Septicemia due to Pasteurella pneumotropica: 16S rRNA sequencing for diagnosis confirmation

Bacteremia due to Pasteurella pneumotropica occurs infrequently. We report a case of septicemia in a 72-year-old woman who had no underlying illness. The microorganism was isolated from 10 blood cultures and identified by conventional and molecular methods. This is the first reported case of P. pneumotropica septicemia in an immunocompetent patient. The history of P. pneumotropica diseases in animals and humans and their varied clinical features are reviewed.     

Use of 16S rRNA gene sequencing for identification of nonfermenting gram-negative bacilli recovered from patients attending a single cystic fibrosis center

During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. Of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. These 46 isolates were genotypically identified as Pseudomonas aeruginosa (19 isolates, 12 patients), Achromobacter xylosoxidans (10 isolates, 8 patients), Stenotrophomonas maltophilia (9 isolates, 9 patients), Burkholderia cepacia genomovar I/III (3 isolates, 3 patients), Burkholderia vietnamiensis (1 isolate), Burkholderia gladioli (1 isolate), and Ralstonia mannitolilytica (3 isolates, 2 patients), a recently recognized species.     

Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing

We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.     

Use of 16S rRNA gene sequencing for identification of "Pseudomonas-like" isolates from sputum of patients with cystic fibrosis

Since nonfermenting, Gram negative bacilli recovered from patients with cystic fibrosis could be misidentified with phenotypic procedures, we used partial 16S ribosomal RNA gene (16S gene) sequencing to identify these "Pseudomonas-like" isolates. 473 isolates were recovered from 66 patients in 2003. Sequencing was used to identify 29 (from 24 patients) of the 473 isolates, showing unclear results with routine tests. PCR with specific primers was carried out to amplify a 995 bp fragment, which was then sequenced. The sequences were analyzed with GenBank database for species assignment. Phenotypic and genotypic results were concordant for 20/29 isolates (10 Pseudomonas aeruginosa, 5 Burkholderia cepacia, 3 Stenotrophomonas maltophilia, 2 Achromobacter xylosoxidans). However, 3 of the 5 B. cepacia isolates were then identified as Burkholderia multivorans with a PCR-RFLP procedure. Phenotypic misidentification was observed for 9/29 isolates: 4 A. xylosoxidans, 1 P. aeruginosa, 1 Bordetella petrii, 1 Bordetella bronchiseptica, 1 Ralstonia respiraculi and 1 Ralstonia mannitolilytica. Partial 16S gene sequencing improved the identification of "Pseudomonas-like" isolates from cystic fibrosis patients, but the accuracy to distinguish between genomovars of the B. cepacia complex was inadequate.     

Utilization of 16S ribosomal DNA sequencing for diagnosis of septicemia due to Neisseria elongata subsp. glycolytica in a neutropenic patient

Septicemia due to Neisseria elongata subsp. glycolytica occurs infrequently. We report a case of septicemia in a patient undergoing antimitotic chemotherapy. Gram-negative coccobacilli were isolated from blood cultures. The identity of the isolate by phenotypic methods was uncertain. In contrast, identity was confirmed by 16S ribosomal DNA sequencing, which appeared to be very useful for correct identification.     

Application of 16S rRNA gene sequencing to identify Bordetella hinzii as the causative agent of fatal septicemia

We report on the first case of fatal septicemia caused by Bordetella hinzii. The causative organism exhibited a biochemical profile identical to that of Bordetella avium with three commercial identification systems (API 20E, API 20 NE, and Vitek GNI+ card). However, its cellular fatty acid profile was not typical for either B. avium or previously reported strains of B. hinzii. Presumptive identification of the patient's isolate was accomplished by traditional biochemical testing, and definitive identification was achieved by 16S rRNA gene sequence analysis. Phenotypic features useful in distinguishing B. hinzii from B. avium were production of alkali from malonate and resistance to several antimicrobial agents.     

Clinical and microbiological features of a cystic fibrosis patient chronically colonized with Pandoraea sputorum identified by combining 16S rRNA sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry

Clonal isolates identified as various nonfermentative Gram-negative bacilli over a 5-year period from sputum cultures of a 30-year-old cystic fibrosis patient were successfully reidentified as Pandoraea sputorum by combining 16S rRNA sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Decreased lung function improved after 1 year of azithromycin and inhaled 7%-hypertonic saline treatment.     

Early prosthetic joint infection due to Ureaplasma urealyticum: Benefit of 16S rRNA gene sequence analysis for diagnosis

Detection of the most frequently bacteria involved in prosthetic joint infection (PJI) is usually performed by conventional cultures. We report a case of early PJI due to Ureaplasma urealyticum, diagnosed by 16S rRNA gene sequence analysis, which highlights the interest of molecular methods if fastidious bacteria are involved in PJI.     

Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing

Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.     

Identification of Mycobacterium neoaurum isolated from a neutropenic patient with catheter-related bacteremia by 16S rRNA sequencing

A rapidly growing pigmented mycobacterial strain with an ambiguous biochemical profile was isolated from the blood culture taken through the Hickman catheter of a 9-year-old girl with acute lymphoblastic leukemia. Whole-cell fatty acid analysis showed that the best match profile was that of Mycobacterium aurum, but the similarity index was only 0.217, meaning that there were no good matches between the isolate and the organisms in the database of the Microbial Identification System. The 16S rRNA gene of the mycobacterial strain was amplified, agarose gel purified, and sequenced. There were 44 base differences between the gene sequence of the isolate and that of M. aurum but only one base difference between the sequence of the isolate and that of Mycobacterium neoaurum, showing that the isolate was indeed a strain of M. neoaurum by using this "gold standard." This represents the first case of M. neoaurum infection documented by 16S rRNA sequencing.     

Pathological confirmation of cystic fibrosis in the fetus following prenatal diagnosis

Prenatal diagnosis of cystic fibrosis is presently based on the determination of microvillar enzyme activities in the amniotic fluid. However, there seems to be no accurate means for confirming the diagnosis of the aborted fetus. During the past year we performed pathological and histopathological examinations on 7 fetuses diagnosed in the second trimester of pregnancy to be affected by cystic fibrosis and compared them with 4 control age-matched fetuses. Glycol-methacrylate-embedded 2-3-mu thick sections of the pancreas, lungs, bronchial tree, and GI tract were stained with toluidine blue, H&E, PAS, and AB-PAS, and examined microscopically. In the controls, PAS-positive granules were dispersed throughout the cytoplasm of most pancreatic acinar and tracheal submucosal glandular cells. In the affected fetuses 2 distinct groups were identified. In one group of 4 fetuses, the pancreatic and tracheal submucosal glands were dilated and contained a weak PAS-positive material. The glandular epithelial cells had very little PAS-positive granules. In this group, the tracheal epithelium was either atrophic or metaplastic and devoid of microvilli. In the second group of 3 fetuses there was less dilation of the glands, and both pancreatic acinar cells and tracheal submucosal glandular epithelial cells contained few PAS-positive granules, which were confined mainly to a perinuclear location. The tracheal epithelial cells contained few microvilli which, when present, appeared thicker and shorter as compared to controls. We feel that histochemical evaluation of pancreatic and bronchial tissue may be of help in the pathological confirmation of cystic fibrosis in human fetuses where the results of the biochemical studies are suggestive of the disease.     

Fatal pulmonary infection due to multidrug-resistant Mycobacterium abscessus in a patient with cystic fibrosis

We report a case of fatal pulmonary infection caused by Mycobacterium abscessus in a young patient with cystic fibrosis, who underwent bipulmonary transplantation after a 1-year history of severe lung disease. Fifteen days after surgery he developed septic fever with progressive deterioration in lung function. M. abscessus, initially isolated from a pleural fluid specimen, was then recovered from repeated blood samples, suggesting a disseminated nature of the mycobacterial disease. Drug susceptibility testing assay, performed on two sequential isolates of the microorganism, showed a pattern of multidrug resistance. Despite aggressive therapy with several antimycobacterial drugs, including clarithromycin, the infection persisted, and the patient died.     

Role of universal 16S rRNA gene PCR and sequencing in diagnosis of prosthetic joint infection

The etiological diagnosis of prosthetic joint infection (PJI) requires the isolation of microorganisms from periprosthetic samples. Microbiological cultures often yield false-positive and false-negative results. 16S rRNA gene PCR combined with sequencing (16SPCR) has proven useful for diagnosing various infections. We performed a prospective study to compare the utility of this approach with that of culture to diagnose PJI using intraoperative periprosthetic samples. We analyzed 176 samples from 40 patients with PJI and 321 samples from 82 noninfected patients using conventional culture and 16SPCR. Three statistical studies were undertaken following a previously validated mathematical model: sample-to-sample analysis, calculation of the number of samples to be studied, and calculation of the number of positive samples necessary to diagnose PJI. When only the number of positive samples is taken into consideration, a 16SPCR-positive result in one sample has good specificity and positive predictive value for PJI (specificity, 96.3%; positive predictive value, 91.7%; and likelihood ratio [LR], 22), while 3 positive cultures with the same microorganism are necessary to achieve similar specificity. The best combination of results for 16SPCR was observed when 5 samples were studied and the same microorganism was detected in 2 of them (sensitivity, 94%; specificity, 100%; and LR, 69.62). The results for 5 samples with 2 positive cultures were 96% and 82%, respectively, and the likelihood ratio was 1.06. 16SPCR is more specific and has a better positive predictive value than culture for diagnosis of PJI. A positive 16SPCR result is largely suggestive of PJI, even when few samples are analyzed; however, culture is generally more sensitive.     

Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool

We investigated the diversity of the primary sequences of 16S rRNA genes among Neisseria meningitidis strains (Men) and evaluated the use of this approach as a molecular subtyping tool. We aligned and compared a 1,417-bp fragment of the 16S rRNA gene from 264 Men strains of serogroups A, B, C, and Y (MenA, MenB, MenC, and MenY, respectively) isolated throughout the world over a 30-year period. Thirty-one positions of difference were found among 49 16S types: differences between types ranged from 1 to 14 positions (0.07 to 0.95%). 16S types and serogroups were highly associated; only 3 out 49 16S types were shared by two or more serogroups. We have identified 16S types that are exclusively associated with strains of certain hypervirulent clones: 16S type 5 with MenA subgroup III, 16S type 4 with the MenB electrophoretic type 5 (ET-5) complex, and 16S types 12 and 13 with MenC of the ET-37 complex. For MenC strains, 16S sequencing provided the highest sensitivity and specificity and the best overall association with the outbreak-related versus sporadic isolates when compared with pulsed-field gel electrophoresis, multilocus enzyme electrophoresis, and multilocus sequence typing. We demonstrated for the first time an unexpected diversity among 16S rRNA genes of Men strains, identified 16S types associated with well-defined hypervirulent clones, and showed the potential of this approach to rapidly identify virulent strains associated with outbreaks and/or an increased incidence of sporadic disease.     

16S rRNA gene sequencing analysis of gut microbiome in a mini-pig diabetes model

Background : Currently, increasing attention is being paid to the important role of in-testinal microbiome in diabetes. However, few studies have evaluated the characteris-tics of gut microbiome in diabetic miniature pigs, despite it being a good model animal for assessing diabetes. Methods : In this study, a mini- pig diabetes model (DM) was established by 9- month high- fat diet (HFD) combined with low- dose streptozotocin, while the animals fed standard chow diet constituted the control group. 16S ribosomal RNA (rRNA) gene sequencing was performed to assess the characteristics of the intestinal microbiome in diabetic mini- pigs. Results : The results showed that microbial structure in diabetic mini- pigs was altered, reflected by increases in levels of Coprococcus_3 and Clostridium_sensu_stricto_1 , which were positively correlated with diabetes, and decreases in levels of the bac-teria Rikenellaceae , Clostridiales_vadinBB60_group , and Bacteroidales_RF16_group , which were inversely correlated with blood glucose and insulin resistance. Moreover, PICRUSt- predicted pathways related to the glycolysis and Entner- Doudoroff super-pathway, enterobactin biosynthesis, and the L - tryptophan biosynthesis were signifi-cantly elevated in the DM group. Conclusion : These results reveal the composition and predictive functions of the in-testinal microbiome in the mini- pig diabetes model, further verifying the relationship between HFD, gut microbiome, and diabetes, and providing novel insights into the application of the mini- pig diabetes model in gut microbiome research.     

Molecular diagnosis of Kingella kingae pericarditis by amplification and sequencing of the 16S rRNA gene

Kingella kingae is a fastidious gram-negative bacillus that is considered an emerging pathogen in pediatric settings but remains less common in adults. Here we describe a case of pericarditis in an immunocompetent adult host. The microorganism was identified directly from the clinical sample by molecular techniques, i.e., 16S rRNA gene amplification and sequencing.     

Use of 16S rRNA gene sequencing to identifyLactobacillus casei in septicaemia secondary to a paraprosthetic enteric fistula

Human infections caused byLactobacillus spp. are rarely reported in the literature. Underlying conditions are frequently reported, and identification of lactobacilli to the species level remains rare. A case ofLactobacillus casei septicaemia secondary to a vascular graft infection is reported. The 16S rRNA sequencing technique was used to definitively identifyLactobacillus casei.     

Characteristics of Bordetella hinzii strains isolated from a cystic fibrosis patient over a 3-year period.

Over a 3-year period, an adult cystic fibrosis patient underwent eight episodes of pulmonary exacerbation of his disease. At least one of two different strains of Bordetella hinzii could be isolated from sputum samples in every instance. The differentiation of B. hinzii from related taxa and its role as an etiologic agent of infections are discussed. The two isolates of B. hinzii reported are the third and fourth human-derived strains described in the literature.     

True microbiota involved in chronic lung infection of cystic fibrosis patients found by culturing and 16S rRNA gene analysis

Patients suffering from cystic fibrosis (CF) develop chronic lung infection. In this study, we investigated the microorganisms present in transplanted CF lungs (n = 5) by standard culturing and 16S rRNA gene analysis. A correspondence between culturing and the molecular methods was observed. In conclusion, standard culturing seems reliable for the identification of the dominating pathogens.