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.