Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology.

Full Laboratory Automation is revolutionizing work habits in an increasing number of clinical microbiology facilities worldwide, generating huge streams of digital images for interpretation. Contextually, deep learning architectures are leading to paradigm shifts in the way computers can assist with difficult visual interpretation tasks in several domains. At the crossroads of these epochal trends, we present a system able to tackle a core task in clinical microbiology, namely the global interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. This is achieved by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture we call DeepColony. Working on a large stream of clinical data and a complete set of 32 pathogens, the proposed system is capable of effectively assist plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of Urinary Tract Infections. Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.

Can the Treatment of Dental Malocclusions Affect the Posture in Children?

OBJECTIVE: The aim of this study was to investigate whether the treatment of the dental malocclusions can affect the postural attitude in children. STUDY DESIGN: Sixty patients aged 9-12 years in mixed dentition were enrolled. The patients underwent an orthodontic evaluation for dental malocclusion and a postural examination by means of a vertical laser line (VLL) and a stabilometric-baropodometric platform. The children were treated with a functional appliance according to the type of malocclusion for two years. The position of the head and of the atlanto-occipital joint (C0-C1) respects to the VLL, the typologies of podalic support and the distribution of the body weight on the feet were evaluated before and after the orthodontic treatment. RESULTS: A significant correction of the position of the head, with a physiological extension of C0-C1, a significant improvement of the typology of podalic support and a homogeneous distribution of the body weight on the feet were observed after the treatment of the malocclusions. Conclusion; From our results, the treatment of dental malocclusion can contribute to ameliorate the postural attitude in children.

Development and evaluation of a multi-antigen serological assay for the intra-vitam diagnosis of Tuberculosis caused by Mycobacterium bovis in pigs.

Bovine Tuberculosis (bTB) is a chronic disease caused by Mycobacterium bovis, affecting cattle and other mammalian species, such as pigs. In the present work, we developed a novel multi-antigen assay (The TB-Luminex multiplex test) to diagnose bTB in pig sera. Moreover, we investigated the seroreactivity to the different antigens employed (MPB83, MPB70, CFP10 and ESAT6) and the possible correlation with bTB lesions distribution in the positive pigs. The serum samples were collected from 59 bTB positive pigs and 186 pigs reared in an officially Tuberculosis free area. Sera were processed according to an optimized protocol for the detection of antibodies by a multiantigen assay using Luminex technology. The positive group showed visible lesions with localized (54.2%) or generalized (45.8%) distribution. Culture confirmed the infection in 62.7% of the cases, and histopathology and intra-vitam assays were used as additional confirmatory tests. Within the set of antigens tested, the immunodominant was MPB83 (positive in 94.9% of the affected pigs), followed by CFP10, MPB70 and ESAT6 (positivity shown in 81.3%, 67.8% and 25.4% of the positive pigs tested, respectively). The best antigens combination was MPB83/CFP10, with a 96.6% sensitivity and 96.8% specificity. Overall, the test showed high sensitivity (98.3% and 86.4%) and specificity (96.2% and 97.8%), if sera were considered positive according to the positivity to a single antigen or at least two antigens, respectively. The TB-Luminex multiplex test results did not give significantly different outcomes according to lesions distribution. Given the present study results, the TB-Luminex multiplex test is a reliable test capable of detecting bTB in most infected pigs with good Se and Sp, regardless of the stage of the disease. In conclusion, multi-antigen tests can be used as individual tests and screening tools for domestic and wild suids within bTB eradication programs.

Development and evaluation of two multi-antigen serological assays for the diagnosis of bovine tuberculosis in cattle.

There is currently an increased interest in the use of serological approaches in combination with traditional cell-mediated immunity-based techniques to improve the detection of tuberculosis (TB)-infected animals. In the present study, we developed and validated two different serological TB-detection assays using four antigens, MPB70, MPB83, ESAT6 and CFP10, and the tuberculin PPDb. A conventional multi-antigen TB-ELISA method and a novel TB multiplex test, based on Luminex technology, were developed to detect antibodies to multiple antigen targets. The performance levels of the two tests were evaluated and compared using selected panels of samples having known TB states. The TB-ELISA test (containing five antigens, including PPDb) had a sensitivity (Se) of 74.2% and a specificity (Sp) of 94.9%, while the TB-Luminex test had higher Se (79.0%) and Sp (99.1%) rates even when only one reactive antigen was used to classify the test as positive. If a more restrictive criterion, requiring two positive antigens to classify the test as positive, was used, then the TB-ELISA's Sp rate increased to 99.8% but the Se decreased to 61.3%, while the TB-Luminex test's Sp rate increased to 100% but the Se decreased to 51.2%. TB-ELISA and TB-Luminex were applied to a panel of 257 sera collected from bTB-positive herds, as determined by a post-mortem inspection. They showed good performance levels, identifying 49 (80.3%) and 48 (78.7%), respectively, of 61 samples that had tested positive by the intradermal tuberculin (IDT) test and/or interferon-gamma assay. In addition, TB-ELISA and TB-Luminex were able to identify 60 and 42 samples as positive, respectively, out of the 196 samples that tested negative to IDT and interferon-gamma at the time of serum collection. Subsequent IDT tests performed after 1-2 months, confirmed the positivity of 18 samples, indicating the strategic value of having two serological assays to detect TB-infected herds that were not reactive to initial IDT testing, thereby allowing for the rapid control of outbreaks and eradication of the disease.

G-CSF treatment of severe congenital neutropenia reverses neutropenia but does not correct the underlying functional deficiency of the neutrophil in defending against microorganisms.

The treatment of children affected by severe congenital neutropenia (SCN) with G-CSF strongly reduces the risk of sepsis by reversing neutropenia. However, SCN patients who respond to the treatment with the growth factor still have an elevated risk of succumbing to sepsis. Because the disease is usually caused by heterozygous mutations of ELA2, a gene encoding for neutrophil elastase (NE), we have investigated in G-CSF-responder and nonresponder patients affected by SCN the expression of polypeptides that constitute the antimicrobial machinery of these cells. In peripheral blood-derived neutrophils of patients with heterozygous mutations of ELA2 who were treated with G-CSF, NE was nearly absent as detected by immunofluorescence and immunoblotting, suggesting that production of the mutant protein interferes with normal gene expression. This defect was associated with abnormal expression of other granule-associated proteins such as myeloperoxidase, lactoferrin, cathepsin G, and human-neutrophil-peptide. Moreover, in one patient with partial response to G-CSF, we observed an impairment of neutrophil antimicrobial activity against Candida albicans, and, to a lower extent against Escherichia coli. Thereby, we propose that the treatment with G-CSF is not sufficient to correct all of the functional deficiency of neutrophils, and this might account for the consistent risk of infections observed in SCN patients.

Combined decrease of defined B and T cell subsets in a group of common variable immunodeficiency patients.

Common variable immunodeficiency disease (CVID) is a primary immune disorder affecting B cells and characterized by hypogammaglobulinemia and recurrent infections. To elucidate the clinical and immunological heterogeneity of this condition, we have studied B and T cell subsets in 25 CVID patients. In eleven of them, we observed a remarkable relative expansion of a B cell subpopulation (CD19(hi)/CD21(lo) cells) characterized by the absence of CD23 and the reduced expression of the chemokine receptors CXCR5 and CCR7. Our analyses demonstrated in these patients that the expansion of CD19(hi)/CD21(lo) cells correlates with a selective decrease of circulating naïve and CD21(hi) memory B lymphocytes. The same group of patients displayed a simultaneous severe reduction of naïve CD4+ T cells associated with decreased levels of T cell receptor excision circles. These observations suggest that a combined defect in generation of B and T subpopulations may account for the abnormal immunophenotype characterizing this subgroup of CVID patients.

Innate immunity defects in Hermansky-Pudlak type 2 syndrome.

Adaptor protein-3 (AP-3) is an ubiquitous cytoplasmic complex that shuttles cargo proteins from the trans-Golgi and a tubular-endosomal compartment to endosome-lysosome-related organelles. Lack of the beta3A subunit of this complex causes Hermansky-Pudlak syndrome type 2, an autosomal recessive disease characterized by partial albinism, prolonged bleeding tendency, and immunodeficiency. To investigate the pathogenesis of immunodeficiency, we studied natural killer (NK) cells and neutrophil functions in 2 previously unreported siblings affected by Hermansky-Pudlak type 2 syndrome. In both patients we observed a dramatic reduction of cytolytic activity of freshly isolated and of IL-2-activated NK cells. Levels of perforin were reduced in unstimulated NK cells, thereby accounting for the impairment of NK cytolitic activity. In addition, analysis of neutrophils in these patients demonstrated that intracellular elastase content was largely reduced while CD63 expression on plasma membrane was substantially increased. Taken together, these observations suggest that type 2 Hermansky-Pudlak syndrome is characterized by defects of innate immunity.

AIRE deficiency in thymus of 2 patients with Omenn syndrome.

Omenn syndrome is a severe primary immunodeficiency with putative autoimmune manifestations of the skin and gastrointestinal tract. The disease is caused by hypomorphic mutations in recombination-activating genes that impair but do not abolish the process of VDJ recombination, leading to the generation of autoreactive T cells with a highly restricted receptor repertoire. Loss of central tolerance in genetically determined autoimmune diseases, e.g., autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy, is associated with defective expression by medullary thymic epithelial cells of AIRE, the transcription activator that induces thymic expression of tissue-specific antigens. Analysis of AIRE expression in the thymi of 2 Omenn syndrome patients and 1 SCID patient, by real-time RT-PCR and immunohistochemistry, demonstrated a profound reduction in the levels of AIRE mRNA and protein in patients as compared with a normal control subject. Lack of AIRE was associated with normal or even increased levels of keratin and lymphotoxin-beta receptor mRNAs, while mRNAs of the self-antigens insulin, cytochrome P450 1a2, and fatty acid-binding protein were undetectable in thymi from immunodeficiency patients. These results demonstrate that deficiency of AIRE expression is observed in severe immunodeficiencies characterized by abnormal T cell development and suggest that in Omenn syndrome, the few residual T cell clones that develop may escape negative selection and thereafter expand in the periphery, causing massive autoimmune reactions.

Congenital neutropenia: advances in diagnosis and treatment.

PURPOSE OF REVIEW: A decade after the availability of hematopoietic growth factors, the long-term outcome of severe congenital neutropenia has dramatically changed. The prolonged survival of neutropenic patients receiving hematopoietic growth factors has drawn attention to the heterogeneity of this disease and to the complications of treatment. The dose of granulocyte colony stimulating factor that is required to obtain normal levels of circulating neutrophils and to prevent fever and infections is quite variable among patients, but is higher in children with severe congenital neutropenia than in those with other conditions of neutropenia. Moreover, leukemic transformation during treatment is not observed in all patients, but is more typical of severe congenital neutropenia and Shwachman-Diamond patients. RECENT FINDINGS: In recent years, the converging efforts of hematologists, immunologists and geneticists have led to the discovery of the genetic and biochemical basis of severe congenital neutropenia; cyclic neutropenia; warts, hypogammaglobulinemia, immunodeficiency, myelokathexis or WHIM syndrome and other rarer conditions associated to neutropenia. SUMMARY: Although the diagnosis of congenital neutropenia includes many disorders of distinct origin and variable prognosis, their treatment is still based on granulocyte colony stimulating factor administration. Understanding the pathogenesis of these forms of neutropenia and their evolution will focus future studies on the mechanisms of normal and pathological myelopoiesis and on the development of the most appropriate treatment for each type of neutropenia.

Functional defects of dendritic cells in patients with CD40 deficiency.

We have recently identified 2 patients with a rare autosomal recessive form of hyper IgM disease, known as HIGM3, caused by mutations in the CD40 gene. These patients had opportunistic infections observed on X-linked hyper IgM syndrome (HIGM), suggesting that the CD40-CD40 ligand interaction is important for promoting T-cell-mediated immunity. To evaluate whether innate immunity signals may substitute CD154 for inducing the maturation of dendritic cells (DCs), we analyzed monocyte-derived DCs in these patients. Monocyte-derived DCs of HIGM3 subjects on ex vivo stimulation with tumor necrosis factor-alpha (TNF-alpha) or lipopolysaccharide (LPS) combined with interferon-gamma (IFN-gamma) normally express all the markers of mature DCs, such as CD83 and DC-LAMP. However, cell surface levels of HLA-DR in mature DCs are reduced, as is costimulatory activity of these cells for allogeneic naive T cells. In addition, CD40-deficient DCs secrete lower amounts of interleukin-12 (IL-12) but larger quantities of IL-10 than control subjects. Finally, analysis of circulating plasmacytoid DCs demonstrates a normal percentage of this subset in CD40-deficient cells, but IFN-alpha secretion in response to herpes simplex virus 1 (HSV-1) infection is severely reduced in patients. These observations suggest that the severe impairment of DC maturation may contribute to the defect of T-cell-mediated immunity observed in HIGM3 patients.