Comparison of chest radiographs against minimum intensity projection reconstruction computed tomography scans for detection of airway stenosis in children with lymphobronchial tuberculosis.

BACKGROUND: Ideally, suspected airway compression in symptomatic children with lymphobronchial tuberculosis (TB) would be diagnosed using modern computed tomography (CT) assisted by coronal minimum intensity projection (MinIP) reconstructions. However, in TB-endemic regions with limited resources, practitioners rely on conventional radiography for diagnosing TB and its complications. Furthermore, airway compression detected on conventional radiographs would upgrade a patient into the severe category according to the new World Health Organization guidelines, precluding the patient from shorter treatment protocols. The accuracy of conventional radiographs in the context of detecting airway compression in children with TB has not been specifically evaluated against an imaging gold standard. OBJECTIVE: We aimed to compare frontal chest radiographs against thick-slab angled coronal CT MinIP in identifying airway stenosis at ten specific sites and to determine observer agreement between the modalities regarding the degree of stenosis. MATERIALS AND METHODS: This retrospective cross-sectional study compared chest radiographs with standardized angled coronal CT MinIP in children with symptomatic lymphobronchial TB at ten predetermined airway locations. Chest radiographs were evaluated by one pediatric radiologist and CT MinIP reconstructions were independently interpreted by three readers. Sensitivity and specificity were calculated using CT MinIP as the gold standard. Stenosis was graded as 1 for mild (1-50%), 2 for moderate (51-75%), 3a for severe (76-99%), and 3b for total occlusion (100%). Agreement between the two modalities regarding severity of stenosis was calculated using the kappa coefficient for each affected site. RESULTS: A total of 37 patients were included in the study. The median age of patients was 14.3 months (interquartile range 8.0-23.2). Three hundred and seventy individual bronchi (10 from each of the 37 patients) were evaluated for stenosis. Chest radiographs showed that 31 out of 37 (84%) patients had stenosis in at least one of ten evaluated sites, most commonly the left main bronchus and bronchus intermedius, and this was confirmed via CT MinIP. The gold standard (CT MinIP) demonstrated stenosis in at least one of ten sites in all 37 patients (100%). Left main bronchus stenosis was detected by chest radiography with a 92.9% sensitivity and 100% specificity. Sensitivity and specificity for bronchus intermedius stenosis were 80% and 75%, respectively. There was substantial agreement for grade of stenosis between chest radiographs and CT (kappa=0.67) for the left main bronchus and moderate agreement (kappa=0.58) for the bronchus intermedius. Severe stenosis was found in 78 bronchi on CT compared to 32 bronchi (Grade 3a: 9, Grade 3b: 23) on chest radiographs. CONCLUSION: The diagnosis of pulmonary TB in children continues to rely heavily on imaging, and we have shown that in young children, chest radiographs had a high sensitivity and specificity for detecting airway stenosis at certain anatomical sites, when adequately visualized, resulting from tuberculous lymph node compression at left main bronchus and bronchus intermedius. For most sites, the interobserver agreement was poor. Stenosis of the left main bronchus and bronchus intermedius should be the focus of chest radiograph interpretation and can assist both diagnosis and classification of patients for treatment.

Comparison of chest radiograph findings in ambulatory and hospitalized children with pulmonary tuberculosis.

BACKGROUND: The diagnosis of childhood tuberculosis (TB) is, in many instances, solely reliant on chest radiographs (CXRs), as they are often the only diagnostic tool available, especially in TB-endemic areas. Accuracy and reliability of CXRs for detecting TB lymphadenopathy may vary between groups depending on severity of presentation and presence of parenchymal disease, which may obscure visualization. OBJECTIVE: To compare CXR findings in ambulatory versus hospitalized children with laboratory confirmed pulmonary TB versus other lower respiratory tract infections (LRTI) and test inter-rater agreement for these findings. MATERIALS AND METHODS: Retrospective review, by two pediatric radiologists, of CXRs performed on children < 12 years old referred for evaluation of LRTI with clinical suspicion of pulmonary TB in inpatient and outpatient settings. Each radiologist commented on imaging findings of parenchymal changes, lymphadenopathy, airway compression and pleural effusion. Frequency of imaging findings was compared between patients based on location and diagnosis and inter-rater agreement was determined. Accuracy of radiographic diagnosis was compared to laboratory testing which served as the gold standard. RESULTS: The number of enrolled patients was 181 (54% males); 69 (38%) were ambulatory and 112 (62%) were hospitalized. Of those enrolled, 87 (48%) were confirmed to have pulmonary TB, while 94 (52%) were other LRTI controls. Lymphadenopathy and airway compression were more common in TB patients than other LRTI controls, regardless of patient location. Parenchymal changes and pleural effusion were more common in hospitalized than ambulatory patients, regardless of patient diagnosis. Agreement for parenchymal changes was higher in the hospitalized group (kappa [κ] = 0.75), while agreement for lymphadenopathy (κ = 0.65) and airway compression (κ = 0.68) was higher in the ambulatory group. The specificity of CXRs for TB diagnosis (> 75%) was higher than the sensitivity (< 50%) for both ambulatory and hospitalized groups. CONCLUSION: Higher frequency of parenchymal changes among hospitalized children may conceal specific imaging findings of TB such as lymphadenopathy, contributing to the poor reliability of CXRs. Despite this, the high specificity of CXRs shown in our results is encouraging for continued use of radiographs for TB diagnosis in both settings.

Clinicians' perspective of picture archiving and communication systems at Charlotte Maxeke Johannesburg Academic Hospital.

Background: Picture archiving and communication systems (PACS) are now an established means of capturing, storing, distribution and viewing of all radiology images. The study was conducted in a quaternary hospital, Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), part of the University of the Witwatersrand teaching circuit, in South Africa. Objectives: To measure the clinicians' perceived benefits and challenges of PACS. To document perceived views on how the current PACS can be improved. Method: This was a cross-sectional observational study over a period of 5 months from September 2021 to January 2022 carried out at CMJAH. Questionnaires were distributed to referring clinicians with PACS experience. Descriptive statistics was conducted. Categorical variables were presented as frequency and percentages. The continuous variables were presented as means ± standard deviation. Results: A survey with a response rate of 54% found the benefits most reported by clinicians were improved patient care, less time needed to review an exam, improved image comparison and consultation efficiency. With respect to perceived challenges, the unavailability of images at the bedside, problems with access and the lack of advanced image manipulating software were noted. The most frequent recommendations on improvements focused on the aforementioned challenges. Conclusion: Hospital-wide PACS was viewed beneficial by most clinicians. Nonetheless, there are a few aspects that deserve attention to improve the functionality and access of the system. Contribution: The findings will assist in future hospital or provincial-wide PACS deployment projects.

Stereotactic breast biopsies: Radiological-pathological concordance in a South African referral unit.

Background: Stereotactic breast biopsies have become the gold standard for tissue diagnosis in non-palpable, sonographically occult breast abnormalities seen on mammogram. Only limited data exist in South Africa on the correlation between imaging findings and stereotactic biopsy histology. Objectives: To describe the mammographic findings and histological diagnosis in patients who underwent stereotactic breast biopsy at a referral hospital. In addition, to evaluate the proportion of malignancy in each Breast Imaging Reporting and Data System (BI-RADS) category. Method: A retrospective review of stereotactic breast biopsies was performed. Imaging characteristics (including BI-RADS category) and histological diagnosis were recorded. Using histopathology, cases were classified as benign, high-risk or malignant. Results: A total of 131 biopsies, from 123 patients, were included in the study. Most biopsies were performed on asymptomatic patients (79.3%, 104/131). The majority were categorised as BI-RADS 4 and demonstrated calcifications. Histology revealed a malignant diagnosis in 40 (30.5%) patients, a high-risk lesion in 8 (6.1%) patients and a benign diagnosis in 83 (63.4%) patients. There was a stepwise increase in the proportion of malignancy from BI-RADS category 3 to 5. When compared with surgical histology, the stereotactic biopsies demonstrated an overall ductal carcinoma in situ (DCIS) underestimation rate of 10.3%. Conclusion: Despite resource restrictions, stereotactic breast biopsies performed in a South African context produce radiological-pathological concordance in keeping with BI-RADS guidelines, as well as with local and international studies.

CT pulmonary angiography findings in HIV-infected patients referred for suspected pulmonary thrombo-embolic disease.

BACKGROUND: South Africa bares a significant burden of HIV and imaging is commonly performed as part of the workup for respiratory distress. OBJECTIVES: The aim of this study was to document the prevalence of pulmonary thrombo-embolic disease (PTED) and other findings in HIV-infected patients referred for CT pulmonary angiography (CTPA) for suspected PTED. METHOD: Forty CTPA studies of documented HIV-infected individuals investigated for suspected PTED during a 1-year period were retrieved, anonymised and interpreted by three consultant radiologists. Inter-reader reliability was calculated using Free Marginal multi-rater Kappa. RESULTS: Fourteen of the forty cases (35%) were positive for PTED. In the pulmonary embolism (PE)-positive group, 57.14% had peripheral disease and 42.86% had both peripheral and central disease. Associated findings in the PE-positive cases were pulmonary infarcts (17.5%), mosaic attenuation (17.5%) and linear atelectasis (7.5%). The most common incidental findings were solid pulmonary nodules (52.5%), non-wedge-shaped consolidation (45%), cardiomegaly (52.5%) and enlarged intra-thoracic lymph nodes (52.5%). Thirty per cent of the study population had findings related directly to the presence of PTED, whilst most cases in the study (77.5%) had pulmonary findings unrelated to PTED. In the PE-negative cases, 55% reported emergent findings that warranted immediate or urgent medical attention. CONCLUSION: Computed tomography pulmonary angiography imaging is critical for diagnosing PE. However, further investigation into the judicious application of CTPA in HIV-infected patients with suspected PTED is required, as CTPA findings in most of the cases in this study were unrelated to PE.

An audit of CT brain findings in adults with new-onset seizures in a resource restricted setting in South Africa.

BACKGROUND: Globally, adults presenting with seizures account for 1% - 2% of visits to emergency departments (EDs), of which 25% are new-onset seizures. Neuroimaging is essential as part of the initial workup. Multiple studies have demonstrated abnormal CT brain (CTB) findings in these patients. OBJECTIVES: To review the CTB findings in adults presenting with new-onset seizures in a resource restricted setting. METHOD: A retrospective review of 531 CTBs was conducted at a tertiary hospital in Gauteng on adults presenting to the ED with new-onset seizures. RESULTS: The mean age of the patients was 45.6 ± 17.1 years, and the male to female ratio was 1.2:1. Generalised and focal seizure types were almost equally represented. Of the total 531 patients, 168 (31.6%) were HIV positive. The CTB findings were abnormal in 257 (48.4%) patients, albeit vascular pathology accounted for 21.9%. Infective pathology accounted for 14.1% with a statistically significant association with HIV (p = 0.003). Trauma related pathology was 2.4%, whilst neoplastic pathology was seen in 3.0%. Other causes included congenital pathology, calcifications, atrophy and gliosis. Clinical factors associated with abnormal CTB findings were age ≥ 40 years, HIV infection, hypertension, focal seizures, low Glasgow Coma Scale (GCS), raised cerebrospinal fluid (CSF) protein and presence of lymphocytes. CONCLUSION: A high yield of abnormal CTB findings was noted in adult patients who presented with new-onset seizures, supporting the use of urgent CTB in patients with certain clinical risk factors. Patients without these risk factors can be scanned within 24-48 h in a resource restricted setting.

An audit of CT brain findings in adults with new-onset seizures in a resource restricted setting in South Africa

Background: Globally, adults presenting with seizures account for 1% ­ 2% of visits to emergency departments (EDs), of which 25% are new-onset seizures. Neuroimaging is essential as part of the initial workup. Multiple studies have demonstrated abnormal CT brain (CTB) findings in these patients. Objectives: To review the CTB findings in adults presenting with new-onset seizures in a resource restricted setting. Method: A retrospective review of 531 CTBs was conducted at a tertiary hospital in Gauteng on adults presenting to the ED with new-onset seizures. Results: The mean age of the patients was 45.6 ± 17.1 years, and the male to female ratio was 1.2:1. Generalised and focal seizure types were almost equally represented. Of the total 531 patients, 168 (31.6%) were HIV positive. The CTB findings were abnormal in 257 (48.4%) patients, albeit vascular pathology accounted for 21.9%. Infective pathology accounted for 14.1% with a statistically significant association with HIV (p = 0.003). Trauma related pathology was 2.4%, whilst neoplastic pathology was seen in 3.0%. Other causes included congenital pathology, calcifications, atrophy and gliosis. Clinical factors associated with abnormal CTB findings were age ≥ 40 years, HIV infection, hypertension, focal seizures, low Glasgow Coma Scale (GCS), raised cerebrospinal fluid (CSF) protein and presence of lymphocytes. Conclusion: A high yield of abnormal CTB findings was noted in adult patients who presented with new-onset seizures, supporting the use of urgent CTB in patients with certain clinical risk factors. Patients without these risk factors can be scanned within 24­48 h in a resource restricted setting.

A proposed CT classification of progressive lung parenchymal injury complicating pediatric lymphobronchial tuberculosis: From reversible to irreversible lung injury.

Lymphobronchial tuberculosis (LBTB) is tuberculous lymphadenopathy affecting the airways, which is particularly common in children with primary TB. Airway compression by lymphadenopathy causes downstream parenchymal pathology, which may ultimately result in irreversible lung destruction, if not treated timeously. Computed tomography (CT) is considered the "gold standard" for detecting mediastinal lymph nodes in children with TB. CT is also the best way of imaging the airways of children with LBTB. The CT findings of the parenchymal complications and associations of LBTB on CT have been described, but no severity classification was provided to aid management decisions. Identifying the parenchymal complications of LBTB and recognizing their severity has clinical relevance. Using prior publications on LBTB and post obstructive lung injury we have used an image bank of CT scans in children with pulmonary TB, presenting with airway symptoms, to create a CT severity staging of lung injury in LBTB. The staging focuses on distinguishing nonsalvageable destruction (nonenhancing or cavitated lung) from salvageable lung parenchymal disease (enhancing and noncavitated) to inform the management decisions, which range from bronchoscopic airway clearance to surgical decompression of the compressing nodes.

A retrospective analysis of time delays in patients presenting with stroke to an academic emergency department.

BACKGROUND: Stroke presents commonly to the emergency department (ED), and is a common cause of morbidity and mortality in South Africa. Early ED presentation and early neuroimaging are required in order for thrombolysis to be a potential therapeutic modality. OBJECTIVES: To determine the time to ED presentation, time to computed tomography (CT) scan and the potential influencing factors for patients with stroke. METHODS: A retrospective record review of all patients who presented with clinical features of stroke to a tertiary academic ED in Johannesburg, South Africa, from 01 January to 31 December 2014. RESULTS: Data from 232 eligible stroke patients were analysed. The median time to presentation to the ED was 33 h with the majority of patients (81.3%) presenting after the 4.5 h window for thrombolysis. The median time to CT was 8 h. Only 3.9% of patients had a CT scan within one hour of arrival. Patients with loss of consciousness were associated with earlier hospital presentation (p = 0.001). None of the patients were thrombolysed. CONCLUSION: Patients with stroke commonly present late to hospital. If we are to make a difference in this group of vulnerable patients, further education and training needs to be emphasised regarding 'time is brain'. Communication and commitment is also required by the emergency medical services, ED and radiology staff in order to prioritise stroke patients and to reduce delays.

A retrospective analysis of time delays in patients presenting with stroke to an academic emergency department

Background: Stroke presents commonly to the emergency department (ED), and is a common cause of morbidity and mortality in South Africa. Early ED presentation and early neuroimaging are required in order for thrombolysis to be a potential therapeutic modality. Objectives: To determine the time to ED presentation, time to computed tomography (CT) scan and the potential influencing factors for patients with stroke. Methods: A retrospective record review of all patients who presented with clinical features of stroke to a tertiary academic ED in Johannesburg, South Africa, from 01 January to 31 December 2014. Results: Data from 232 eligible stroke patients were analysed. The median time to presentation to the ED was 33 h with the majority of patients (81.3%) presenting after the 4.5 h window for thrombolysis. The median time to CT was 8 h. Only 3.9% of patients had a CT scan within one hour of arrival. Patients with loss of consciousness were associated with earlier hospital presentation (p = 0.001). None of the patients were thrombolysed. Conclusion: Patients with stroke commonly present late to hospital. If we are to make a difference in this group of vulnerable patients, further education and training needs to be emphasised regarding 'time is brain'. Communication and commitment is also required by the emergency medical services, ED and radiology staff in order to prioritise stroke patients and to reduce delays

Pilot Educational Intervention and Feasibility Assessment of Breast Ultrasound in Rural South Africa.

PURPOSE: Breast cancer is the leading cause of cancer death in women worldwide, with high mortality in low- and middle-income countries because of a lack of detection, diagnosis, and treatment. With mammography unavailable, ultrasound offers an alternative for downstaging. The literature reports successful training in various domains, but a focus on the breast is novel. We assessed the feasibility (knowledge acquisition, perceived usefulness, and self-efficacy) of breast ultrasound training for nonphysician providers. METHODS: Training was implemented for 12 providers at Hlokomela Clinic in Hoedspruit, South Africa, over 3 weeks. Didactic presentations and example cases were followed by a presurvey and test (n = 12). All providers received hands-on training with nurses as models; five providers trained with patients. A post-test (n = 12) assessed knowledge acquisition and a postsurvey (n = 10) assessed perceived program usefulness and provider self-efficacy. RESULTS: The pre- to post-test averages improved by 68% in total and in four competencies (foundational knowledge, descriptive categories, benign v malignant, and lesion identification). On the postsurvey, providers expressed that ultrasound could significantly influence breast cancer detection (9.1 out of 10), treatment (7.9 out of 10), and survival (8.7 out of 10) in their community and endorsed moderate confidence in their scanning (6.3 out of 10) and interpreting abilities (5.6 out of 10). CONCLUSION: Our research supports the feasibility of breast ultrasound training as part of a breast education program in low- and middle-income countries. Pre- and post-test results and observed proficiency indicate that training nonphysician providers is achievable; postsurvey responses indicate program acceptance, community-based ownership, and provider self-efficacy with ultrasound. Future work may show that breast ultrasound is viable for early detection where mammography is unavailable.

Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.

Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

Digital platform for improving non-radiologists' and radiologists' interpretation of chest radiographs for suspected tuberculosis - a method for supporting task-shifting in developing countries.

BACKGROUND: Shifting X-ray interpretation to non-radiologists can help to address radiologist shortages in developing countries. OBJECTIVE: To determine the change in accuracy of non-radiologists and radiologists for the radiographic diagnosis of paediatric tuberculosis after a short skill-development course. MATERIALS AND METHODS: Participants interpreted 15 paediatric chest radiographs before and after a 30-minute course using three possible responses: (1) diagnostic for tuberculosis, (2) abnormal but inconclusive for diagnosis of tuberculosis and (3) normal. We compared proportions of correct diagnoses, sensitivity, and specificity, before and after the course. RESULTS: We included 256 participants comprising 229 non-radiologists (134 radiographers, 32 paediatricians, 39 Médecins Sans Frontières clinicians and 24 physicians including paediatricians) and 27 radiologists. Mean change proportions of correct diagnosis ranged from -27% to 53% for individuals and 9% to 20% for groups. All groups showed a statistically significant improvement. Mean change in diagnostic sensitivity ranged from -38% to 100% for individuals and from 16% to 41% for groups. All groups showed a statistically significant improvement. Mean change in specificity ranged from -57% to 57% for individuals and from -15% to -4% for groups. The decrease was statistically significant for physicians, paediatricians and radiographers. CONCLUSION: The course resulted in increased correct diagnoses and improved sensitivity at the expense of specificity.

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4.

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

Complete genome sequence of Anabaena variabilis ATCC 29413.

Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogenases that function under different environmental conditions and is capable of photoautotrophic growth in the light and true heterotrophic growth in the dark using fructose as both carbon and energy source. While this strain was first isolated in 1964 in Mississippi and named Anabaena flos-aquae MSU A-37, it clusters phylogenetically with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile, growing well at approximately 40(°) C. Here we provide some additional characteristics of the strain, and an analysis of the complete genome sequence.

Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring.

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations.

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.

Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.

Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).

Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.