Preventive veterinary medicine

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GeneXpert MTB/RIF is a reliable molecular diagnostic tool capable of detecting Mycobacterium tuberculosis (MTB) and identifying genetic determinants of rifampicin (RIF) resistance. This study aimed to assess physicians’ diagnostic decision-making processes for TB based on GeneXpert MTB/RIF results and how this affected the initiation of multidrug resistance (MDR) treatment. This study employed a mixed method: data were collected retrospectively from the medical records of TB patients and in-depth interviews were conducted with healthcare workers in areas with a high TB burden in Thailand. A total of 2,030 complete TB records from 2 patient groups were reviewed, including 1443 suspected cases with negative smear results and 587 with high risk of MDR-TB. GeneXpert MTB/RIF was routinely used to assist the physicians in their decision-making for the diagnosis of pulmonary tuberculosis (PTB) and the initiation of MDR-TB treatment. The physicians used it as a “rule-in test” for all patients with negative chest X-rays (CXR) and smear results, to ensure timely treatment. Approximately one-fourth of the patients with negative CXR/smear and GeneXpert MTB/RIF results were diagnosed with PTB by the physicians, who based their decisions on other evidence, such as clinical symptoms, and did not use GeneXpert MTB/RIF as a “rule-out test.” GeneXpert MTB/RIF proved effective in early detection within a day, thereby radically shortening the time required to initiate second-line drug treatment. Despite its high sensitivity for detecting PTB and MDR-TB, GeneXpert MTB/RIF had contradictory results (false positive and/or false negative) for 21.8% of cases among patients with negative smear results and 41.1% of cases among patients with high risk of MDR-TB. Therefore, physicians still used the results of other conventional tests in their decision-making process. It is recommended that GeneXpert MTB/RIF should be established at all points of care and be used as the initial test for PTB and MDR-TB diagnosis.

/pdf/evaluation-of-the-use-of-genexpert-mtb-rif-in-a-zone-with-1iaeoi8y.pdf

Evaluation of the use of GeneXpert MTB/RIF in a zone with high burden of tuberculosis in Thailand

Tuberculosis (TB) is one of the top 10 causes of death worldwide. It is challenging to find methods of diagnosis of active pulmonary TB that are sensitive enough to detect cases for proper treatment before unintentional transmission. Droplet digital PCR (ddPCR) is a highly sensitive method to detect genetic material of pathogens, but it has rarely been used for diagnosis of TB. This study compared the sensitivity of ddPCR with that of GeneXpert and AFB smear microscopy in 180 leftover sputum samples from patients suspected of having TB on the basis of clinical symptoms and radiography. Absolute quantification of copy numbers of MTB-specific genes was possible using ddPCR targeting the mpt64 gene. Among the 180 samples, 41.1% were diagnosed as having TB using ddPCR. The sensitivities of AFB smear microscopy, GeneXpert and ddPCR were 41.9%, 82.4% and 100%, respectively. AFB smear microscopy and GeneXpert both had a specificity of 100%, and the specificity of ddPCR was 95.3%. The accuracy of ddPCR (97.2%) is higher than that of GeneXpert (92.7%). This robust ddPCR system could potentially be used as a method for early diagnosis of TB.

/pdf/detection-of-mycobacterium-tuberculosis-complex-in-sputum-3gro1hxz.pdf

Detection of Mycobacterium tuberculosis Complex in Sputum Samples Using Droplet Digital PCR Targeting mpt64

Background Fungal infections are common in HIV-infected individuals and significantly contribute to mortality. However, a substantial number of cases are undiagnosed before death. Objective To determine the frequency of fungal pathogens in autopsy studies of people who died with HIV In Africa. Methods We conducted a scoping review of autopsy studies conducted in Africa. Data sources PubMed, Scopus, Web of Science, Embase, Google Scholar, and African Journal Online. Study eligibility criteria The review encompasses studies published from inception to September 2023, and no language restrictions were imposed during the search process. We included studies that reported histopathological or microbiological evidence for the diagnosis of fungal infections and other pathogens. Data synthesis Data was summarised using descriptive statistics and no meta-analysis was performed. Results We examined 30 articles reporting studies conducted between 1991 and 2019, encompassing a total of 13,066 HIV-infected decedents across 10 African countries. In five studies, the autopsy type was not specified. Among those studies with specified autopsy types, 20 involved complete diagnostic autopsies, while 5 were categorized as partial or minimally invasive autopsies. There were 2,333 pathogens identified, with 946 (40.5%) being mycobacteria, 856 (36.7%) fungal, 231 (3.8%) viral, 208 (8.9%) parasitic, and 92 (3.9%) bacterial. Of the 856 fungal pathogens identified, 654 (28.0%) were Cryptococcus species, 167 (7.2%) Pneumocystis jirovecii, 16 (0.69%) Histoplasma species, 15 (0.64%) Aspergillus species, and 4 (0.17%) Candida species. Other major non-fungal pathogens identified were cytomegalovirus 172 (7.37%) and Toxoplasma gondii 173 (7.42%). Conclusions Invasive fungal infections occur in over one-third of people who succumb to HIV in Africa. In addition to cryptococcosis and PCP, integrating other priority fungal pathogen detection and management strategies into the broader framework of HIV care in Africa is recommended. This involves increasing awareness regarding the impact of fungal infections in advanced HIV disease and strengthening diagnostic and treatment capacity. 

Frequency of Fungal Pathogens in Autopsy Studies of People who died with HIV in Africa: A Scoping Review

Tuberculosis (TB) is a leading cause of morbidity and mortality worldwide. Control of TB is lingering by the lack of diagnostic tests that are simple, rapid, yet accurate. Thus, smear-negative pulmonary TB often misses the diagnosis. The study evaluated the performance of GeneXpert MTB/RIF assay for the detection of Mycobacterium tuberculosis (MTB).The study was carried out from June to December 2016 in Nepal Tuberculosis Center, Bhaktapur, Nepal. A total of 173 sputum samples were collected and processed by microscopy [Auramine-O staining and Ziehl-Neelsen (ZN) staining], followed by GeneXpert MTB/RIF assay and culture in Lowenstein-Jensen (LJ) medium.Of 173 sputum samples, 162 (93.6%) were smear-negative. Of 162 smear-negative sputum samples, 35 (21.6%) were confirmed to have MTB by culture, and 31 (19.1%) by GeneXpert MTB/RIF assay. Of 31 GeneXpert-positive samples, 25 (80.6%) were susceptible, 4 (12.9%) were resistant, and 2 (6.45%) were intermediate to rifampicin. The sensitivity, specificity, positive predictive value, and negative predictive value of GeneXpert MTB/RIF assay for smear-negative sputum samples were 74.3%, 96.6%, 86.7%, and 92%, respectively. The GeneXpert MTB/RIF has a substantial diagnostic agreement of 90.91% with culture (Cohen's Kappa coefficient = 0.73).The diagnostic performance of GeneXpert MTB/RIF assay was almost on par with culture, and thus can be relied upon for MTB detection in smear-negative sputum samples. 

/pdf/diagnostic-performance-of-genexpert-mtb-rif-in-detecting-mtb-3v4f4rrm.pdf

Diagnostic performance of GeneXpert MTB/RIF in detecting MTB in smear-negative presumptive TB patients

Intestinal parasitosis is one of the chief causes of health problems associated with domesticated and free-range ducks particularly in developing  countries. Among the various health problems amoebiasis and helminthic infection are still significant among ducks (Anas platyrhynchos Linnaeus, 1758) in Nepal. We report the status of intestinal parasitosis, particularly the prevalence and associated risk factors of gastrointestinal parasites of ducks reared in three different locations (Bishnu-Devi, Kanchan-Basti and Balambu) of Chandragiri Municipality from November 2016 to February 2017 using opportunistic random method. A total of 120 faecal samples collected in clean, dry and screw-capped plastic containers from six different locations were examined for the presence of parasites using formol-ether concentration method and modified Ziehl Neelsen staining technique, sodium chloride floatation and zinc sulphate sedimentation methods. Overall parasite positive rate was 81.67% (98/120). Positive rate of nematodes was highest (74.49%; 73/98) followed by cestodes (52.04%; 51/9) and protozoans (41.84%; 41/98) (P<0.05). A total of 78 (65.00%) samples showed single infections and 20 (16.67%) samples showed mixed infection (χ2 = 5.55; P<0.05). Statistical analysis indicated that locations were insignificantly associated with the infection by gastrointestinal tract parasites in the study areas. A total of eight (8) genera of parasites were identified which include two genera of protozoa, five genera of nematodes and one genera of cestodes. Of these, Ascaridia galli (21.67%) was found to have the highest prevalence and Isospora sp. (6.67%) to be the lowest. Gastrointestinal tract parasites were the major biological constraints contributing tothe low productivity of ducks and hampered the economic benefits obtained from the sector. Improvement of biosecurity measures for household duck farms through educating and motivating household farmers could help mitigate the effects of parasitic infection on production.
Keywords: Duck, Nematode, Cestode, Kathmandu, Chandragiri

/pdf/gastrointestinal-parasites-of-domesticated-duck-anas-1sjf4ubxqt.pdf

Gastrointestinal parasites of domesticated duck (Anas platyrhynchos Linnaeus, 1758) in Chandragiri municipality, Kathmandu, Nepal

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Diagnostic performance of GeneXpert MTB/RIF in detecting MTB in smear-negative presumptive TB patients

Gastrointestinal parasites of domesticated duck (Anas platyrhynchos Linnaeus, 1758) in Chandragiri municipality, Kathmandu, Nepal