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. szulgairevealed 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.

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.

Nine strains isolated from mycetoma patients and received as Streptomyces somaliensis were the subject of a polyphasic taxonomic study. The organisms shared chemical markers consistent with their classification in the genus Streptomyces and formed two distinct monophyletic subclades in the Streptomyces 16S rRNA gene tree. The first subclade contained four organisms, including the type strain of S. somaliensis, and the second clade the remaining five strains which had almost identical 16S rRNA sequences. Members of the two subclades were sharply separated using DNA:DNA relatedness and phenotypic data which also showed that the subclade 1 strains formed an heterogeneous group. In contrast, the subclade 2 strains were assigned to a single genomic species and had identical phenotypic profiles. It is evident from these data that the subclade 2 strains should be recognised as a new species of Streptomyces. The name proposed for this new species is Streptomyces sudanensis sp. nov. The type strain is SD 504(T) (DSM = 41923(T) = NRRL B-24575(T)).

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.

Two hundred and fifty-two representatives of the genera Cuvynebacteuium, Gorduna, Mycobactevium, Nocardia, Rkoducuccus and Tsukamurella were degraded by alkaline hydrolysis and their mycolic acids extracted as methyl esters following phase-transfer-catalysed esterification. When the mycolic acid methyl esters were treated with a mixture of acetonitrile and toluene all mycobacterial mycolates formed copious white precipitates whereas all but 5 out of the 106 non-mycobacterial mycolates remained in solution. The precipitated methyl mycolates and the dried soluble mycolates were compared by pyrolysis gas chromatography and silica gel thin-layer chromatography. O n pyrolysis, the precipitated methyl mycolates from mycobacteria yielded fatty acid methyl esters with 20 to 26 carbon atoms whereas those from the remaining taxa produced shorter-chain esters. Mycobacteria and Tsukamurella paurometabolu gave multispot mycolic acid patterns on thin-layer chromatography of their methyl esters whereas those from the remaining strains gave single spots. Our results indicate that Rhodococcus chlouophanolicus strains contain mycolic acids typical of mycabacteria, It can be concluded that the mycolic acid precipitation test provides a simple and reliable way of distinguishing mycobacteria from all other prokaryotes, notably from other mycolic-acid-containing taxa.

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.

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.

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.