Diversity and geographic distribution of soil streptomycetes with antagonistic potential against actinomycetoma-causing Streptomyces sudanensis in Sudan and South Sudan.

BACKGROUND: Production of antibiotics to inhibit competitors affects soil microbial community composition and contributes to disease suppression. In this work, we characterized whether Streptomyces bacteria, prolific antibiotics producers, inhibit a soil borne human pathogenic microorganism, Streptomyces sudanensis. S. sudanensis represents the major causal agent of actinomycetoma - a largely under-studied and dreadful subcutaneous disease of humans in the tropics and subtropics. The objective of this study was to evaluate the in vitro S. sudanensis inhibitory potential of soil streptomycetes isolated from different sites in Sudan, including areas with frequent (mycetoma belt) and rare actinomycetoma cases of illness. RESULTS: Using selective media, 173 Streptomyces isolates were recovered from 17 sites representing three ecoregions and different vegetation and ecological subdivisions in Sudan. In total, 115 strains of the 173 (66.5%) displayed antagonism against S. sudanensis with different levels of inhibition. Strains isolated from the South Saharan steppe and woodlands ecoregion (Northern Sudan) exhibited higher inhibitory potential than those strains isolated from the East Sudanian savanna ecoregion located in the south and southeastern Sudan, or the strains isolated from the Sahelian Acacia savanna ecoregion located in central and western Sudan. According to 16S rRNA gene sequence analysis, isolates were predominantly related to Streptomyces werraensis, S. enissocaesilis, S. griseostramineus and S. prasinosporus. Three clusters of isolates were related to strains that have previously been isolated from human and animal actinomycetoma cases: SD524 (Streptomyces sp. subclade 6), SD528 (Streptomyces griseostramineus) and SD552 (Streptomyces werraensis). CONCLUSION: The in vitro inhibitory potential against S. sudanensis was proven for more than half of the soil streptomycetes isolates in this study and this potential may contribute to suppressing the abundance and virulence of S. sudanensis. The streptomycetes isolated from the mycetoma free South Saharan steppe ecoregion show the highest average inhibitory potential. Further analyses suggest that mainly soil properties and rainfall modulate the structure and function of Streptomyces species, including their antagonistic activity against S. sudanensis.

DNA Gyrase and Topoisomerase IV Mutations and their effect on Quinolones Resistant Proteus mirabilis among UTIs Patients.

OBJECTIVE: This study aimed to highlight the importance of mutations within Proteus mirabilis genome that are related to fluoroquinolone resistance. METHODS: This is a cross sectional study performed in different teaching hospitals in Khartoum State from June 2016 to May 2017. A total of (120) P mirabilis isolates from patients with symptoms of UTIs attending different hospitals in Khartoum State were examined. First, modified Kurby Bauer method was performed for phenotypical detection of resistant isolates. Then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) followed by sequencing were applied for detection of mutations in GyrA, GyrB, ParC and ParE genes of isolates. RESULTS: P. mirabilis showed 30% resistance to ciprofloxacin. All samples revealed mutation at (serine 83) of GyrA and (serine 84) of ParC by Hinf1 restriction endonuclease digestion. Sequencing was performed for 12 samples. For each gene, two resistant and one susceptible strains were randomly selected. The mutations associated with ciprofloxacin resistant P. mirabilis were as follows; (1/3) GyrA (Ser 83 to Ile) and (2/3) ParC (Ser 81 to Ile). Also it revealed silent mutations at codons of GyrB 474 leucine (3/3), 585 valine (2/3), 612 histidine (1/3) and 639 asparagine (1/3) and ParE 469 isoleucine (2/3), 531 aspartic (2/3) and 533 glycine (1/3). CONCLUSIONS: Ciprofloxacin resistance in P. mirabilis could be monitored through detection of mutations within DNA gyrase (encoded by gyrA and gyrB) and topoisomerase IV (encoded by parC and parE).

Changes of th1 and th2 cytokines levels among sudanese tuberculosis patients during treatment.

Background: The interaction of T cells with infected macrophages depends on the interplay of cytokines produced in each cell, and this mechanism is a key to protective immunity against Mycobacterium tuberculosis. Extensive research has been devoted to studying the changes in systemic cytokine levels in patients with tuberculosis (TB), but the results are inconclusive. Determine Th1 and Th2 cytokine immune response levels among new TB patients compared to follow-up and healthy control. . Design: Cross-sectional laboratory-based study. Setting: Immunology Laboratory, National Center for Research. Methods: Blood samples (n = 145) were collected from confirmed new TB cases, follow-up TB cases, and from healthy controls. Participants were initially diagnosed by microcopy using Ziehl-Neelsen smear method and confirmed by polymerase chain reaction using IS6110. Cytokine levels (interleukin-10 [IL-10], tumor necrosis factor alpha [TNF-α], and Interferon-gamma [IFN-γ]) were measured directly from plasma using sandwich enzyme-linked immunosorbent assay. Main Outcome Measures: Measuring Th1 cytokines (IFN-γ and TNF-α) and Th2 cytokine (IL-10). One hundred and forty-five cases (new TB cases, 85; follow-up, 25; and healthy control, 35) were included in this study. Results: The study population were mainly males (70.3%) compared to females (29.7%) and 87.5% aged between 21 to 60 year. The plasma IFN-γ levels were found significantly higher in new TB cases (mean 35.38 pg/m; confidence interval: 29.32-41.43) than in the follow-up patients and the healthy control (P = 0.000). There were no significant differences in TNF-α and IL-10 levels among the new TB cases and the follow-up and healthy control (P = 0.852 and P = 0.340, respectively). Conclusions: Direct plasma IFN-γ level can be used in TB patient follow-up as a recovery marker as it correlated well with the appearance of the disease and treatment response.

Increasing Prevalence of Methicillin-resistant Staphylococcus aureus among Hospital and Community acquired Infections in Khartoum State, Sudan.

BACKGROUND: Staphylococcus aureus is an important bacterium that can cause many diseases. Methicillin-resistant S.aureus (MRSA) is often sub-categorized as Hospital or Community acquired infection. MRSA causes serious problems, such as bloodstream and surgical site infections or pneumonia. OBJECTIVES: The present study aimed to identify S. aureus by 16SrRNA using PCR, estimate the antibiotic susceptibility pattern and determine the prevalence of MRSA among Hospital and community acquired infections. METHODS: A cross-sectional laboratory-based study was conducted during the period from November 2020 to January 2021. Conventional methods were used to identify S. aureus and isolate confirmation was performed by PCR targeting 16SrRNA gene. All isolated organisms were tested for their in-vitro antimicrobial susceptibility. RESULT: Among the enrolled patients (n, 300), MRSA was observed in 185 (61.7%). The highest frequency was shown in the age group over 45 years old (46.7%). The result also showed a high frequency of S. aureus among community infections (81.7%), MRSA in hospital acquired infections was 10.7% while 51% was community acquired. The antimicrobial susceptibilities against MRSA isolates showed high sensitivity to Ceftriaxone 90.0%). Most infections caused by MRSA isolates were respiratory tract infection (RTI) (28.3%) and Septicemia (22.5%). CONCLUSION: The present study highlighted a high proportion of MRSA in clinical settings at Khartoum State. Antibiotic susceptibility results showed that Ceftriaxone was the drug of choice against MRSA isolates. Overuse and misuse of antibiotics, along with self-medication, seem to be the cause of antibiotic resistance, thus should be avoided.

Isolation and Identification of Streptomyces spp. from Desert and Savanna Soils in Sudan.

The purpose of this study was to investigate streptomycete populations in desert and savanna ecozones in Sudan and to identify species based on 16S rRNA gene sequences. A total of 49 different Streptomyces phenotypes (22 from sites representing the desert and semi-desert ecozone; 27 representing the savanna ecozone) have been included in the study. The isolates were characterized phenotypically and confirmed using 16S rRNA gene sequence analysis. The two ecozones showed both similarities and uniqueness in the types of isolates. The shared species were in cluster 1 (Streptomyces (S.) werraensis), cluster 2 (Streptomyces sp.), cluster 3 (S. griseomycini-like), and cluster 7 (S. rochei). The desert ecozone revealed unique species in cluster 9 (Streptomyces sp.) and cluster 10 (S. griseomycini). Whereas, the savanna ecozone revealed unique species in cluster 4 (Streptomyces sp.), cluster 5 (S. albogriseolus/ S. griseoincarnatus), cluster 6 (S. djakartensis), and cluster 8 (Streptomyces sp.). Streptomycetes are widely distributed in both desert and the savanna ecozones and many of these require full descriptions. Extending knowledge on Streptomyces communities and their dynamics in different ecological zones and their potential antibiotic production is needed.

Nocardiosis in Sudan: Current Situation and Future Perspective.

BACKGROUND: Infections caused by Nocardia are rare, but misguided to clinicians, especially if there is a delay in the diagnosis and/or low response to chemotherapy. The incidence of nocardiosis is increasing constantly worldwide, and the situation is getting worse if we consider immunocompromised individuals, such as human immune virus (HIV) positive patients since they are at higher risk. Surgical amputation, although not common, but should be considered as a result in some cases that cause partial disability. AIMS: To throw light on the situation of nocardiosis in Sudan, the possible reasons for the increased prevalence are investigated and discussed the possible strategies for prevention and control. Data Review: PubMed investigations were adopted using terms that included nocardiosis in Sudan as well as in other parts of the world. Part of the review has been retrieved from the main library of the postgraduate college, University of Khartoum and University of Newcastle upon Tyne. FINDINGS: In Sudan, nocardiosis revealed wide geographical distribution; different cases were reported from western, middle as well as the northern parts of the country. Moreover, several clinical presentations were seen. While pulmonary, coetaneous and subcutaneous infections represent the primary types caused by Nocardia, disseminated infection in two or more organs had also been reported. As in all other infectious diseases, opportunistic nocardiosis is more prevalent among HIV patients. Zoonotic transmission of the disease was also proved; several cases of bovine and caprine mastitis were due to one or another species of Nocardia. The effect of ecology on the prevalence and pathogenicity of Nocardia is proved by the isolation of Nocardia and other actinomycetes from Sudanese soil, which represents the most probable source of infection. Regarding treatment, effective results are usually obtained by the use of sulfonamides and thirdgeneration cephalosporins. However, surgical interference is also used when necessary, such as in cases of drainage of abscesses. CONCLUSION: Since the description of Nocardia by Edmond Nocard in 1888, it started to be well known worldwide. In Sudan, however, the awareness regarding this bacterium is still below the level and is only due to the end of the fifties of the twentieth century, which is relatively late. Hence, attention towards this neglected pathogen may lead to early recognition and prompt treatment, resulting in complete cure.

Epidemiological Trends of Cutaneous Leishmaniasis in Al-Madinah Al-Munawarah Province, Western Region of Saudi Arabia.

OBJECTIVE: To investigate the epidemiological trends of cutaneous leishmaniasis (CL) in Al-Madinah Al-Munawarah, western region of KSA. MATERIALS AND METHODS: Four hundred and sixty-seven parasitologically confirmed CL cases attending Al-Meeqat Hospital, Al-Madinah, during 2012-2015, were included in this study. RESULTS: Both Saudi and non-Saudi nationals were infected, with the highest infection rate being among Saudis (68.7%). Males were more affected than females as 86.9% of the total CL cases were males. Moreover, CL was prevalent in all age groups with higher frequency among young adults and adolescents (23.1% and 22.7%, respectively). Interestingly, almost all the patients in the adolescent and child age groups were Saudis (96.2% and 93.5%, respectively). Considering geographical distribution, the highest percentage of the cases (40.5%) were from the northern parts of Al-Madinah province while the eastern parts reported the least infection rate (7.3%). Few cases (2.5%) were supposed to encounter the infection abroad. Additionally, the frequency of infection was found to follow a seasonal distribution. Regarding treatment, pentostam, ketoconazole, or cryotherapy were the treatment options usually used. CONCLUSION: CL is prevalent in Al-Madinah Al-Munawarah area and new foci are being introduced. Thus, detailed studies with large surveillances regarding vector and reservoir hosts in and around the area are needed.

Burden of Multidrug Resistant Mycobacterium tuberculosis Among New Cases in Al-Madinah Al-Monawarah, Saudi Arabia.

BACKGROUND: The pattern of Mycobacterium tuberculosis susceptibility to first line drugs and multidrug resistance in Al-Madinah Al-Munawarah, a seasonally overcrowded are during Hajj and Omrah, is not well studied. OBJECTIVE: This study aimed to investigate anti-tuberculosis drug resistance and its distribution among new cases in Al-Madinah Al-Monawarah. METHODS: Study subjects included 622 patients with first time confirmed TB referred to the central tuberculosis laboratory in Al-Madinah between January 2012 and December 2014. RESULTS: Out of the 622 isolates, 99 (15.9%) were Mycobacteria Other Than Tuberculosis (MOTTS) and 25 (4.0%), three of which (12%) were children under five years of age, revealed multidrug resistance (MDR). Monoresistance to isoniazid (H) was (1.8%), to rifampin (R) was (1.4%), to streptomycin (S) was (1.9 %) to ethambutol (E) was (1.1 %) and to pyrazinamide (Z) was (2.1%). CONCLUSION: Being among the new cases, multidrug resistant tuberculosis (MDR TB) is supposed to be caused by strains which are originally multidrug resistant. Neither nationality nor gender was found to be associated with MDR TB. Since 12% of MDR cases were among children, a probability of primary infection with MDR strains is to be considered. Moreover, mass gathering during Hajj and Omrah seasons does not seem to increase the burden of MDR in the region. However, further investigation is needed to molecularly characterize MDR isolates and their phylogenetics and geographical origin.

Elevated TGF-beta levels in drug-resistant visceral leishmaniasis.

BACKGROUND: Poor and neglected populations in Africa are particularly affected with visceral leishmaniasis. The widespread emergence of resistance to pentavalent antimonials occurs globally and the unavailability of a vaccine in clinical use constitutes a major obstacle in disease control. OBJECTIVE: To investigate the cytokine profile in human visceral leishmaniasis. DESIGN: A cross-sectional laboratory-based study. SETTING: Single center study carried out at the Institute of Endemic Diseases, University of Khartoum, Sudan. PATIENTS AND METHODS: Soluble lysates of L major and L donovani were used to stimulate the lymphocytes of two groups of confirmed VL patients (group 1 [n=20] had respond to pentostam treatment and group 2 [n=5] were recorded as drug resistant after follow up) in a cellular proliferation assay and the levels of IFNg, IL-10, TNFa and TGFb were detected by cytokine ELISA. MAIN OUTCOME MEASURES: Levels of IFNg, TNFa, IL-10 and TGFb. RESULTS: A significant increase of IFNg and TNFa levels were reported in stimulated cells of drug susceptible and drug resistant groups, but no significant difference in IL-10 production was observed between the different antigens or between the patients groups. TGFb from stimulated lymphocytes was secreted in statistically significant amounts in patients reported as drug resistant in response to both L major and L donovani antigens (P < .001). CONCLUSIONS: In VL patients, IFNg and TNFa are extremely produced in response to in vitro re-stimulation which means that the parasitic infection, although virulent and chronic, does not render patients as immunocompromised. However, TGFb is mostly associated with treatment failure. LIMITATIONS: This study assessed secretory TGFb. A study with a larger sample size to assess TGFb gene expression and to follow its intracytoplasmic synthesis in drug resistant VL patients is recommended.

Challenges in diagnosing tuberculosis in children: a comparative study from Sudan.

OBJECTIVES: The diagnosis of tuberculosis (TB) in children is challenging due to insufficient specimen material and the scarcity of bacilli in specimens. This study aimed to evaluate methods for diagnosing TB in children in Sudan. METHODS: Patients (N=197) were subjected to the tuberculin skin test (TST). Gastric lavage or sputum specimens were then collected, processed, and cultured as per standard procedures. RESULTS: Culture on Löwenstein-Jensen medium, the reference standard, revealed growth in 16.2% of the specimens. Comparative analysis showed that 43.7% were positive for the TST (sensitivity 100%, specificity 67.3%), 8.1% were positive by Ziehl-Neelsen stain (sensitivity 43.8%, specificity 98.8%), 11.2% by auramine stain (sensitivity 56.3%, specificity 98.8%), and 17.8% were positive for PCR amplification of the IS6110 sequence (sensitivity 100%, specificity 98.8%). CONCLUSIONS: It is concluded that whilst TST and IS6110 achieved 100% sensitivity based on the reference standard of culture, the latter was more specific. The TST is recommended for routine diagnosis and the use of PCR for particular cases, depending on the facilities and the urgency.

Absence of the mecA Gene in Methicillin Resistant Staphylococcus aureus Isolated from Different Clinical Specimens in Shendi City, Sudan.

Absolute dependence on mecA gene as the defining standard in determining the resistance of S. aureus to methicillin became the subject of distrust by many researchers. The present study aimed to determine the frequency of mecA gene in methicillin resistant S. aureus (MRSA) isolates using polymerase chain reaction and to correlate its presence to conventional method. In this regard, two hundred S. aureus isolates were collected from patients with different diseases attending different hospitals in Shandi City, Sudan. Phenotypic Kirby-Bauer method confirmed the existence of methicillin resistant S. aureus in 61.5% of the subjected isolates with MICs ranging from 4 µg/mL to 256 µg/mL when using E-test. However, when amplifying a 310 bp fragment of the mecA gene by PCR, twelve out of the 123 MRSA isolates (9.8%) were mecA negative, whereas all the 77 methicillin sensitive S. aureus (MSSA) were mecA negative. In conclusion, this study drew attention to the credibility of the mecA gene and its usefulness in the detection of all MRSA strains without referring to the traditional methods. Hence, it is highly recommended to consider alternative mechanisms for ß-lactam resistance that may compete with mecA gene in the emergence of MRSA phenomenon in the community.

Polymerase Chain Reaction targeting insertion sequence IS6110 for the diagnosis of pulmonary tuberculosis among Sudanese children and young adults.

This study was carried out in Khartoum State during the period from January 2011 to December 2013 to improve the rate of detection of Mycobacterium tuberculosis (MTB) in children with symptoms of tuberculosis (TB) infection using different conventional and advanced diagnostic techniques. One hundred and ninety-seven specimens of gastric lavage and sputum were collected from different hospitals in Khartoum State, including Elbolok Hospital, Jafar Ibn Owf Hospital, Elasha'ab Teaching Hospital, Soba University Hospital and Academy Charity Hospital. All children participating in the study were subjected to the Mantoux test after obtaining appropriate consent injected by 5 tuberculin units of tuberculin purified protein derivative, and the results were recorded after three days. Specimens were decontaminated and inoculated on Lowenstein-Jensen media according to the modified Petroff's method. Two smears were prepared and stained by Ziehl-Neelsen stain and Auramine fluorescent dye; bacterial DNA was extracted from each specimen by using phenol chloroform method, and then the Polymerase Chain Reaction technique was adopted to detect Insertion Sequence IS6110 gene of MTB in these specimens. This study showed that the positive results for TST, ZN, Auramine, Culture and PCR were 86 (43.7%), 16 (8.1%), 22 (11.2%), 32 (16.2%) and 35(17.8%), respectively. The study concluded that the PCR technique is the most sensitive and specific technique for a quick identification of MTB in gastric lavage and sputum from children who are unable to expectorate a good quality sputum sample or who are diagnosed as negative using conventional diagnostic methods.

Multi-drug resistance tuberculosis (MDR-TB) in Kassala State, Eastern Sudan.

This study investigates the prevalence of drug resistance and mutations in rpoB gene among Mycobacterium tuberculosis isolates from Kassala State, Sudan. In a cross-sectional study during 2011, sputum specimens (n = 90) were examined microscopically and grown cultures were identified by analysing IS6110 insertion sequence. Antimicrobial sensitivity and mutations in the rpoB gene were determined. Of the 90 specimens found which were positive for acid-fast bacilli (AFB), 65 (72.2%) showed growth of mycobacteria. Sixty (66.7%) of these were M. tuberculosis, 5 (5.6%) were rapidly growing mycobacteria and 10 (11.1%) revealed no growth. Of the 60 M. tuberculosis, 31 (51.7%) were drug resistant, including 18 multidrug resistant TB (30%), and 15 (83.3%) demonstrated mutations in the rpoB gene. Isoniazid and rifampicin revealed the highest resistance rates (64.5%, 61.3%, respectively). In conclusion, drug resistance M. tuberculosis in Kassala State was high (30%) and was found to be mainly (83.3%) due to mutations in the rpoB gene.

Prevalence of Nocardia species among HIV-positive patients with suspected tuberculosis.

The objective of the study was to determine the frequency of nocardiosis in HIV-positive and HIV-negative individuals clinically suspected of having tuberculosis (TB). The study population (n = 171) were those who attended chest hospitals in Khartoum State, Sudan, between January and March 2010. The patients suffered from pulmonary infections with positive acid-fast bacilli. Blood (n = 171) and sputum (n = 171) samples were collected simultaneously. Blood samples were tested serologically for the presence of antibodies using HIV/Intensified Combination Prevention (ICP) test and sputum were cultured onto Lowenstein Jensen slants according to standard methods. Isolates showing rapid growth characteristic of Nocardiae were subcultured and subsequently identified using glucose yeast extract agar medium. All candidates in the study population (n = 171) suffered from pulmonary infections, nocardiosis was diagnosed in 4% (n = 7), HIV-positive cases were 17 (9.9%). Five Nocardia species were isolated from HIV-negative patients whereas two were from HIV-positive patients. Nocardia spp. cause pulmonary infections (4.09%) in both immunocompetent (2.92%) as well as immunocompromised (1.17%) patients who attend chest clinics in Sudan.