia. It is suggested that colonic investigation should be considered in patients with Gemella endocarditis, in whom no other source is apparent.

A case of septic arthritis due to infection with Gemella morbillorum

Gemella morbillorum is a facultatively anaerobic Gram-positive coccus which forms part of the normal flora of the oro-pharynx and the upper respiratory tract. It rarely causes human infection but has been described previously in cases of empyema and lung abscess, septic shock, endocarditis, meningitis, and osteomyelitis. We describe a case of septic arthritis due to G. morbillorum occurring in an otherwise healthy 42-year old man and review previous reports of infection in the literature.

An unusual case of brain abscess by Gemella morbillorum

A case of deep brain abscess by Gemella morbillorum is described. Due to high fever, lethargy, severe headache, and the risk of intraventricular rupture of the suppurative lesion, a CT-guided stereotactic aspiration of the abscess was successfully performed. The patient responded well to a 6-week course of meropenem, metronidazole, and fluconazole. Gemella spp. should not be considered as trivial commensals of the mucous membranes, but appear as emerging pathogens involved in endocarditis, septic shock, and necrotizing pneumonia, as well as in serious intracranial infections.

Streptococci dominate the diverse flora within buccal cells

Previously, we reported that intracellular Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythensis were present within buccal epithelial cells from human subjects, as lesser components of a polymicrobial flora. In this study, we further characterized that intracellular flora by using the same double-labeling techniques to identify Fusobacterium nucleatum, Prevotella intermedia, oral Campylobacter species, Eikenella corrodens, Treponema denticola, Gemella haemolysans, Granulicatella adiacens, and total streptococci within buccal epithelial cells. All those species were found within buccal cells. In every case, species recognized by green-labeled species-specific probes were accompanied by other bacteria recognized only by a red-labeled universal probe. Streptococci appeared to be a major component of the polymicrobial intracellular flora, being present at a level from one to two logs greater than the next most common species (G. adiacens). This is similar to what is observed in oral biofilms, where diverse species interact in complex communities that often are dominated by streptococci.

Ocular infection secondary to gemella

PURPOSE

To report four cases of ocular infection caused by Gemella species.

METHODS

Microbial identification was carried out using the MicroScan Walkaway system (Dade Behring) and/or Vitek-2 (bioMérieux) and susceptibility testing with either Kirby-Bauer disc diffusion and/or Vitek-2. The paper is presented as an interventional case report.

RESULTS

Four patients developed infection due to Gemella species. All responded to vancomycin or fortified aminoglycosides and broad-spectrum antibiotics.

CONCLUSION

Gemella spp. can cause opportunistic infections in the eye.

[Microflora of the mucous membrane of human tonsils in the normal state and in pathology]

A total of 50 healthy persons and 50 chronic tonsillitis patients were examined with the use of the bacteriological method. The microflora of tonsillar mucous membrane was represented by 8 genera of facultative anaerobic microorganisms. In the biocenosis of the tonsillar mucosa of the healthy subjects the occurrence of Streptococcus was 1.5-fold greater than in that of the patients; microorganisms of the genus Staphylococcus prevailed on the tonsillar mucosa of chronic tonsillitis patients 1.3-fold prevailed more often and Klebsiella and Neisseria prevailed 4-fold more often. Among the microorganisms isolated from the patients, cultures simultaneously having two or more pathogenicity markers occurred twice as often as among the representatives of the microbiocenosis obtained from the healthy subjects. The microflora of the tonsillar mucosa of the chronic tonsillitis patients was characterized by resistance to penicillins, macrolides and aminoglygosides, but was simultaneously sensitive to lincosamides and glycopeptides.

Pleural empyema associated with Gemella morbillorum: report of a case and review of the literature

Gemella morbillorum, a microaerophilic Gram-positive coccus, is a natural inhabitant of the human oropharyngeal, gastrointestinal and urogenital flora. However, it is an infrequently isolated organism and a rare cause of pulmonary or pleural infections. We report on a 26-y-old male subject with a past medical history of epilepsy and intravenous drug abuse, who presented with imminent sepsis and respiratory failure. Computed tomography of the thorax revealed a pleuropulmonary consolidation of the left lower lobe, and ultrasound guided thoracentesis resulted in aspiration of pus. Microbiological analysis revealed Gemella morbillorum in the pleural fluid. Thoracic drainage and antibiotic therapy resulted in full recovery. We discuss previous cases of pleuropulmonary infections due to Gemella morbillorum and review the available literature of this rare occurrence.

In vitro inhibition of SARS virus replication by human interferons

Four different types of human interferon, interferon-beta (IFN-beta), recombinant IFN-alpha2a and IFN-alpha2b and natural IFN-alpha were tested for antiviral activity against SARS-coronavirus. The experiments were performed using in vitro cultivated monkey Vero E6 cells. IFN-beta was found to be the most highly active antiviral agent, followed by natural IFN-alpha, whereas the 2 recombinant IFN-alpha2 species were poorly active in the system used. These results suggest that IFN-beta as well as natural IFN-alpha may be used for the treatment of SARS.