Open Access Original Research Article

GeneXpert MTB/RIF as a Rapid Diagnostic tool for Diagnosis of Pulmonary, Extra-pulmonary Tuberculosis and Rifampicin Resistance in the Egyptian Population

Sahar A. M. Ali, Reem M. Hassan, Mona M. K. Shehata

Journal of Advances in Microbiology, Page 1-14
DOI: 10.9734/JAMB/2018/45101

Rapid and accurate detection of Mycobacterium tuberculosis complex (MTBC) with early detection of drug-resistance is mandatory for the effective control of TB.

Aim: An evaluation of the performance of the GeneXpert MTB/RIF assay in the diagnosis of pulmonary and extra-pulmonary TB and Rifampicin (RIF) resistance.

Materials and Methods: 420 patients with clinical or radiological suspicion of Tuberculosis were included in this study. GeneXpert MTB/RIF (Cepheid, Sunnyvale, USA) was used for diagnosis of pulmonary, extra-pulmonary tuberculosis and Rifampicin-resistance. Comparison of our results was done with the results of acid-fast bacilli (AFB) smear microscopy and the culture method (as a standard method). Rifampicin resistance results were compared to drug susceptibility testing (DST) as a gold standard method.  Sequencing of the rpoB gene was done for the Rifampicin-resistant isolates using genetic analyser ABI prism 3130 XL (Applied Biosystems, USA). 

Results: TB was diagnosed in 23.7% of patients suspected to have pulmonary TB and in 12.5% of patients suspected of having extra-pulmonary TB. The GeneXpert MTB/RIF detected MTB with an overall sensitivity of 88.7% (63/71), specificity of 97.8% (224/229), PPV of 92.6% and NPV of 96.5%. There was a highly statistically significant difference between GeneXpert MTB/RIF and AFB smear microscopy, in pulmonary and extra-pulmonary cases. RIF resistance was identified by DST in 2.3% (2/86) TB culture positive specimens; both of which were multidrug-resistant (MDR). The GeneXpert MTB/RIF assay showed RIF resistance in all specimens identified as RIF resistant by DST in addition to one specimen identified as RIF susceptible by DST. The results of gene sequencing were in concordance with that obtained from GeneXpert MTB/RIF.

Conclusions: Our findings inforce the use of GeneXpert MTB/RIF as a prompt rapid diagnostic tool for early diagnosis of pulmonary TB especially in smear-negative and extra-pulmonary tuberculosis with the early detection of Rifampicin resistance.

Open Access Original Research Article

Lactic Acid Bacteria Profile of Some Selected Food Products and Their Ability to Produce Bacteriocins

Godwin E. John, Josiah A. Lennox

Journal of Advances in Microbiology, Page 1-8
DOI: 10.9734/JAMB/2018/45134

Lactic acid bacteria (LAB) commonly used as starter cultures in foods is known to produce antimicrobial substances such as bacteriocins, hydrogen peroxide and organic acids. They have great potential as food biopreservatives. The present study was aimed at profiling lactic acid bacteria of some selected food products and bacteriocin production from various food products. Different food samples comprising four each of cucumber, fresh fish, fresh milk (nunu), meat, ogi, cheese, yoghurt, and tapioca making it a total of thirty two (32) was bought in area markets in Calabar Metropolis. Serial dilutions of these samples were prepared and inoculated by pour plate method on MRS medium and incubated. It was observed that the lactic acid bacteria loads ranged from 1.11±0.41 × 102 cfu/ml(g) for fresh milk to 4.62 × 103 cfu/ml(g) for cheese. As for the distinct colonies, cheese had the highest 22 while silage had the lowest 9. Others were 21 for fresh milk, 20 for fufu, 19 for ogi, 18 for yoghurt, 15 for meat, 14 for cucumber and 12 for fish. The isolates were identified based on morphological, physiological and biochemical analysis using API 50 CHL kit. One hundred and fifty five morphologically distinct colonies of lactic acid bacteria isolated from these food samples were screened for bacteriocin production. Only 26 of these were found to be bacteriocin-positive indicating their ability to produce bacteriocin. The isolates identified included Lactobacillus sp, Leuconostoc sp, Lactococcus spp, Enterococcus sp and Pediococcus sp. This research extends our knowledge of the ubiquitous distribution of lactic acid bacteria in foods. These bacteriocin positive isolates can, therefore, be used in food preservation and control of food borne pathogens.

Open Access Original Research Article

Efficacy of Different Alcohol-based Hand Disinfectants in Reduction of Hand Contamination among Food Handlers in Alexandria, Egypt

Hadir EL-Kady

Journal of Advances in Microbiology, Page 1-13
DOI: 10.9734/JAMB/2018/45345

Aims: To assess hand contamination among food handlers working at the cafeterias of Pharos University and to compare the efficacy of different alcohol-based hand rubs (ABHRs) in reducing hand contamination among them during routine work.

Study Design:  Pre/post test quasi experimental study.

Place and Duration of Study: The study was carried out in the period from April to August 2018 and included fifty volunteered food handlers at the cafeterias of Pharos University, Alexandria, Egypt.

Methodology: Dominant hand direct finger-print samples were collected from the fifty participants during a pre-intervention visit to estimate the prevalence of hand contamination. In four following visits, another 400 finger-print samples were collected before and after applying four different hand disinfectants: three liquid ABHRs and a hand-rubbing gel. Samples were microbiologically examined for identification of contaminants. The different formulae were evaluated regarding their efficacy in reducing the count of hand contaminants.

Results: Thirty out of fifty (60%) of the finger-print samples were positive for one or more microbial contaminants. Coagulase-negative staphylococci (CNS) were the most prevalent isolates; detected in 66% of samples. The isolation rate of potential food borne contaminants was significantly higher among food handlers who served for less than five years (80%), compared to only 16.7% among those who served for more than ten years (P=0.001). The isolation rate of contaminants was significantly lower among participants who washed their hands after visiting the toilet (45.8%), compared to 73.1% among those who didn’t (p=0.05). A significant percentage reduction in the microbial count was recorded for all formulae used; with the gel hand rub being the least reducing formula.

Conclusion: Hand contamination with food borne pathogens is highly prevalent among food handlers. Liquid formulae of hand disinfectants containing propanol, applied for 15 seconds, are more efficient than those containing ethanol and than the gel formulae.

Open Access Original Research Article

Production of Modified Rapid Serum Agglutination Antigen for Sero-diagnosis of Contagious Bovine Pleuropneumonia (CBPP)

Raghad A. H. Onsa, F. M. Hamid, E. I. Elshafie, E. A. Muna, G. E. Mohammed

Journal of Advances in Microbiology, Page 1-7
DOI: 10.9734/JAMB/2018/44503

Aims: This work was conducted to develop rapid serum agglutination test for Contagious Bovine Pleuropneumonia (CBPP) serodiagnosis.

Study Design: Production of two types of antigen, one from T1/44 reference strain of Mycoplasma mycoides sub sp.  mycoides (Mmm) and the other from local strain (RH). 

Place and Duration of Study: This study was carried out at Mycoplasma department Central Veterinary Research Lab (CVRL) in Sudan during 2016-2018.

Methodology: The antigens have been developed using standard methods and evaluated using standard reference serum, c.ELISA and Latex Agglutination test. Statistical analysis using Chi-square test and Kappa agreement were applied.  

Results: The sensitivity of the developed stained antigen from T1/44 strain (SAT1) was 100% in comparison of 92% and 95% of SAT2 (RH local strain) and LAT, respectively, The developed SAT2 antigen revealed satisfied specificity results (70%), which is higher than SAT1 (31%) and LAT (59.6%).

Conclusion: From these results we found that SAT2 which is produced from local strain- proved to be more specific and highly sensitive. The SAT2 combines low cost and high specificity and easy applicable in field, without need for any specialist training or equipment.

Open Access Original Research Article

Bioremediation of Illegally Refined Crude Oil Residue Using Soybean Waste and Cow Dung

S. I. Douglas, O. F. Ikirikoba

Journal of Advances in Microbiology, Page 1-8
DOI: 10.9734/JAMB/2018/45588

Aims: This study was carried out to compare the effectiveness of soybean wastes and cow dung as an organic treatment for stimulating the hydrocarbon utilising Bacteria.

Study Design:  In the laboratory, about 1000g of soil samples were weighed and transferred in to sterile pots labelled EP1, EP2, and EP3. The biostimulants were respectively transferred into the pots accordingly. The setup was watered and tilled once a week to provide moisture and oxygen for the organisms

Place and Duration of Study: Kpo fire contaminated soil samples were collected in plastic bag from four different points in marine base, Port Harcourt, Rivers State, Nigeria. The GPS of the location is given as N4°46’11.1252” E7°1’38.1324. The study was from March to April, 2018.

Methodology: The standard plate count method was used for the enumeration of the total heterotrophic and hydrocarbon utilising bacteria. One gram (1 g) of soil sample was weighed and aseptically transferred into test tube containing 9ml sterile normal saline. This was serially diluted to 10-6. 10-2 and 10-4 dilutions were inoculated onto the mineral salt medium and nutrient agar medium respectively. Inoculated plates were spread using sterile bent glass rod and incubation at 37 0C followed. The duration of incubation were 24 hours and 5-8 days for the total heterotrophic bacteria and total hydrocarbon utilising bacteria respectively. This was done for all the soil samples.

Results: The total heterotrophic bacterial loads revealed that the EP1 (control) ranged from 3.15 to 4.613 Log10Cfu/g. The EP2 ranged from 4.9 to 7.4 Log10Cfu/g while the EP3 ranged from 5.2 to 7.6 Log10Cfu/g. The hydrocarbon utilising bacterial loads revealed that EP1 (control) ranged from 1.0 to 4.2 Log10Cfu/g. The EP2 ranged from 4.7 to 6.9 Log10Cfu/g while the EP3 ranged from 4.9 to 7.4 Log10Cfu/g. The HUB identified in this study were Citrobacter species, Bacillus species, Serratia species, Clostridium species, Micrococcus species Pseudomonas species, Proteus species and Enterobacter species.

Conclusion: From the investigation of the bioremediation potential of contaminated soil supplemented with soybean wastes and those supplemented cow dungs, it was observed that both stimulants yielded good results and can be used as organic stimulants. Furthermore, this study has shown that the cow dung stimulants yielded better results than soybean waste simulants.