The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry.

Nitrogen removal is an important process for wastewater ponds prior to effluent release. Bacteria and archaea can drive nitrogen removal if they possess the genes required to metabolize nitrogen. In the tropical savanna of northern Australia, we identified the previously unresolved microbial communities responsible for nitrogen cycling in a multi-pond wastewater stabilization system by measuring genomic DNA and cDNA for the following: nifH (nitrogen fixation); nosZ (denitrification); hzsA (anammox); archaeal AamoA and bacterial BamoA (ammonia oxidation); nxrB (nitrite oxidation); and nrfA (dissimilatory NO3 reduction to NH3). By collecting 160 DNA and 40 cDNA wastewater samples and measuring nitrogen (N)-cycling genes using a functional gene array, we found that genes from all steps of the N cycle were present and, except for nxrB, were also expressed. As expected, N-cycling communities showed daily, seasonal, and yearly shifts. However, contrary to our prediction, probes from most functional groups, excluding nosZ and AamoA, were different between ponds. Further, different genes that perform the same N-cycling role sometimes had different trends over space and time, resulting in only weak correlations between the different functional communities. Although N-cycling communities were correlated with wastewater nitrogen levels and physico-chemistry, the relationship was not strong enough to reliably predict the presence or diversity of N-cycling microbes. The complex and dynamic response of these genes to other functional groups and the changing physico-chemical environment provides insight into why altering wastewater pond conditions can result an abundance of some gene variants while others are lost.

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx.

BACKGROUND: Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Non-invasive upper airway sampling is an alternative method for monitoring airway microbiota; however, there are limited data describing the relationship of such results with lung microbiota in young children. In this study, we compared the upper and lower airway microbiota in young children to determine whether non-invasive upper airway sampling procedures provide a reliable measure of either lung microbiota or clinically defined differences. RESULTS: The microbiota in oropharyngeal (OP) swabs, nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) from 78 children (median age 2.2 years) with and without lung disease were characterised using 16S rRNA gene sequencing. Permutational multivariate analysis of variance (PERMANOVA) detected significant differences between the microbiota in BAL and those in both OP swabs (p = 0.0001, Pseudo-F = 12.2, df = 1) and NP swabs (p = 0.0001; Pseudo-F = 21.9, df = 1) with the NP and BAL microbiota more different than the OP and BAL, as indicated by a higher Pseudo-F value. The microbiota in combined OP and NP data (upper airways) provided a more comprehensive representation of BAL microbiota, but significant differences between the upper airway and BAL microbiota remained, albeit with a considerably smaller Pseudo-F (PERMANOVA p = 0.0001; Pseudo-F = 4.9, df = 1). Despite this overall difference, paired BAL and upper airway (OP and NP) microbiota were >50 % similar among 69 % of children. Furthermore, canonical analysis of principal coordinates (CAP analysis) detected significant differences between the microbiota from clinically defined groups when analysing either BAL (eigenvalues >0.8; misclassification rate 26.5 %) or the combined OP and NP data (eigenvalues >0.8; misclassification rate 12.2 %). CONCLUSIONS: Upper airway sampling provided an imperfect, but reliable, representation of the BAL microbiota for most children in this study. We recommend inclusion of both OP and NP specimens when non-invasive upper airway sampling is needed to assess airway microbiota in young children who do not expectorate. The results of the CAP analysis suggest lower and upper airway microbiota profiles may differentiate children with chronic suppurative lung disease from those with persistent bacterial bronchitis; however, further research is needed to confirm this observation.

The melioidosis agent Burkholderia pseudomallei and related opportunistic pathogens detected in faecal matter of wildlife and livestock in northern Australia.

The Darwin region in northern Australia has experienced rapid population growth in recent years, and with it, an increased incidence of melioidosis. Previous studies in Darwin have associated the environmental presence of Burkholderia pseudomallei, the causative agent of melioidosis, with anthropogenic land usage and proximity to animals. In our study, we estimated the occurrence of B. pseudomallei and Burkholderia spp. relatives in faecal matter of wildlife, livestock and domestic animals in the Darwin region. A total of 357 faecal samples were collected and bacteria isolated through culture and direct DNA extraction after enrichment in selective media. Identification of B. pseudomallei, B. ubonensis, and other Burkholderia spp. was carried out using TTS1, Bu550, and recA BUR3-BUR4 quantitative PCR assays, respectively. B. pseudomallei was detected in seven faecal samples from wallabies and a chicken. B. cepacia complex spp. and Pandoraea spp. were cultured from wallaby faecal samples, and B. cenocepacia and B. cepacia were also isolated from livestock animals. Various bacteria isolated in this study represent opportunistic human pathogens, raising the possibility that faecal shedding contributes to the expanding geographical distribution of not just B. pseudomallei but other Burkholderiaceae that can cause human disease.

Association of the melioidosis agent Burkholderia pseudomallei with water parameters in rural water supplies in Northern Australia.

We analyzed water parameters and the occurrence of the melioidosis agent Burkholderia pseudomallei in 47 water bores in Northern Australia. B. pseudomallei was associated with soft, acidic bore water of low salinity but high iron levels. This finding aids in identifying water supplies at risk of contamination with this pathogenic bacterium.

[Super intensive treatment followed by bone marrow autograft in cases of hematologic neoplasms and solid tumors]. / Traitements supraintensifs suivis d'une autogreffe de moelle osseuse en cas de néoplasies hématologiques et de tumeurs solides.

Thirty-one patients underwent autologous bone marrow transplantation (ABMT) after intensive radio and/or chemotherapy. On 18 occasions, bone marrows were treated in vitro with either Asta-Z 7557, Asta-Z 7654 or the rat monoclonal antibody Campath-1M and complement. Sixteen patients were transplanted for acute leukemia: 6 patients were in first complete remission (CR), 5 in CR greater than 1 and 5 in relapse. Twelve out of fourteen evaluable patients have relapsed. Two patients transplanted in CR 2 and CR 1 remain in CR after 9.5 and 12 months respectively. Nine patients were transplanted for aggressive lymphoma: four patients were in CR 1, 2 in CR greater than 1, 1 in first relapse and 2 refractory to best available second line chemotherapy. All 3 achieved CR after ABMT. Nine patients are evaluable: 4 relapsed and 5 remain in CR at 5, 6.5, 21, 25 and 39 months, this last patient transplanted in a refractory state, the others in CR 1. Four patients were transplanted for refractory Hodgkin's disease: 3 patients are evaluable. One patient achieved complete remission which lasted 9 months. Two patients were transplanted for relapsed solid tumors and achieved a partial response. In conclusion, the response rate is encouraging for patients transplanted during active and sometimes refractory phases of the diseases (8/13 evaluable patients achieved CR). However, for the whole group of patients, including those transplanted for acute leukemia in CR 1, the relapse rate was high. Durable remissions were achieved for patients with aggressive lymphoma who were transplanted early in the disease.

Quantity and nature of residual bone marrow T cells after treatment of the marrow with Campath-1.

Precise characterization of T-cell depletion in marrows used for transplantation is necessary for the evaluation of their potential contribution to engraftment and to graft-versus-host disease. A limiting dilution culture method that allows the determination of small numbers of bone marrow T cells is described. It can detect less than one T cell in 10(4) cells. Bone marrow T-cell depletion with the rat monoclonal antibody Campath-1 and fresh human complement results in a median decrease of 1.7 log (range, 1.6-2.1 log) of marrow T cells. A 2.7 to 3.3-log reduction is obtained when peripheral blood T cells are treated. A second incubation with fresh complement removes additional T cells from peripheral blood and from marrow samples, indicating the importance of bystander marrow cells to complement activity. The assay system described also allows the phenotypic study of responding cells growing in culture. These studies demonstrate that, after treatment with Campath-1 plus complement, no T-subset imbalance occurs. Furthermore, the T cells in these cultures are derived from mature T cells contained in the samples.

[In vivo detection of alloreactive T cells of the donor in graft versus host disease]. / Détection in vivo de cellules T alloréactives du donneur pendant la maladie de greffe contre hôte (mGcH).

A male patient with severe aplastic anemia who had rejected a first T cell depleted graft from his HLA-identical sister was retransplanted from the same donor without T cell depletion and using an intensified conditioning regimen. After 8 weeks acute graft versus host disease (GVHD) developed and peripheral blood mononuclear cells (PBMC) were obtained. After in vitro restimulation and following limiting dilution cloning, 15 proliferative (PLT) and 25 cytolytic (CTL) T cell lines specific for host PBMC but unreactive to donor PBMC were isolated. Only 1 of 10 clones which could be expanded sufficiently for testing recognized a target cell (haploidentical sister), and in only 4 instances could a restriction element be found in a panel study (3 times HLA-A2; once HLA-BW49) of 13 unrelated stimulators. Of the 8 CTL clones testable after expansion, none showed a clear restriction and none recognized any of the family cells. Our data demonstrate that anti-patient reactive PLT and CTL lines can be found in PBMC. In no instance was segregation with HLA found. Only HLA-class I restriction was detectable.

[Effect of T-cell depletion of the graft on graft survival and graft vs host disease]. / Effets sur la prise de greffe et la maladie de greffe contre hôte (mGcH) de la déplétion des cellules T du greffon.

A limiting dilution culture method has been developed which allows the detection of small numbers of residual marrow T cells following their depletion with the monoclonal antibody Campath-I and autologous complement. In seven consecutive patients the degree of T cell depletion obtained was 1.82 (1.27-2.82) log. The number of nucleated cells per kg decreased by 50% and the number of CFU-GM per kg decreased by 60%. In all except one case marrow cellularity was found to be satisfactory 3 weeks after the transplant. Peripheral engraftment of granulocytes (greater than 500/mm3 on day 20, greater than 1000/mm3 on day 27), lymphocytes (greater than 500 on day 39, greater than 1000 on day 66), platelets (greater than 20,000 and self-sustained after day 24) and red blood cells (day to last infusion = 19) indicated a delay in recovery of lymphocytes and possibly granulocytes, but not platelets or red blood cells, compared to the engraftment seen in non-T depleted patients. No correlation between nucleated cells infused, GFU-GM and engraftment was found. However, the extent of T cell depletion apparently affects lymphocyte, and possibly granulocyte, recovery. The delay in lymphoid engraftment is also reflected by nonresponsiveness to alloantigens during the first 6-9 months following marrow grafting in the absence of graft vs. host disease.

[Quantitative determination of human bone marrow T cells following in vitro depletion by Campath-1 monoclonal antibody]. / Détermination quantitative des cellules T humaines médullaires après déplétion in vitro par l'anticorps monoclonal Campath-1.

Bone marrow T cell depletion is an effective graft vs host disease prophylaxis in allogeneic bone marrow transplantation. Standard methods of identifying T cells are not sensitive enough to determine small numbers of residual T cells following T cell depletion. A rapid and sensitive method, using limiting dilution culture technology and radionucleotide labelling and allowing the detection of 1/10(4)-1/10(5) residual T cells, has been developed. Its usefulness in the evaluation of the number of T cells after monoclonal antibody (Campath-1) + autologous complement marrow treatment is demonstrated.

[In vivo detection of alloreactive T cells of host origin after rejection of HLA-identical allogeneic bone marrow transplant]. / Détection in vivo de cellules T alloréactives d'origine de l'hôte après rejet de greffe de moelle osseuse allogénique HLA-identique.

Rejection and graft vs host disease after HLA-identical allogeneic bone marrow transplantation are probably due to in-vivo T-cell reactivity against non-MHC antigens. Peripheral blood lymphocytes from a patient transplanted for aplastic anemia have been obtained during graft failure and tested for their alloreactivity towards unrelated and marrow donor lymphocytes. Their caryotype was determined. Our results demonstrate (1) alloreactive T cells of host origin and (2) the presence of donor-specific host cells in vivo, providing evidence for rejection following in vivo sensitization to non-MHC antigens.