Microsporum gypseum Infection Among Two Related Families With a Zoonotic Aspect: A Prospective Case Series

Background and purpose The Microsporum gypseum complex is a globally distributed group of geophilic dermatophytes that primarily affect animals but can also rarely cause dermatomycoses in humans. With some regional and occupational variations, tinea corporis is the most prevalent presentation of the infection. The aim of this study was to report on the diagnosis and treatment of dermatophytosis cases among related families, and their pets, from southern Saudi Arabia. Up-to-date information on dermatophytes and dermatophytosis is needed. Methods This is a prospective case series undertaken at the Dermatology Outpatient Clinic of King Khalid University, Saudi Arabia. Six patients with suspected dermatophytosis were received at our hospital in 2022 and have been followed for recovery with or without scars. Characteristics of fungal pathogens were examined phenotypically on the basis of microscopic and growth characteristics, and laboratory data were used to initiate treatment with oral fluconazole, topical terbinafine cream, or oral itraconazole. Results Clinical features and culture results confirmed tinea capitis and tinea corporis caused by M. gypseum, which was also present in a pet cat. Tinea capitis cases (n = 4) did not respond to fluconazole and terbinafine treatment, but treatment with itraconazole resulted in a full recovery. Tinea corporis cases (n = 2) were treated with terbinafine, which resulted in a full recovery within four weeks, with no signs of scarring. Conclusions M. gypseum presents with serious persistent lesions and is extremely contagious. Treatment is durable but challenging, and breaking the transmission chain is more difficult.

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.

Knowledge, Attitudes, and Practices Regarding Brucellosis among Parents in Aseer Region, Southwestern Saudi Arabia

This study aimed to investigate the knowledge, attitudes, and practices regarding brucellosis among parents in the Aseer region of southwestern Saudi Arabia in order to estimate the population sectors that are at high risk for accidental exposure to brucellosis. This was a cross-sectional survey conducted in 2018, including 311 participants representing various genders, ages, and levels of education. Bivariate analysis showed a significant association of good awareness of the disease with the male gender and higher education levels. Of the 311 participants, 90.0% had good knowledge, whereas 10.0% showed inadequate knowledge about brucellosis. Practices and attitudes regarding brucellosis were satisfactory as participants did not eat meat from their own animals (52.7%), did not practice slaughtering (71.4%), did not participate in the birth of animals (91.3%), were not exposed to abortion in animals (93.2%), and practiced burial of aborted animal fetuses (59.2%). The practice regarding brucellosis was unsatisfactory as 66.6% never wore gloves when dealing with animals. The study concluded that the majority of parents showed fair and positive knowledge, attitudes, and practices regarding brucellosis and found that gender and education were determinants of satisfactory awareness.

Susceptibility of hospital-acquired uropathogens to first-line antimicrobial agents at a tertiary health-care hospital, Saudi Arabia

Context

Management of urinary tract infections (UTIs) is caused by antibiotic resistance uropathogens.

Aim

This study aimed to determine the important uropathogens and their resistance to first-line urinary tract antimicrobial agents.

Settings and Design

The region of Aseer, Southern Saudi Arabia, between 2013 and 2016.

Materials and Methods

A total of 1506 isolates were recovered from the urine samples of patients that were identified and tested against nine first-line UTI antimicrobial agents. Laboratory analysis was done as per the standard methods. Confirmation of bacterial identity and antimicrobial susceptibility assay was achieved by the VITEK 2 automated system.

Statistical Analysis Used

Statistical Package for the Social Sciences software version 21.0 was used for the statistical analysis.

Results

The dominant uropathogens were Escherichia coli (E. coli) 507 (33.7%); Klebsiella pneumoniae (K. pneumoniae), 229 (15.21%); Pseudomonas aeruginosa, 153 (10.2%); Acinetobacter baumannii, 80 (5.3%); Enterococcus faecalis, 71 (4.7%); and Proteus mirabilis, 61 (4.1%). Of all culture-positive uropathogens, 51.5% were resistant to the 39 agents, whereas 48.5% were sensitive (P = 0.7969). Regarding the susceptibility to the first-line agent, the most effective against the dominant (in vitro) agents against E. coli were fosfomycin and nitrofurantoin (93.5%) and (85.4%), respectively. Whereas those worked well against K. pneumoniae were cefoxitin (57.1).

Conclusions

The present study recommends the use of fosfomycin, cefoxitin, nitrofurantoin, and amoxicillin/clavulanate as the first choice UTIs treatment given their relatively high in vitro activity against major uropathogens. Knowledge of the bacterial species and their antimicrobial sensitivity patterns are always necessary to serve as a base for selecting the empirical treatment of UTIs as resistance rates vary geographically and with time.

Increased mRNA expression of key cytokines among suspected cases of Pneumocystis jirovecii infection

Background

Pneumocystis pneumonia (PCP) is a fatal infectious disease caused by Pneumocystis jirovecii (PJP). The major factor relevant to morbidity and mortality seems to be the host inflammatory reaction. The objective of this study was to evaluate the role of IL-2, IL-4, IL-10, and IL-13 cytokine mRNA expression among suspected P. jirovecii infection.

Methods

This was a cross-sectional analytical study undertaken in Aseer region, Saudi Arabia. One hundred suspected PCP cases and 100 healthy controls were included in the study. Basic clinical manifestations, radiological findings, microbiological and immunological findings were extracted from the hospital records from January 2019 to August 2019, Pneumocystis detection was done by immune-fluorescent staining (IFAT, Gomorimethanamine silver staining (GMSS), Giemsa staining, Toluidine blue O (TBO), and Pneumocystis RT-PCR.

Results

Increased more than 5 fold, 3 fold, 4 fold, and 7 fold of IL-2, IL-4, IL-10, and IL-13 mRNA expression were observed in PCP cases compared to controls. Higher expression of IL-2 mRNA was connected with crept, wheezing and chest X-ray findings like central perihilar infiltrate, patchy infiltrate, consolidation, hilar lymphadenopathy, pneumothorax, pleural effusion which showed higher expression compared to counterpart (p< 0.0001). Higher expression of IL-4 mRNA was found to be significantly associated with weight loss (p=0.002), dyspnea (p=0.003), crept (p=0.01), and chest X-ray findings (p< 0.0001). Significantly increased expression of IL-10 mRNA was observed to be associated with weight loss, dyspnea, night sweats, wheezing, and different findings of chest X-ray compared to their counterparts, whereas, IL-13 mRNA was observed in cases with fever. Suspected cases of PCP confirmed positive by IFTA with higher IL-2, IL-4, and IL-10 mRNA expression compared to negative cases. RT-PCR confirmed PCP cases had significantly higher expression of IL-2, IL-4, and IL-10 as well as IL-13 mRNA compared to negative cases. Positive detected cases by GMSS showed higher IL-2, IL-10 mRNA expression, while Giemsa showed only higher IL-4 mRNA expression compared to negative cases.

Conclusion

Confirmed cases of P. jirovecii showed higher IL-2, IL-4, IL-10, and IL-13 mRNA expression comparatively to negative cases. Increased expression of cytokines may be indicative of infection severity and could help in patients’ management.

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.

Rising Klebsiella pneumoniae Infections and Its Expanding Drug Resistance in the Intensive Care Unit of a Tertiary Healthcare Hospital, Saudi Arabia

Nosocomial infections caused by Klebsiella pneumoniae and other Gram-negative organisms have emerged as a significant health problem especially in intensive care units (ICU). This study aims to examine K. pneumoniae infections in the ICU of Aseer Central Hospital and to determine their antimicrobial susceptibility and their relationship to patients' clinical outcomes. This is a retrospective observational study done in a tertiary care center in the Aseer region in Saudi Arabia. The study spanned from January 2018 to December 2019. Demographic, microbiologic, and patient outcomes were collected from 276 patients with various infections. Identification of isolates and in vitro susceptibility to 32 antimicrobial agents were done by the Vitek 2 automated system (bioMérieux, Marcy-l'Étoile, France). Prevalence of K. pneumoniae bacteria, their susceptibility to antimicrobials, and effect on clinical outcome were studied. Two hundred seventy-six K. pneumoniae were recovered from ICU patients with various infections. K. pneumoniae isolates (n=276) were collected mainly from the respiratory tract (61%) and K. pneumoniae represented 39% of the major causal agents of ICU infections, followed by Acinetobacter spp. (30%), Pseudomonas aeruginosa (10.0%), Escherichia coli (7%), and others (14%). The mortality among the 276 ICU patients was 33.3%; K. pneumoniae was connected to 42% of the cases and 67% of the total deaths were between 50 and 90 years of age. K. pneumoniae demonstrated high sensitivity and hence can be recommended for in vivo treatment for tigecycline (81%), cefazolin (77.2%), colistin (64.9%), and to a lesser extent norfloxacin (60%) and imipenem (55.5%). High resistance was detected for ampicillin (100%), extended-spectrum β-lactamases-sulbactam (ESBL-SCM) (100%), piperacillin (100%), and ceftazidime (92.5%). Resistance to carbapenems was elevated in ertapenem (65.2%) and meropenem (61.7%). The increase of K. pneumoniae represents a threat to ICU patients, although K. pneumoniae infections were results rather than the causes, as it was connected to almost half of the ICU mortalities. Tigecycline alone or in combination with colistin on high-dose regimens could be a more effective therapy for treating carbapenem-resistant K. pneumoniae infections.

A multimodality approach to decreasing ICU infections by hydrogen peroxide, silver cations, and compartmentalization

PURPOSE

Hospital-acquired infections in the Intensive Care Unit (ICU) account for an increase in morbidity and mortality leading to serious health complications. This study aims to determine the effect of a multimodality approach including disinfection and physical separation on the infections prevailing in ICU.

METHODS

The study employed prospective cross-over analysis to assess the 738 individuals (560 males and 178 females) at the ICU, Aseer Central Hospital, Saudi Arabia. The intervention programs were carried out for 3 years (2013-2015). It included the application of hydrogen peroxide and silver cations, physical separation, and compartmentalization of ICU. Acinetobacter spp., E. coli, and staphylococci were isolated, identified, and used to evaluate the efficacy of the intervention program.

RESULTS

The results provide endotracheal tube as the main specimen type (34.7%) followed by blood (29.1%), tracheal secretion (7.7%), wound (6%), urine (5.7%), throat swab (5.4%), sputum (3.7%), and other specimens (7.7%). It also showed the infection rate decreased from 14.3% to 4% in the last three months after continuous interventions (R² = 0.44). There was a decrease in the occurrence of bacteria after an intervention (p = 0.036).

CONCLUSION

The outcome of the study revealed that mist and separation measures offered a significant decrease in infections at the ICU as per the measurement of the most hazardous nosocomial pathogens.

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.

Basidiobolus haptosporus-like fungus as a causal agent of gastrointestinal basidiobolomycosis

Basidiobolus species were isolated from colonic biopsy samples of patients with gastrointestinal basidiobolomycosis (GIB) in southern Saudi Arabia. Isolated fungi were initially identified using classical mycological tools and confirmed by sequence analysis of the large subunit ribosomal RNA gene. Phenotypic tests revealed zygomycete-like fungi which conform to those of Basidiobolus species. Five sequenced strains formed a monophyletic clade in the 28S ribosomal RNA gene phylogenetic tree. They shared 99.97% similarity with B. haptosporus and 99.97% with B. haptosporus var. minor, and relatively lower similarity with B. ranarum (99.925%). The study suggests a new and a serious causal agent of GIB related to Basidiobolus haptosporus. These isolates are not related to B. ranarum, which is commonly linked to this disease.

Sero-prevalence and risk factors of brucellosis among suspected febrile patients attending a referral hospital in southern Saudi Arabia (2014-2018)

BACKGROUND

Human brucellosis is an infectious zoonotic disease caused by Brucella spp. It is one of the most public health problems that remains largely neglected in developing counties, including Saudi Arabia. Brucellosis is particularly prevalent among rural people who have constant contact with livestock.

METHODS

A cross-sectional sero-epidemiological study conducted in Aseer Central Hospital, South Saudi Arabia, between 2014 and 2018 among 7567 patients. Serum samples were analyzed for Brucella antibodies using slide agglutination test. Serology results and patient's demographic data were analyzed by GraphPad Prism. Results were presented as mean ± SEM and differences between two groups were assessed by t-test and p < 0.05 was considered significant.

RESULTS

The prevalence of brucellosis among the admitted suspected 7567 cases was 12.8% (10.4-15.7%; CI 95%). The highest prevalence rate was detected during 2015, the rate decreased to the lowest level during the last three years (p < 0.05). Higher rate of brucellosis was observed among males than females (p < 0.05) and most cases were reported during summer season (p < 0.05). The highest prevalence rate was observed in age group 21-40 year old (40.5%) followed by 41-60 years (27.7%). The lowest prevalence rate was noticed in old and young children (15 and 3%, respectively). Cross-transmission of brucellosis was seen within family (1%) and high titers (> 1280) was noticed in 22% of the hospitalized patients. The major symptoms were fatigue, hyperhidrosis, fever and joint pain.

CONCLUSION

Our findings showed a high prevalence of human brucellosis among suspected patients in Aseer region. This indicates that clinical suspicion is a valid criterion and the endemic nature of the disease. The disease status requires early laboratory detection and confirmation to start prompt treatment to decrease patients suffering.

Fungal peritonitis caused by Pichia kudriavzevii following sleeve gastrectomy

A 23-year-old female, who had undergone a sleeve gastrectomy two weeks earlier, presented with abdominal complaints. A CT scan showed portal vein thrombosis, bowel ischemia, and intra-abdominal sepsis. Anastomosis and antibiotic therapy were not successful, and the patient went into multi-organ failure and died. Multiple cultures revealed a yeast fungus confirmed as Pichia kudriavzevii using rRNA gene sequencing. We report the first case of peritonitis in association with P kudriavzevii. In addition to the abdominal complications and surgical interventions, the yeast was found to have significantly contributed to the patient's death. SIMILAR CASES PUBLISHED: None. CONFLICT OF INTEREST: None.

Trend analysis of bacterial uropathogens and their susceptibility pattern: A 4-year (2013-2016) study from Aseer region, Saudi Arabia

Purpose:

To analyze the prevalence and resistance rates of bacterial agents causing urinary tract infections (UTIs) in Aseer, Saudi Arabia (2013–2016).

Patients and Methods:

This was a 4-year (2013–2016) retrospective study undertaken in Aseer Central Hospital, Saudi Arabia. A total of 49,779 urine and other UT specimens obtained from patients suspected of having a UTI were analyzed. Urine specimens were inoculated onto cystine lactose electrolyte deficient agar following standard procedures. Cultures showing significant bacteriuria were subjected to identification and sensitivity testing using VITEK 2 system. Data of patients and uropathogens were assembled, checked, and analyzed using SPSS software.

Results:

Culture positive samples were 49,779 (59.9% males, 40.1% females; P = 0.000). Year trend showed significant variations (P = 0.000) and the forecast trend line hypothesized a clear rise. Age groups 70–79 years were the most vulnerable group (22.3%). Gram-negative bacilli were 91.8% and the major species were Escherichia coli - 39.7%, Klebsiella pneumoniae - 15.8%; Pseudomonas aeruginosa - 13.8%, Proteus mirabilis - 10.6%, and Acinetobacter baumannii - 5%. Antimicrobials with high sensitivity rate were linezolid (99.1%), daptomycin (89.3%), vancomycin (86.7%), teicoplanin (85.5%), ertapenem (85.1%), fosfomycin (82.1%), and tigecycline (80.2%). High resistant rates to uropathogens were encountered with cephalothin (89.8%), nalidixic acid (86.7%), and ampicillin (81.9%).

Conclusions:

The majority of uropathogens were resistant to antibiotics commonly used in clinical practice. Linezolid, daptomycin, and vancomycin showed the lowest resistance to all uropathogens; this can be revised for empirical treatment of UTIs. Continuous surveillance of uropathogens and their susceptibility is important.

Fungal keratitis caused by a rare ocular pathogen, Gjaerumia minor: A case report

Fungal keratitis is an important infection of the eye that may cause devastating effects. Keratitis caused by fungi has been described in many parts of the world mainly in tropical countries. The objective of this study is to report a serious eye infection in an adult with a known history of diabetes caused by an uncommon yeast fungus with details of clinical findings and laboratory investigations. Left eye visual acuity was no perception of light due to end stage neovascular glaucoma. The patient was pseudophakic in both eyes. Culture of a corneal scraping showed yeast like organism on Sabouraud dextrose agar. Gjaerumia minor, a rare yeast but with history of a pulmonary infection in the region, was confirmed with 98% similarity in the large subunit ribosomal RNA gene (accession KY690175). Topical Amphotericin B and oral fluconazole were initiated. The patient showed gradual improvement, epithelial defect healed, infiltration steadily regressed and hypopyon disappeared. We report the first case of fungal keratitis caused by G. minor in Saudi Arabia. Fungal Keratitis should be considered in cases where clinical response to the conventional antibacterial antibiotic treatment is not optimal.

Multidrug resistance Acinetobacter species at the intensive care unit, Aseer Central Hospital, Saudi Arabia: A one year analysis

OBJECTIVE

To identify and to determine the antimicrobial susceptibility of Acinetobacter baumannii (A. baumannii) clinical isolates from ICU at Aseer Central Hospital.

METHODS

The study was conducted in the Intensive Care Unit, Aseer Central Hospital, Saudi Arabia over 13 months period (2014-2015). Acinetobacter species (n = 105) were isolated from various clinical samples. Isolates were identified using selected phenotypic criteria and confirmed using the Vitek 2 automated system. This system was used to determine the susceptibilities of 21 antimicrobial agents. Patients, isolates and drug data were analyzed using the SPSS statistical software package to determine some epidemiological and microbiological patterns.

RESULTS

Of the 105 stains, A. baumannii accounted for 49 (46.67%), A. baumannii complex, 19 (18.09%), A. baumannii/haemolyticus 32 (30.47), Acinetobacter haemolyticus 4 (3.81%), Acinetobater lwoffii 1 (0.95%) and unidentified Acinetobater species 2 (1.3%). Of the 105 Acinetobacter strains, 103 (98.1%) were found multidrug resistant (MDR). A. baumannii strain were 100% sensitive to colistin and 74.5% to trimethoprim + sulfamethoxazole. The remaining 19 antimicrobial agents revealed low or no sensitivities: amikacin 16.3%; ampicillin 7.7%; ceftazidime, 7.3%. Distribution of similar sensitivities was shown by other Acinetobacter species. Mean number of isolates from males and females indicates no statistical variation (P = 0.867) whereas age groups showed significant differences (P = 0.008) as it is clear from the high percentage of infected individuals more than 60 years followed by those aged 20-29 years old (19.05%). Upper respiratory tract (30.48%), lower respiratory tract (47.65%) and subcutaneous tissue (9.5%) were the main sources of Acinetobacter spp. but mean numbers of isolates from these specimens indicate no discrepancy between specimens (P = 0.731).

CONCLUSIONS

Acinetobacter species including A. baumannii were found MDR (98.1%) according to the current Acinetobacter spp. antimicrobial categorization. Approximately half of these strains were A. baumannii. All Acinetobacter species were 100% sensitive to colistin and to some extent to trimethoprim + sulfamethoxazole (74.5%). ICU-acquired pneumonia among patients over 60 years of age who spend prolong times at artificial ventilations made up the majority of the cases.

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.

Severe pneumonia with a massive pleural effusion in a child caused by Tilletiopsis minor: the first case from Saudi Arabia

Tilletiopsis minor, a blastoconidia-forming yeast, was isolated from a 4-year-old boy suffering from severe pneumonia. Chest x-rays revealed the progression of widespread and multiple nodular lesions, nonsymmetrical interstitial and airspace infiltrates, and consolidations. Creamy yellow, irregular, wrinkled yeast-like organisms were isolated from the pleural fluid specimens when cultured on Sabouraud dextrose agar for 5 days and incubated at 30°C. Microscopically, the organisms showed broad, irregular filaments with blastoconidia but no budding cells. Manual bench tests and automated phenotypic analyses failed to recognize the organism. This unique and rare organism (AB7-11; DSM 29469) was identified using the sequence analysis of the internal transcribed spacer region of the nuclear ribosomal DNA. It showed a precise alignment with the type strains of T minor. Subsequent to this diagnosis, and the earlier nonre.sponse to vancomycin and meropenem, the patient was put on liposomal amphotericin. However, the condition continued to deteriorate, and then, intravenous voriconazole was added to control the infection. Finally, the patient's condition improved, and he was discharged in good condition after 1 month of stay in the hospital.

Chronic rhinofacial basidiobolomycosis caused by Basidiobolus ranarum: Report of a case from Aseer Region, Kingdom of Saudi Arabia

We present a case of fungal sinusitis caused by Basidiobolus ranarum in a 22-year-old male patient with chronic rhinosinusitis in Aseer region, Kingdom of Saudi Arabia. The patient was admitted with nasal obstruction accompanied by itching, sneezing, rhinorrhea, epistaxis and recurrent headache. Axial computed tomography (CT) scan of the paranasal sinuses showed a clear left facial swelling chronic inflammation and granulomata. Basidiobolus ranarum fungus was isolated on Sabouraud dextrose agar from a biopsy specimen. The organism was characterized by flat, yellowish-grey, glabrous, becoming radially folded fungus that under the microscope showed broad vegetative hyaline hyphae that bear zygospores with protuberances. The patient made good recovery and was discharged home with no recurrences after receiving oral itraconazole and removal of the polyps surgically.

Is there is an association between the presence of Staphylococcus species and occurrence of vernal keratoconjunctivitis?

Purpose

The aim of this study was to identify the association of normal bacterial flora with vernal keratoconjunctivitis (VKC) occurrence in VKC and non-VKC groups.

Methods

Conjunctival specimens were collected from 18 VKC patients and 22 healthy controls, cultured and identified following standard methods. The association between the presence of bacteria and occurrence of VKC was analyzed using Chi square statistic.

Results

Comparable bacterial growth was observed in VKC (77.8%) as well as control group (77.2%) (p = 0.970). Analysis of individual bacterial revealed that Staphylococcus aureus was detected more frequently in VKC (27.78% vs. 4.55% in control, p = 0.041) and Staphylococcus epidermidis was found much more commonly in the control eyes (45.45% in control vs. 5.56% in VKC, p = 0.005).

Conclusions

An aggravating role of S. aureus colonization in the occurrence of VKC, and a possible role of S. epidermidis against the occurrence of VKC were concluded.

Comparison of phenotypic characteristics and antimicrobial resistance patterns of clinical Escherichia coli collected from two unrelated geographical areas

Background:

Antimicrobial resistance among pathogenic Escherichia coli is an increasing problem especially in developing countries.

Aims:

To compare between resistance patterns of E. coli collected from two unrelated geographical areas.

Methods:

A descriptive comparative study was conducted between May 2010 and August 2011. E. coli (n= 402) collected from hospitals in Khartoum state, Sudan and in Aseer region, Saudi Arabia were studied. Identification and antimicrobial susceptibility testing of isolates were performed following standard methods. Multi-drug resistance (MDR) was defined as non-susceptibility to ≥ three antimicrobials.

Results:

Of the 402 E. coli isolates studied, MDR patterns were significantly higher among isolates from Sudan than Saudi Arabia [92.2% (214/232) vs. 70.6% (120/170)] (p = 0.000). The resistance rates of E. coli isolates were recorded as follows (Sudan and Saudi Arabia): High to moderate resistance to amoxicillin (97.7% and 94.2%), trimethoprim-sulfamethoxazole (88.3% and 82.5%), tetracycline (77.1% and 74.2%), amoxicillin- clavulanic acid (51.4% and 70%), ceftriaxone (64% and 52.4%) and ciprofloxacin (58.4% and 40%). Low resistance was to ceftazidime (35% and 20%), gentamicin (35% and 17.5%) and nitrofurantoin (22.4% and 11.7%). Resistance to amikacin was uncommon (1.9% and 5%). Significant differences (p < 0.05) in resistance rates of isolates between both countries in term to patient’s gender and age. The most frequent MDR phenotypes among isolates were to 7(15.9%) in Khartoum state and to 3(20.8%) in Aseer region.

Conclusions:

Variation and emerging of antimicrobial resistance among pathogenic E. coli isolates was observed in both regions. Continuous monitoring of resistance profiles, locally and international surveillance programs are required.

Current Perspectives on Mycobacterium farcinogenes and Mycobacterium senegalense, the Causal Agents of Bovine Farcy

Mycobacterium farcinogenes and M. senegalense are the causal agents of bovine farcy, a chronic, progressive disease of the skin and lymphatics of zebu cattle. The disease, which is prevalent mainly in sub-Saharan Africa, was in earlier times thought to be caused by Nocardia farcinica and can be described as one of the neglected diseases in cattle. Some aspects of the disease have been investigated during the last five decades but the major development had been in the bacteriological, chemotaxonomic, and phylogenetic aspects. Molecular analyses confirmed that M. farcinogenes and M. senegalense fall in a subclade together with M. houstonense and M. fortuitum. This subclade is closely related to the one accommodating M. peregrinum, M. porcinum, M. septicum, M. neworleansense, and M. alvei. DNA probes were designed from 16S-23S rRNA internal transcribed spacer and could be used for the rapid diagnosis of bovine farcy. An ELISA assay has been evaluated for the serodiagnosis of the disease. The zoonotic potentials of M. farcinogenes and M. senegalense are unknown; few studies reported the isolation of M. senegalense and M. farcinogenes from human clinical sources but not from environmental sources or from other domestic or wild animals.

Vaginal infections among pregnant women at Omdurman Maternity Hospital in Khartoum, Sudan

Introduction: Microbial infections of the vagina in pregnant women are health problems that lead to serious medical complications and consequences. This study aimed to investigate and determine antimicrobial susceptibilities of the causative agents of vaginal infections in pregnant women. Methodology: A cross-sectional study of pregnant women (n = 200) was conducted between August and December 2008 at Omdurman Maternity Hospital, Khartoum, Sudan. Vaginal and cervical swabs were obtained from each subject and processed for isolation and identification of pathogenic microorganisms using standard methods of wet mount preparation, direct Gram smear, Nugent scoring system, direct immunofluorescence, and cultural techniques. Antimicrobial susceptibility testing of bacterial isolates was performed using standard procedures. Statistical analysis was done using SPSS program version 12.0.1. A p value < 0.05 was considered statistically significant. Results: Of the 200 pregnant women enrolled, BV was detected in 49.8%, followed by Chlamydia trachomatis (31.3%) and Candida albicans (16.6%), with low frequencies of Neisseria gonorrhoeae (1.8%) and Trichomonas vaginalis (0.5%). Higher infection rates were recorded among subjects in the third trimester (71.6%) than in the second trimester of gestation (28.4%). No significant association (p = 0.7) between history of abortions and C. trachomatis infections was found. Gentamicin was the most active agent against Gram-positive and Gram-negative bacteria. Clarythromycin was the most active against Mycoplasma species. Conclusions: Pregnant women with vaginal complaints revealed various positive microbiology results. Such cases may require specific medication. Routine culture of vaginal and cervical samples should be performed on all pregnant women during prenatal visits.

Candida and other yeasts of clinical importance in Aseer region, southern Saudi Arabia. Presentation of isolates from the routine laboratory setting

OBJECTIVES

To isolate, identify, and determine the prevalence of Candida and other yeasts of clinical importance in Aseer region, Saudi Arabia.

METHODS

This is a cross-sectional study involving retrospective analysis of 6100 samples submitted to the Microbiology Laboratory, Aseer Central Hospital, Abha, Saudi Arabia between 2011 and 2012, and prospective isolation and identification of 84 isolates recovered from various clinical specimens presented to the Microbiology Laboratory between 2012 and 2013 using the classic morphological schemes and the Vitek 2 automated system.

RESULTS

The results of the retrospective analysis (2011-2012) indicated that of the 6100 various clinical specimens submitted to the routine microbiology analysis, 143 (2.35%) revealed the presence of Candida spp. The distribution of the 143 Candida spp according to specimens was as follows: urine 72%, sputum 10.5%, endotracheal tube 7%, blood 4.2%, catheter tip 2.1%, throat swab 2.1%, eye swab 0.7%, wound exudates 0.7%, and cerebrospinal fluid 0.7%. The results of the prospective study (2012-2013), which involved the identification of yeast recovered from 84 specimens indicated that Candida albicans 28.6% was the predominant species, followed by Candida parapsilosis 21.4%, Candida tropicalis 14.3%, and Candida lusitaniae 9.5%.

CONCLUSIONS

Along with the commonly encountered Candida albicans, Candida parapsilosis, Candida tropicalis, and Candida lusitaniae were detected with significant rates. Many other Candida species and some other pathogenic yeasts have been detected for the first time in the region. Urinary tract samples were the main source of Candida species.

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.

Isolation of a rare Nocardia wallacei from an HIV-positive patient with pulmonary infection in Southern Saudi Arabia

This study aimed to clarify the taxonomic position of an actinomycete isolated from an HIV-positive male patient with pulmonary complications in Asir, southern region of Saudi Arabia. The strain was found to have phenotypic properties typical of nocardiae and 16S rRNA gene analysis clustered the isolate with Nocardia wallacei (accession KC677696) in the phylogenetic branch of the amikacin resistance Nocardia transvalensis complex. We consider that nocardiosis is usually missed or misdiagnosed clinically and recognition of these bacteria based on phenotypic tests is strenuous, but definitive identification is attainable by molecular methods.

Prevalence of Extended-spectrum β-Lactamases-producing Escherichia coli from Hospitals in Khartoum State, Sudan

OBJECTIVE

This study aimed to determine the prevalence and assess antimicrobial susceptibility of extended- spectrum β-lactamase-producing Escherichia coli isolated from clinical specimens of patients at hospitals in Khartoum State, Sudan.

METHODS

During April to August 2011, a total of 232 E. coli isolates were collected from various clinical specimens of patients. Isolates were identified, tested for antimicrobial susceptibility and screened for ESBL production as per standard methods. The double-disk diffusion method was used to confirm ESBL production using antimicrobial disks of ceftazidime (30 μg), cefotaxime (30 μg), with or without clavulanic acid (10 μg). A zone difference of >5 mm between disks was considered indicative of ESBL production.

RESULTS

Out of 232 E. coli isolates, 70 (30.2%) were found to be positive for ESBL by the applied phenotypic methods. ESBL-producing isolates yielded high resistance rates for trimethoprim-sulfamethoxazole (98.6%), tetracycline (88.6%), nalidixic acid (81.4%) and ciprofloxacin (81.4%). The highest antimicrobial activities of ESBL-producing isolates were observed for amikacin (95.7%), followed by tobramicin (74.3%) and nitrofurantoin (68.6%). Resistance to quinolones, aminoglycosides, trimethoprim-sulfamethoxazole, tetracycline, nitrofurantoin and chloramphenicol was higher in ESBL than non-ESBL isolates (p<0.05). The frequency of ESBL-producing isolates varied among hospitals (18.2% to 45.1%), although a high prevalence was recorded as 45.1% at Khartoum Teaching Hospital. Wound specimens were the most common source of ESBL-producing isolates. The proportion of ESBL-producing E. coli did not differ significantly between adults and children (31% vs. 27%).

CONCLUSION

The prevalence of ESBL-producing E. coli detected in this study is of great concern, which requires sound infection control measures including antimicrobial management and detection of ESBL-producing isolates.

Distribution of Class I integrons and their effect on the prevalence of multi-drug resistant Escherichia coli clinical isolates from Sudan

OBJECTIVE

To analyze integrons gene cassettes Class I among Escherichia coli (E. coli) isolates from Sudan and to determine their effect on the prevalence of resistance to antimicrobials.

METHODS

This cross-sectional study was conducted at 6 hospitals in Khartoum State, Sudan between April and August 2011. Escherichia coli (n=133) isolated from clinical specimens of patients were included. Isolates were identified and tested for antimicrobial susceptibility following standard procedures. Multi-drug resistance (MDR) patterns was defined as non-susceptibility to &#8805;3 antimicrobials. Class I integrons was detected by polymerase chain reaction, and gene cassettes were characterized via sequencing analysis.

RESULTS

Of the 133 E. coli isolates, 40.6% (n=54) harbored Class I integrons. All the 54 integron carriage, E. coli was found to be MDR strains. Integron carriage isolates confer higher levels of resistance than any other isolates (p<0.05) such as amoxicillin-clavulanic acid (66.7% versus 36.7%), ceftazidime (46.3% versus 17.7%), chloramphenicol (29.6% versus 7.6%), ciprofloxacin (70.4% versus 43%), tetracycline (88.9% versus 57%) and trimethoprim-sulfamethoxazole (98.1% versus 69.6%). Sequencing of gene cassettes harbored mostly dihydrofolate reductase (dfrA), which encodes resistance to trimethoprim and aminoglycoside adenyltransferase (aadA) that encodes resistance to streptomycin. The most frequent combination types were dfrA17 and aadA5 genes.

CONCLUSION

Class I integrons were quite common and its carriage contributed significantly to the emergence of MDR among E. coli. Nevertheless, factors leading to the wide spread of integrons are still to be determined.

Prevalence of Bacterial Pathogens in Aseer Region, Kingdom of Saudi Arabia: Emphasis on Antimicrobial Susceptibility of Staphylococcus aureus

OBJECTIVES

This short study aims to determine the prevalence of various bacterial pathogens causing infections in the Aseer regions, and to also assess the distribution of Staphylococcus aureus in relation to different body sites as well as their in vitro antimicrobial susceptibility profile.

METHODS

Clinical specimens (n=9831) from various infections diagnosed at Aseer Central Hospital (ACH) and Abha General Hospital (AGH), were analyzed bacteriologically. Confirmed S. aureus isolates (n=210) were tested against 44 antibacterial agents as per standard methods.

RESULTS

Bacterial pathogens were recovered from 24.9% of the samples. The results revealed that Escherichia coli, Klebsiella pneumoniae, Enterococcus spp. and S. aureus to be the main etiological agents, while purulent exudates of wounds and abscesses were the main source of S. aureus. Out of the 210 S. aureus isolates; 77 (38.5%) were recovered from purulent exudates of wounds and abscesses of the examined patients and 53 (26.5%) were from high vaginal discharges, while other body sites exhibited different rates of S. aureus. On the other hand, 45% of the 210 S. aureus isolates were found to be multidrug resistant S. aureus (MRSA).

CONCLUSION

The results from this study revealed that Escherichia coli and staphylococci were the main etiological agents, while purulent exudates of wounds and abscesses were the main source of S. aureus. Also, a higher rate of MRSA was detected.

Increased multi-drug resistant Escherichia coli from hospitals in Khartoum state, Sudan

BACKGROUND

Multidrug-resistant Escherichia coli (MDR E. coli) has become a major public health concern in Sudan and many countries, causing failure in treatment with consequent huge health burden.

OBJECTIVES

To determine the prevalence and susceptibility of MDR E. coli isolated from patients in hospitals at Khartoum State.

METHODS

Between May to August 2011, E. coli (n = 232) isolated from clinical specimens, identified, tested their antimicrobials susceptibility and screened for extend spectrum â-lactamase production as per standard methods.

RESULTS

Of the 232 E. coli isolates, the majority were from urine (65.1%). MDR E. coli were present in 214 (92.2%). Of these, the resistance rates were recorded to: amoxicillin 97.7%, cefuroxime 92.5%, trimethoprim-sulfamethoxazole 88.3%, tetracycline 77.1%, nalidixic acid 72%, ceftriaxone 64%, ciprofloxacin 58.4%, ofloxacin 55.1%, amoxicillin-clavulanate 50.4%, ceftazidime, gentamicin 35% each, nitrofurantoin 22.4%, chloramphenicol, tobramicin 18.2% each and amikacin 1.9%. Overall MDR E. coli, 53.3% were resistant to > 7 antimicrobial agents and ESBL was detected in 32.7%. Isolates from males were more resistant than those from females (p < 0.05).

CONCLUSIONS

Drug-resistance surveillance and epidemiological analysis of patient data is need periodically and can be informative for appropriate management of antimicrobial resistance.

Comparison of conventional and non-conventional techniques for the diagnosis of bovine brucellosis in Sudan

The objective of the present study was to detect brucellosis in suspected dairy cattle in Khartoum State, Sudan using the conventional serological tests and tests done on milk in comparison to a PCR-based technique. Milk and blood samples collected simultaneously from suspected brucellosis cows (n = 147) in 12 different dairy farms around Khartoum State were used in the study. Overall, 54 (36.7%) of the total milk samples were positive according to the milk ring test (MRT), while 29 (19.7%) of the serum samples were positive according to the Rose Bengal test (RBT); microscopy on modified Ziehl-Neelsen-stained slides detected 13.6% of the cases, and recovery of Brucella species on both Brucella medium and tryptic soya agar was 7.5%. Thirty-three (22.4%) samples were found positive on PCR-amplified IS711 which were then taken as positive brucellosis cases. The differences of RBT and PCR-IS711 from MRT were highly significant (P < 0.05). MRT detected more cases of bovine brucellosis compared to RBT, PCR, microscopy, and culture. MRT is recommended as a noninvasive test compared to RBT, and it is less expensive compared to PCR and culture.

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.

Variable antibiotic susceptibility patterns among Streptomyces species causing actinomycetoma in man and animals

BACKGROUND

Drug therapy is recommended in conjunction with surgery in treatment of actinomycetoma. The specific prescription depends on the type of bacteria (actinomycetoma) or fungi (eumycetoma) causing the disease and their in vitro antimicrobial susceptibility.

OBJECTIVES

To investigate the antimicrobial susceptibility among isolates of Streptomyces spp. isolated from cases of actinomycetoma in man and animals in Sudan.

METHODS

Streptomyces strains (n = 18) isolated from cases of actinomycetoma were tested in vitro against 15 commonly prescribed antibacterial agents using MIC agar dilution method as per standard guidelines.

RESULTS

Streptomyces strains isolated from actinomycetoma fall into various phenotypic groups. All of the strains were inhibited by novobiocin (8 μg/mL), gentamycin (8, 32 μg/mL) and doxycycline (32 μg/mL). Fusidic acid (64 μg/mL) inhibited 94.4% of the strains; bacitracin, streptomycin, cephaloridine, clindamycin, ampicillin, rifampicin and tetracycline (64 μg/mL) inhibited between 61.1 and 77.8% of the strains. All strains were found resistant to amphotericin B (64 μg/mL), penicillin (20 μg/mL) and sulphamethoxazole (64 μg/mL).

CONCLUSIONS

Saprophytic Streptomyces spp. cause actinomycetoma in man and animal belong to separate phenotypes and have a wide range of susceptibility patterns to antimicrobial agents, which pose a lot of difficulties in selecting effective in vivo treatment for actinomycetoma.

The treatment of bovine dermatophilosis and its effect on some haematological and blood chemical parameters

In this study, the authors evaluated parenteral treatment of zebu cattle, with naturally and experimentally induced bovine dermatophilosis, in western Sudan, using four different antibiotic treatments. In terms of recovery rate, weight gain, avoiding relapse and preventing death, gentamycin was found to be the most effective treatment, followed by a combination of penicillin and streptomycin and, finally, long-acting oxytetracycline. However, enrofloxacin was not successful. A significant improvement in the red blood cell count was noticed among cattle treated with penicillin-streptomycin (p = 0.021) and gentamycin (p = 0.029). All treated cattle, except those treated with enrofloxacin, showed a significant improvement in mean corpuscular haemoglobin concentration (p = 0.021); mean corpuscular volume (p = 0.021), and white blood cell count (p < 0.021). Significant improvements were observed among treated cattle in their total levels of protein, calcium (p = 0.021) and cholesterol (p < 0.05), when compared to untreated cattle infected with Dermatophilus congolensis. This study recommends gentamycin as a drug of choice for the parenteral treatment of dermatophilosis. Treatment was not only effective in early, mild cases but also useful among moderately and heavily affected cattle. According to the observations of the authors, when no intervention took place, the condition of moderately and heavily affected cattle deteriorated and/or resulted in death.

Comparative assays of the rpoB gene for identification of Mycobacterium tuberculosis isolated from patients in Sudan

OBJECTIVES

To characterise mycobacterial clinical isolates based on amplification of the rpoB gene.

SETTING

One hundred and thirty-five mycobacterial isolates cultured from suspected pulmonary tuberculosis (TB) patients were identified phenotypically. Molecular characterisation of the isolates was performed based on amplification of the rpoB gene, using duplex polymerase chain reaction (DPCR), PCR-restriction fragment length polymorphism (RFLP) and nested PCR-based sequence analysis techniques.

RESULTS

The DPCR assay identified 129 of 135 (95.5%) clinical isolates as Mycobacterium tuberculosis complex species. Restriction enzyme analysis of the rpoB PCR product using Hind II identified 134 of the 135 (99.3%) isolates as M. tuberculosis complex, while nested PCR sequence analysis of the rpoB gene identified 133/133 examined isolates (100%) as M. tuberculosis species. No mycobacteria other than M. tuberculosis (MOTT) were detected among the studied isolates.

CONCLUSION

DPCR, PCR/RFLP Hind II and nested PCR sequence analysis of the rpoB gene techniques showed comparable efficiency in the characterisation of Mycobacterium isolates. Nested PCR sequence analysis of the rpoB gene was superior to PCR/RFLP for characterisation of suspected M. tuberculosis isolates, while the DPCR technique showed less sensitivity. As PCR-RFLP requires less sophisticated laboratory facilities than nested PCR sequence analysis, it would be more appropriate to be adopted for accurate characterisation of mycobacteria in countries with a weak infrastructure.

Unusual manifestation of a concurrent demodectic and sarcoptic mange in a Zebu-Friesian cross-bred heifer

We describe a rare case of a concurrent demodectic and sarcoptic mange in a 2-year-old heifer in Khartoum, Sudan. The lesions were massive lumps of granulomatous tumour-like dermatitis with thick, nodular folds mainly covering the head, neck and shoulders. Histopathological examination of the lesions revealed the presence of both Demodex bovis and Sarcoptes scabiei. The animal died regardless of the anti-parasitic treatment it received.

Evaluation of a PCR-amplified IS6110 insertion element in the rapid diagnosis of pulmonary tuberculosis in comparison to microscopic methods in Sudan

OBJECTIVE

The aim of this study was to evaluate the sensitivity and specificity of a polymerase chain reaction (PCR)-based method (IS6110 insertion site) in the diagnosis of pulmonary tuberculosis in sputum samples in comparison to smears by using culture on Loewenstein-Jensen medium as a standard.

METHODS

The study was conducted during the period 1999 through to 2000, at Khartoum Teaching Hospital, Sudan, on 200 sputum samples. The samples were collected from patients suspected of having pulmonary tuberculosis, were examined using a PCR amplified IS6110 insertion element in comparison to Ziehl-Neelsen stained smears in terms of sensitivity and specificity. Culture on Loewenstein-Jensen medium was used as the standard to control the 2 tests.

RESULTS

Microscope sensitivity was found to be 65.4% and the specificity was 90.5%, whereas sensitivity of the IS6110 was 88.5% and specificity was 98.6%.

CONCLUSION

The study concluded that though IS6110 sensitivity was 13.1% higher than smear method, it provided a significant improvement in specificity for the diagnosis of pulmonary tuberculosis. Improvement is still needed to increase the sensitivity of the IS6110 methods by decreasing the number of the false negative samples before its use can be at routine levels.

Nocardia farcinica - a significant cause of mastitis in goats in Sudan : short communication

Fifteen of 100 mastitic milk samples from goats suffering from mastitis were tentatively identified as members of the genus Nocardia on the basis of selected phenotypic and chemotaxonomic characteristics. Six of the 15 strains were confirmed as Nocardia farcinica by 16S rDNA gene sequencing and subsequent aligning with relevant actinomycetes found in electronic databases and 2 by other identification criteria. N. farcinica is a serious cause of mastitis with a significant prevalence (15%) among the examined goats. Efforts are needed to optimise and simplify isolation and identification methods.

Identification of acid fast bacteria from caseous lesions in cattle in Sudan

One-hundred-and-twenty caseous lesions collected from slaughtered cattle at selected slaughterhouses in Sudan were processed for the detection of acid-fast bacteria (AFB). Sixty-four of the 120 samples showed AFB on microscopic examination after staining with the Ziehl-Neelsen method. Accordingly, it was estimated that 64 (53.3%) of the 120 caseous (purulent) lesions among the samples were due to AFB whereas 56 (46.7%) were due to other causes. Growth on Lowenstein-Jensen slants was obtained in 54 of the 120 samples. The isolated AFB were tentatively identified using microscopic and cultural characteristics. Confirmation of the phenotypic clusters was achieved by analysing the mycolic acids contents and PCR-amplification of the IS6110 insertion sequences. The above two methods have allowed the identification of Mycobacterium bovis and M. farcinogenes, the major AFB isolated from cattle in Sudan. The remaining AFB, which were negative for the above two tests, were further identified by sequencing the 16S rRNA gene. The above strategy thus allowed the identification of the isolated strains as follows: 25 (46%) M. bovis; 21 (39.9%) M. farcinogenes; 4 (7.4%) M. tuberculosis; 1 (1.9%) M. avium; 1 (1.9%) Nocardia sp., 2 (3.7%) unidentified AFB. The isolation of M. farcinogenes and M. tuberculosis, from pulmonary lymph nodes represented important findings.

Streptomyces sp., a cause of fistulous withers in donkeys

Four of 10 donkeys, which showed lesions simulating fistulous withers, were examined clinically with the aim to cultivate and identify the causal agent. Aspiated purulent materials were subjected to bacteriological examination. The causal organisms were recovered in Tryptic Soya agar medium when incubated aerobically at 37 degrees C for up to 5 days. These organisms were found to be actinomycetes-like, Gam positive with stable branching filaments and to form heavy aerial hyphae on colony surface. The isolated organisms ere tentatively identified as Streptomyces sp. on the basis of morphological and cultural characteristics. The initial sequences analysis of the 16S rDNA gene conformed that one of the isolates (SD551) falls within the phylogenetic clade, which encompasses the genus Streptomyces. Studies are underway to further describe the disease and its causal agent. The report represents a good evidence to incriminate Streptomyces in the aetiology of the fistulous withers.

Molecular analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with persistent disease in the Khartoum region of Sudan

SETTING

Patients with positive smears for acid-fast bacilli were enrolled at tuberculosis (TB) clinics in the Khartoum region of Sudan.

OBJECTIVE

To identify the presence of drug resistant genotypes in M. tuberculosis isolates which are difficult to treat.

METHODS

Genus specific PCR-SSCP was performed to confirm the presence of M. tuberculosis in clinical isolates. Genotypic drug resistance testing was performed by mutation analysis and spoligotyping was used to monitor transmission and to identify epidemic strains.

RESULTS

Fifty (48%) of the original 105 samples were classified as M. tuberculosis. Four (4%) of the samples were typed as mycobacteria other than TB, while the remaining (n =50) samples were refractory to further molecular analysis. The fifty amplifiable M. tuberculosis samples were used for subsequent mutation analysis and typing. Mutations were identified in the genes conferring resistance to INH (kat G, 12%), RIF (rpoB, 8%), SM (r psL and rrs, 30%) and EMB (embB, 4%). Two of the samples (4%) had mutations in genes associated to both INH and RIF and can be classified as MDR-TB. Thirty-three percent (13/39) of the persistant tuberculosis cases (5/18 treatment failure; 5/14 relapse; 3/7 defaulter) had mutations accounting for drug resistance. A total of 27 different spoligotypes were identified from 49/50 samples. Twenty-nine (59%) of the isolates were grouped into one of seven clusters, while 20 (41%) showed unique patterns. One patient was infected with M. bovis.

CONCLUSION

This is the first molecular approach to characterize clinical isolates of M. tuberculosis from Sudan. The results show that drug resistance is indeed a serious problem and it may compliment the efforts of the National Tuberculosis Programme to improve strategies to control this disease.

Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense strains based on 16S-23S ribosomal DNA internal transcribed spacer sequences

16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA sequence analyses were performed on Mycobacterium farcinogenes and M. senegalense strains and 26 strains of other rapidly growing mycobacteria to investigate the phylogenetic structure of bovine farcy mycobacteria within the M. fortuitum complex. M. farcinogenes and M. senegalense were indistinguishable in their 5"-end 16S rDNA but showed both considerable interspecies spacer sequence divergence and a high level of intraspecies sequence stability. A rapid detection assay using PCR and hybridization with species-specific probes was developed. The assay was specific among 46 species other than M. farcinogenes and M. senegalense and correctly identified all M. farcinogenes and M. senegalense strains. PCR- and 16S-23S rDNA sequence-based detection will be a valuable approach for diagnosis of the causal agents of African bovine farcy in cattle.

Nocardia africana sp. nov., a new pathogen isolated from patients with pulmonary infections

Eight actinomycete strains, isolated from 8 out of 400 sputum samples examined, taken from patients with pulmonary diseases at the Chest Unit of Khartoum Teaching Hospital in the Sudan, were provisionally assigned to the genus Nocardia according to morphological criteria. These isolates were studied further in order to establish their taxonomic status. They were found to have morphological and chemical properties typical of nocardiae and formed a monophyletic clade in the 16S ribosomal DNA tree together with Nocardia vaccinii. The strains showed a unique pattern of phenotypic properties that distinguished them from representatives of recognized Nocardia species, including Nocardia vaccinii. The strains were considered to merit species status and were designated Nocardia africana sp. nov. The findings of the present study are consistent with the view that pulmonary nocardiosis may occur in a substantial proportion of patients who exhibit chronic lung diseases in African countries. It is important, therefore, that clinicians in such countries consider this condition, especially when patients with respiratory infections fail to respond to antitubercular therapy.

Serotaxonomic analysis of glycolipids from Mycobacterium chelonae-M. fortuitum complex and bovine farcy strains

The antigenicity and cross-reactivity of glycolipids from strains of bovine farcy and the Mycobacterium chelonae-M. fortuitum complex were analyzed using the ELISA technique. Purified alkali-stable glycopeptidolipids (GPLs) with a characteristic dimethylrhamnosyl sugar unit extracted from M. abscessus, M. chelonae, M. peregrinum and M. senegalense, gave very strong reactions with sera against members of the same four species. Particularly strong cross-reactions were evident between M. peregrinum and M. senegalense. These GPLs reacted more weakly with antisera against the other mycobacteria tested, though clear reactions were noticed with M. farcinogenes and M. fortuitum and also with M. bovis BCG, M. phlei, and M. tuberculosis strains. Alkali-labile diacyl trehalose (DAT) and triacyl trehalose (TAT) from M. fortuitum reacted with homologous sera, and with that against M. tuberculosis. Traces of uncharacterized acyl trehaloses isolated from two strains of M. farcinogenes gave comparatively weak reactions. Mycobacteria labeled M. farcinogenes and M. senegalense produced glucosylated trehalose-based glycolipids (GTs) and the studies showed that the major type was antigenic. These glycolipids cross-reacted strongly with M. senegalense NCTC 4524 but not with the type strain of M. senegalense. On the basis of the chemical patterns and the antigenicity of the GPLs it is evident that M. peregrinum and M. senegalense are particularly closely related and these species show a very close affinity to M. abscessus-M. chelonae.

Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences

Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii, M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai, M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgai revealed ITS sequence similarities of 93 and 88%, respectively. M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.