Immunohistochemistry and real-time Polymerase Chain Reaction: importance in the diagnosis of intestinal tuberculosis in a Peruvian population.

INTRODUCTION: The diagnosis of intestinal tuberculosis is challenging even nowadays. This study aims to report the positivity rates of new diagnostic methods such as immunohistochemistry and Real-Time Polymerase Chain Reaction in patients with intestinal tuberculosis, as well as describe the pathological and endoscopic features of intestinal tuberculosis in our population. METHODS: This was a retrospective observational study conducted in patients diagnosed with intestinal tuberculosis, between 2010 to 2023 from the Hospital Nacional Daniel Alcides Carrion and a Private Pathology Center, both located in Peru. Clinical data was obtained, histologic features were independently re-evaluated by three pathologists; and immunohistochemistry and real-time Polymerase Chain Reaction evaluation were performed. The 33 patients with intestinal tuberculosis who fulfilled the inclusion criteria were recruited. RESULTS: Immunohistochemistry was positive in 90.9% of cases, while real-time Polymerase Chain Reaction was positive in 38.7%. The ileocecal region was the most affected area (33.3%), and the most frequent endoscopic appearance was an ulcer (63.6%). Most of the granulomas were composed solely of epithelioid histiocytes (75.8%). Crypt architectural disarray was the second most frequent histologic finding (78.8%) after granulomas, but most of them were mild. CONCLUSION: Since immunohistochemistry does not require an intact cell wall, it demonstrates higher sensitivity compared to Ziehl-Neelsen staining. Therefore, it could be helpful for the diagnosis of paucibacillary tuberculosis.

Differentiation of intestinal tuberculosis and Crohn's disease through an explainable machine learning method.

Differentiation between Crohn's disease and intestinal tuberculosis is difficult but crucial for medical decisions. This study aims to develop an effective framework to distinguish these two diseases through an explainable machine learning (ML) model. After feature selection, a total of nine variables are extracted, including intestinal surgery, abdominal, bloody stool, PPD, knot, ESAT-6, CFP-10, intestinal dilatation and comb sign. Besides, we compared the predictive performance of the ML methods with traditional statistical methods. This work also provides insights into the ML model's outcome through the SHAP method for the first time. A cohort consisting of 200 patients' data (CD = 160, ITB = 40) is used in training and validating models. Results illustrate that the XGBoost algorithm outperforms other classifiers in terms of area under the receiver operating characteristic curve (AUC), sensitivity, specificity, precision and Matthews correlation coefficient (MCC), yielding values of 0.891, 0.813, 0.969, 0.867 and 0.801 respectively. More importantly, the prediction outcomes of XGBoost can be effectively explained through the SHAP method. The proposed framework proves that the effectiveness of distinguishing CD from ITB through interpretable machine learning, which can obtain a global explanation but also an explanation for individual patients.

Recent updates in diagnosis of abdominal tuberculosis with emphasis on nucleic acid amplification tests.

INTRODUCTION: Abdominal tuberculosis (TB) is a common epitome of extrapulmonary TB (EPTB), wherein peritoneal and intestinal TB are the most prevalent forms. Diagnosis of abdominal TB is a daunting challenge owing to variable anatomical locations, paucibacillary nature of specimens and atypical clinical presentations that mimic other abdominal diseases, such as Crohn's disease and malignancies. In this review, we made a comprehensive study on the diagnosis of abdominal TB. AREA COVERED: Various modalities employed for abdominal TB diagnosis include clinical features, imaging, bacteriological tests (smear/culture), histopathological/cytological observations, interferon-gamma release assays and nucleic acid amplification tests (NAATs). Among NAATs, loop-mediated isothermal amplification assay, PCR, multiplex-PCR, nested PCR, real-time PCR and GeneXpert® MTB/RIF were discussed. Identification of circulating Mycobacterium tuberculosis cell-free DNA by real-time PCR within ascitic fluids is another useful approach. EXPERT OPINION: Several novel molecular/immunological methods, such as GeneXpert Ultra, aptamer-linked immobilized sorbent assay, immuno-PCR (I-PCR) and nanoparticle-based I-PCR have recently been developed for detecting pulmonary TB and several EPTB types, which may also be explored for abdominal TB diagnosis. Precise and prompt diagnosis of abdominal TB may initiate an early therapy so as to reduce the complications, i.e. abdominal pain, ascites, abdominal distension, intestinal obstruction/perforation, etc., and avoid surgical involvement.Plain Language SummaryAbdominal tuberculosis (TB) is a manifestation of extrapulmonary TB (EPTB), where peritoneal and intestinal TB are two major forms. Diagnosis of abdominal TB is difficult owing to low bacterial load present in clinical samples and non-specific clinical presentations as it mimics other diseases such as inflammatory bowel diseases, abdominal malignancies, etc. Bacteriological tests (smear/culture) almost fail owing to poor sensitivities and it is not always possible to get representative tissue samples for histopathological and cytological observations. In recent years, molecular tests i.e. nucleic acid amplification tests (NAATs), such as PCR/multiplex-PCR (M-PCR), nested PCR and GeneXpert are widely employed. Markedly, PCR/M-PCR and nested PCR exhibited reasonable good sensitivities/specificities, while GeneXpert revealed low sensitivity in most of the studies but high specificity, thus it could assist in differential diagnosis of intestinal TB and Crohn's disease. Further, novel molecular/immunological tests employed for pulmonary TB and other EPTB types were described and those tests can also be utilized to diagnose abdominal TB. Reliable and rapid diagnosis of abdominal TB would initiate an early start of anti-tubercular therapy and reduce the severe complications.

Differential prevalence of pathobionts and host gene polymorphisms in chronic inflammatory intestinal diseases: Crohn's disease and intestinal tuberculosis.

BACKGROUND AND OBJECTIVES: Crohn's disease (CD) and Intestinal tuberculosis (ITB) are chronic inflammatory ulcero-constrictive intestinal diseases with similar phenotype. Although both are disease models of chronic inflammation and their clinical presentations, imaging, histological and endoscopic findings are very similar, yet their etiologies are diverse. Hence, we aimed to look at differences in the prevalence of pathobionts like adherent-invasive Escherichia coli (AIEC), Listeria monocytogenes, Campylobacter jejuni and Yersinia enterocolitica in CD and ITB as well as their associations with host-associated genetic polymorphisms in genes majorly involved in pathways of microbial handling and immune responses. METHODS: The study cohort included 142 subjects (69 patients with CD, 32 with ITB and 41 controls). RT- PCR amplification was used to detect the presence of AIEC, L. monocytogenes, C. jejuni, and Y. enterocolitica DNA in colonic mucosal biopsies. Additionally, we tested three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and one SNP in TNFRSF1A (rs4149570) by real-time PCR with SYBR green from peripheral blood samples in this cohort. RESULTS: In patients with CD, AIEC was most frequently present (16/ 69, 23.19%) followed by L. monocytogenes (14/69, 20.29%), C. jejuni (9/69, 13.04%), and Y. enterocolitica (7/69, 10.14%). Among them, L. monocytogenes and Y. enterocolitica were significantly associated with CD (p = 0.02). In addition, we identified all the three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and TNFRSF1A (rs4149570) with a significant difference in frequency in patients with CD compared with ITB and controls (p<0.05). CONCLUSION: Higher prevalence of host gene polymorphisms, as well as the presence of pathobionts, was seen in the colonic mucosa of patients with CD as compared to ITB, although both are disease models of chronic inflammation.

Application value of tissue tuberculosis antigen combined with Xpert MTB/RIF detection in differential diagnoses of intestinal tuberculosis and Crohn's disease.

BACKGROUND: The purpose of this study was to examine the value of Xpert MTB/RIF assay and detection of additional Mycobacterium tuberculosis complex (MTBC) species antigens from intestinal tissue samples in differentiating intestinal tuberculosis (ITB) from Crohn's disease (CD). METHODS: Several clinical specimens of intestinal tissue obtained by either endoscopic biopsy or surgical excision were used for mycobacteriologic solid cultures,Xpert MTB/RIF assays, immunohistochemistry, and histological examinations. Four antigens (38KDa, ESAT-6, MPT64, and Ag85 complex) of MTBC in the intestinal tissue were detected by immunohistochemical analysis. RESULTS: The study included 42 patients with ITB and 46 with CD. Perianal lesions and longitudinal ulcers were more common in patients with CD, while caseating granuloma and annular ulcers were more common in patients with ITB. The positive rate of MTBC detected by Xpert MTB/RIF in intestinal tissues of patients with ITB was 33.33%, which was significantly higher than that in patients with CD and that detected using acid-fast staining smears. It was also higher than that detected by tissue MTBC culture, but the difference was not statistically significant. The positive MPT64 expression rate in patients with ITB was 40.48%, which was significantly higher than that observed in patients with CD. The sensitivity of parallelly combined detection of tuberculosis protein MPT64 and Xpert MTB/RIF in diagnosing ITB was 50.0%. CONCLUSIONS: The detection of Xpert MTB/RIF in intestinal tissue is a rapid and useful method for establishing an early diagnosis of ITB. The detection of MTBC using Xpert MTB/RIF and MPT64 antigen in intestinal tissues has a definitive value in the differential diagnosis ofITB and CD. The combination of these two methods can improve the detection sensitivity.

Diagnostic accuracy of the Xpert MTB/RIF assay for abdominal tuberculosis: a systematic review and meta-analysis.

BACKGROUND: We performed a meta-analysis to determine diagnostic accuracy of Xpert MTB/RIF for diagnosis of abdominal (intestinal or peritoneal) tuberculosis (TB) in various tissues (intestinal, omental/peritoneal tissue or ascitic fluid). METHODS: Electronic databases were searched for observational studies on use of Xpert MTB/RIF in ascitic fluid, peritoneal, or omental tissue for diagnosis of peritoneal and intestinal TB. We calculated the pooled sensitivity, specificity and diagnostic odds ratio of Xpert MTB/RIF for diagnosis of peritoneal TB in comparison to composite reference standard (CRS) and culture, and in comparison to CRS for intestinal TB. RESULTS: Twenty-five observational studies were included. The pooled sensitivity and specificity as assessed with peritoneal culture from ascites as an Index test was 64% (95% Confidence Interval [C.I.] 49-76%) and 97% (95% C.I., 95-99%) respectively and with peritoneal CRS was 30% (95% C.I., 22-40%) and 100% (95% C.I., 98-100%) respectively. In the intestinal group, the pooled sensitivity and specificity of Xpert MTB/RIF was 23% (95% C.I., 16-32%) and 100% (95% C.I., 52-100%). The AUC of peritoneal culture and intestinal tissue was 0.935 and 0.499. CONCLUSION: Xpert MTB/RIF has modest sensitivity for diagnosis of peritoneal and intestinal tuberculosis but has a good specificity. PROSPERO REGISTRATION: CRD42020140545.

Obstructed ileocaecal tuberculosis with splenic tuberculosis and solid pseudopapillary tumour of tail of pancreas in an immunocompetent woman.

A 22-year-old young woman presented with fever, lower abdominal pain and vomiting for 20 days. She had persistent fever and abdominal pain. Fever panel was negative. Clinical features were suggestive of subacute small bowel obstruction. Contrast-enhanced CT abdomen showed thickening of distal ileum, ileocaecal junction and caecum with conglomerate necrotic nodal mass in the ileocolic mesentry along with a lesion in the tail of pancreas. Patient was discussed with multidisciplinary team and decided to undergo a single-stage procedure after adequate nutritional optimisation. During optimisation, she underwent acute obstruction and hence taken up for emergency laparotomy proceeded to right haemicolectomy with distal pancreatectomy and splenectomy 4 weeks after the time of admission. Histopathology showed ileocaecal tuberculosis and solid pseudopapillary tumour with margins free of tumour. Approach of obstructed ileocaecal tuberculosis in the setting of incidental diagnosis of solid pseudopapillary tumour of pancreas in a moribund patient was challenging.

How can gastro-intestinal tuberculosis diagnosis be improved? A prospective cohort study.

BACKGROUND: Gastrointestinal tuberculosis (TB) is diagnostically challenging; therefore, many cases are treated presumptively. We aimed to describe features and outcomes of gastrointestinal TB, determine whether a clinical algorithm could distinguish TB from non-TB diagnoses, and calculate accuracy of diagnostic tests. METHODS: We conducted a prospective cohort study of hospitalized patients in Kota Kinabalu, Malaysia, with suspected gastrointestinal TB. We recorded clinical and laboratory characteristics and outcomes. Tissue samples were submitted for histology, microscopy, culture and GeneXpert MTB/RIF®. Patients were followed for up to 2 years. RESULTS: Among 88 patients with suspected gastrointestinal TB, 69 were included in analyses; 52 (75%) had a final diagnosis of gastrointestinal TB; 17 had a non-TB diagnosis. People with TB were younger (42.7 versus 61.5 years, p = 0.01) and more likely to have weight loss (91% versus 64%, p = 0.03). An algorithm using age < 44, weight loss, cough, fever, no vomiting, albumin > 26 g/L, platelets > 340 × 109/L and immunocompromise had good specificity (96.2%) in predicting TB, but very poor sensitivity (16.0%). GeneXpert® performed very well on gastrointestinal biopsies (sensitivity 95.7% versus 35.0% for culture against a gold standard composite case definition of confirmed TB). Most patients (79%) successfully completed treatment and no treatment failure occurred, however adverse events (21%) and mortality (13%) among TB cases were high. We found no evidence that 6 months of treatment was inferior to longer courses. CONCLUSIONS: The prospective design provides important insights for clinicians managing gastrointestinal TB. We recommend wider implementation of high-performing diagnostic tests such as GeneXpert® on extra-pulmonary samples.

Clinicopathological profile of gastrointestinal tuberculosis: a multinational ID-IRI study.

Data are relatively scarce on gastro-intestinal tuberculosis (GITB). Most studies are old and from single centers, or did not include immunosuppressed patients. Thus, we aimed to determine the clinical, radiological, and laboratory profiles of GITB. We included adults with proven GITB treated between 2000 and 2018. Patients were enrolled from 21 referral centers in 8 countries (Belgium, Egypt, France, Italy, Kazakhstan, Saudi Arabia, UK, and Turkey). One hundred four patients were included. Terminal ileum (n = 46, 44.2%), small intestines except terminal ileum (n = 36, 34.6%), colon (n = 29, 27.8%), stomach (n = 6, 5.7%), and perianal (one patient) were the sites of GITB. One-third of all patients were immunosuppressed. Sixteen patients had diabetes, 8 had chronic renal failure, 5 were HIV positive, 4 had liver cirrhosis, and 3 had malignancies. Intestinal biopsy samples were cultured in 75 cases (78.1%) and TB was isolated in 65 patients (86.6%). PCR were performed to 37 (35.6%) biopsy samples and of these, 35 (94.6%) were positive. Ascites samples were cultured in 19 patients and M. tuberculosis was isolated in 11 (57.9%). Upper gastrointestinal endoscopy was performed to 40 patients (38.5%) and colonoscopy in 74 (71.1%). Surgical interventions were frequently the source of diagnostic samples (25 laparoscopy/20 laparotomy, n = 45, 43.3%). Patients were treated with standard and second-line anti-TB medications. Ultimately, 4 (3.8%) patients died and 2 (1.9%) cases relapsed. There was a high incidence of underlying immunosuppression in GITB patients. A high degree of clinical suspicion is necessary to initiate appropriate and timely diagnostic procedures; many patients are first diagnosed at surgery.

[Duodenal obstruction and upper gastrointestinal bleeding as the initial presentation of an isolated duodenal tuberculosis]. / Obstrucción duodenal y hemorragia digestiva alta como presentación inicial de una tuberculosis duodenal aislada.

Primary duodenal tuberculosis is rare, even in endemic regions. The diagnosis poses a major challenge and requires a high index of suspicion, supported by imaging studies, microbiology, and histopatology obtained by endoscopic or surgical biopsy. We report the case of a 31-year-old man, without HIV infection or any previous history of tuberculosis, who presented with duodenal obstruction. After exploratory laparotomy, he presented a duodenal stenosis and upper gastrointestinal bleeding. A total of four diagnostic procedures (one laparotomy and three endoscopies) were performed, all of which included biopsies. Only the last endoscopy made with the technique "biopsy upon biopsy" showed the presence of acid fast bacilli and granulomas. The diagnosis of tuberculosis was confirmed by polymerase chain reaction in duodenal tissue. There was no evidence of involvement of other organs by tuberculosis. The patient had an excellent therapeutic response.

Imaging in discriminating intestinal tuberculosis and Crohn's disease: past, present and the future.

Introduction: Intestinal tuberculosis (ITB) and Crohn's disease (CD) have similar clinical presentation, but require different treatment approaches. Despite advances in various endoscopic, imaging, microbiological, and histological techniques, the differentiation of these two entities is often difficult. Newer radiological and image acquisition modalities have now become indispensable tools for evaluation of these two diseases.Areas covered: This review summarizes the currently available literature on various radiological investigations to differentiate ITB from CD. This review also enumerates the newer modalities in image acquisition techniques and their potential role for differentiating these two diseases. At present abdominal computed tomography (CT) scan is used as a first line investigation for differentiating ITB from CD. Magnetic resonance imaging (MRI) is preferred in pediatric patients and for follow-up studies.Expert opinion: Role of newer modalities like contrast enhanced abdominal ultrasound, perfusion CT, advanced MRI and positron emission tomography (PET) is evolving and requires further exploration. Till further robust studies are available, differentiation between ITB and CD requires use of a combination of clinical, endoscopic, serological, histological, and radiological parameters rather than relying on a single test.

Genomic Polymorphism Associated with the Emergence of Virulent Isolates of Mycobacterium bovis in the Nile Delta.

Mycobacterium bovis is responsible for bovine tuberculosis in both animals and humans. Despite being one of the most important global zoonotic disease, data related to the ecology and pathogenicity of bovine tuberculosis is scarce, especially in developing countries. In this report, we examined the dynamics of M. bovis transmission among dairy cattle in the Nile Delta of Egypt. Animals belonging to 27 herds from 7 governorates were tested by the Single Intradermal Comparative Skin Tuberculin (SICST), as a preliminary screen for the presence of bovine tuberculosis. Positive SICST reactors were identified in 3% of the animals spread among 40% of the examined herds. Post-mortem examination of slaughtered reactors confirmed the presence of both pulmonary and/or digestive forms of tuberculosis in > 50% of the examined animals. Targeted and whole-genome analysis of M. bovis isolates indicated the emergences of a predominant spoligotype (SB0268) between 2013-2015, suggesting a recent clonal spread of this isolate within the Nile Delta. Surprisingly, 2 isolates belonged to M. bovis BCG group, which are not allowed for animal vaccination in Egypt, while the rest of isolates belonged to the virulent M. bovis clonal complex European 2 present in Latin America and several European countries. Analysis of strain virulence in the murine model of tuberculosis indicated the emergence of a more virulent strain (MBE4) with a specific genotype. More analysis is needed to understand the molecular basis for successful spread of virulent isolates of bovine tuberculosis among animals and to establish genotype/phenotype association.

Obstrucción duodenal y hemorragia digestiva alta como presentación inicial de una tuberculosis duodenal aislada / Duodenal obstruction and upper gastrointestinal bleeding as the initial presentation of an isolated duodenal tuberculosis

Resumen La tuberculosis duodenal primaria es muy infrecuente, incluso en regiones endémicas. El diagnóstico plantea un gran reto, y requiere un alto índice de sospecha, apoyado en estudios de imágenes, microbiología, e histopatología obtenida por biopsia endoscópica o quirúrgica. Presentamos el caso de un varón de 31 años, sin infección por VIH ni antecedente de tuberculosis, que debutó con una obstrucción duodenal. Posterior a una laparatomía exploradora presentó una estenosis duodenal y una hemorragia digestiva alta. Luego de varias biopsias no concluyentes, sólo la última, realizada con la técnica "biopsia sobre biopsia", demostró la presencia de granulomas con bacilos ácido-alcohol resistentes. El diagnóstico de tuberculosis fue confirmado por reacción de polimerasa en cadena de tejido duodenal. No se evidenció compromiso de otros órganos. La respuesta terapéutica fue excelente.

Primary duodenal tuberculosis is rare, even in endemic regions. The diagnosis poses a major challenge and requires a high index of suspicion, supported by imaging studies, microbiology, and histopatology obtained by endoscopic or surgical biopsy. We report the case of a 31-year-old man, without HIV infection or any previous history of tuberculosis, who presented with duodenal obstruction. After exploratory laparotomy, he presented a duodenal stenosis and upper gastrointestinal bleeding. A total of four diagnostic procedures (one laparotomy and three endoscopies) were performed, all of which included biopsies. Only the last endoscopy made with the technique "biopsy upon biopsy" showed the presence of acid fast bacilli and granulomas. The diagnosis of tuberculosis was confirmed by polymerase chain reaction in duodenal tissue. There was no evidence of involvement of other organs by tuberculosis. The patient had an excellent therapeutic response.

Differentiating Crohn's disease from intestinal tuberculosis.

Differentiating Crohn's disease (CD) and intestinal tuberculosis (ITB) has remained a dilemma for most of the clinicians in the developing world, which are endemic for ITB, and where the disease burden of inflammatory bowel disease is on the rise. Although, there are certain clinical (diarrhea/hematochezia/perianal disease common in CD; fever/night sweats common in ITB), endoscopic (longitudinal/aphthous ulcers common in CD; transverse ulcers/patulous ileocaecal valve common in ITB), histologic (caseating/confluent/large granuloma common in ITB; microgranuloma common in CD), microbiologic (positive stain/culture for acid fast-bacillus in ITB), radiologic (long segment involvement/comb sign/skip lesions common in CD; necrotic lymph node/contiguous ileocaecal involvement common in ITB), and serologic differences between CD and ITB, the only exclusive features are caseation necrosis on biopsy, positive smear for acid-fast bacillus (AFB) and/or AFB culture, and necrotic lymph node on cross-sectional imaging in ITB. However, these exclusive features are limited by poor sensitivity, and this has led to the development of multiple multi-parametric predictive models. These models are also limited by complex formulae, small sample size and lack of validation across other populations. Several new parameters have come up including the latest Bayesian meta-analysis, enumeration of peripheral blood T-regulatory cells, and updated computed tomography based predictive score. However, therapeutic anti-tubercular therapy (ATT) trial, and subsequent clinical and endoscopic response to ATT is still required in a significant proportion of patients to establish the diagnosis. Therapeutic ATT trial is associated with a delay in the diagnosis of CD, and there is a need for better modalities for improved differentiation and reduction in the need for ATT trial.

Primary enterolithiasis with intestinal tuberculosis: rare presentation of a common disease.

Enterolithiasis is the formation of intestinal calculi due to stasis. Tubercular strictures resulting in intestinal stasis provide a favourable environment for enterolith formation. Intestinal tuberculosis occurs commonly in India, but coexistent enterolithiasis has been reported rarely. We are describing three cases of enterolithiasis secondary to tubercular intestinal strictures among female patients in the fourth to fifth decades of life, all of them having pulmonary tuberculosis in the past. All the cases presented with features of subacute intestinal obstruction. X-ray abdomen done for all of them revealed single to multiple round, oval and rectangular, radio-opaque shadows suggestive of stones. Coexistence of enterolithiasis with intestinal tuberculosis may worsen the symptoms of intestinal obstruction and surgery remains the mainstay of treatment. All the patients underwent exploratory laparotomy, resection and anastomosis of the diseased bowel and antitubercular therapy was started. Two patients responded well to the treatment and the third one expired due to cardiac comorbidity.

[Gastric tuberculosis in an elderly patient:a case report].

A woman in her 70s presented to our hospital with epigastric pain, back pain, and weight loss. Esophagogastroduodenoscopy was performed, and numerous protuberances, which were suspected to be submucosal tumors, were found at the gastric corpus. The patient was diagnosed with gastric tuberculosis based on the biopsy results of these protuberances. Histopathological analysis demonstrated non-caseating epithelioid granuloma. A positive culture for Mycobacterium tuberculosis was also obtained on gastric juice analysis and confirmed using polymerase chain reaction assay. In the rapidly aging population in Japan, our findings emphasize on the importance of differentiating gastrointestinal tuberculosis, including gastric tuberculosis, from other diseases. This case may provide information about the development of gastric tuberculosis.