Effect of sputum quality and role of Xpert® MTB/ RIF assay for detection of smear-negative pulmonary tuberculosis in same-day diagnosis strategy in Addis Ababa, Ethiopia

Background

There is limited information on the performance of the Xpert® MTB/RIF test for diagnosis of smear-negative pulmonary tuberculosis (SNPT) and rifampicin resistance (RR) in the same-day diagnosis approach. The effects of sputum quality and other factors affecting the Xpert performance are also under-investigated.

Objective

This study aimed to determine the performance of the Xpert® MTB/RIF test for detection of SNPT and RR in the same-day diagnosis strategy and the effect of sputum quality and other factors on its performance.

Methods

A cross-sectional study was conducted from August 2017 to January 2018 across 16 health facilities in Addis Ababa, Ethiopia. Two spot sputum samples were collected from 418 presumptive SNPT patients, tested with Xpert® MTB/RIF, then compared to tuberculosis culture. Additionally, culture isolates were tested for RR by BACTEC MGIT™ 960 drug susceptibility testing (DST) and MTBDRplus version 2.

Results

The Xpert® MTB/RIF test detected 24 (5.7%) SNPT cases, with a sensitivity of 92.3% (75.9% - 97.9%) and specificity of 99.2% (97.8% - 99.7%) compared with tuberculosis culture. Xpert® MTB/RIF also detected three (11.58%) RR strains with 100.0% concordance with BACTEC MGIT™ 960 DST and MTBDRplus results. Three blood-stained SNPT samples were positive by Xpert (30.0%), which was 6.9 times higher compared to salivary sputum (odds ratio: 6.9, 95% confidence interval: 1.36-34.96, p = 0.020).

Conclusion

The performance of the Xpert® MTB/RIF to detect SNPT and RR in same-day diagnosis is high. However, SNPT positivity varies among sputum qualities, and good sample collection is necessary for better test performance.

A High Level of Antimicrobial Resistance in Gram-Positive Cocci Isolates from Different Clinical Samples Among Patients Referred to Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia

Background

Gram-positive cocci are clinically important pathogens that cause infections and their development of antibiotic resistance continues to pose a severe threat to public health. Therefore, this study aims to investigate the level of antimicrobial resistance among Gram-positive cocci isolated from different clinical samples among patients referred to Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia.

Methods

From January to April 2018, a cross-sectional study was conducted at Arsho Advanced Medical Laboratory. Seven hundred ninety-two (792) different clinical samples were obtained from 792 individuals and inoculated into blood culture bottles and Blood Agar base. Bacterial identification was done using the number, type, and morphology of colonies, as well as Gram staining, catalase testing, and coagulase test after isolation of pure growth on culture media using the standard operating procedure. VITEK 2 compact system was used for bacterial identification and drug susceptibility testing. The information entry and analysis were performed by using SPSS version 20.

Results

Out of 792 clinical samples cultured, the prevalence of Gram-positive cocci was 12.6% (n=100/792). The most frequent one is S. aureus 54% (n=54/100) followed by coagulase-negative Staphylococcus species 42% (n=42/100), S. agalactiae 1% (n=1/100) and E. faecalis 3% (n=3/100). Penicillin showed the highest resistance rate 85% (n=85/100), followed by sulfamethoxazole/trimethoprim (47%), and oxacillin (38%); however, highest sensitivity was seen towards linezolid 97% (n=97/100) and vancomycin 94% (n=94/100). The total multi-drug resistance (MDR) Gram-positive cocci were 44% (n=44/100).

Conclusion

This study demonstrated high antimicrobial resistance and multi-drug resistance. This suggests that the importance of continuous monitoring of antimicrobial resistance patterns is crucial for selecting the suitable drug for treatment and infection prevention.

High Trichophyton violaceum-Induced Tinea Capitis with Isolation of Many Non-Dermatophyte Molds in Scalp Scrapings in Patients Referred to a Dermatology Clinic in Addis Ababa, Ethiopia

Objective

This work aimed to determine the magnitude of tinea capitis, the diversity and species composition of fungi, and the predominant dermatophytes implicated in causing tinea capitis.

Methods

A prospective, cross-sectional study was conducted at a dermatology clinic. Scalp scrapings were collected and cultured, and dermatophyte and non-dermatophyte molds were identified.

Results

Of 364 scalp scrapings, fungi were recovered from 301 (82.7%) clinical samples. About 60.7% of the samples were collected from women, while 39.3% were collected from male study subjects. The association between the magnitude of scalp ringworm and gender was not statistically significant (P = 0.105). Two hundred eighty study subjects were less than 15 years of age, of which 254 were culture positive. The association of tinea capitis and the age of patients was statistically significant (P = 0). Three hundred forty-nine fungal isolates were isolated, of which 54.2% were dermatophytes, while 45.8% were non-dermatophyte molds. The occurrence of dermatophytes in their decreasing order was T. violaceum (138; 73%), Trichophyton mentagrophytes (18; 9.5%), Trichophyton tonsurans (16; 8.5%), Trichophyton verrucosum (8; 4.5%), Microsporum audouinii (7; 3.7%), Trichophyton schoenleinii (1; 0.5%), and Trichophyton soudanense (1; 0.5%).

Conclusion

A high prevalence rate of T. violaceum-induced tinea capitis was reported. The magnitude of scalp ringworm in adults was remarkably high. Therefore, conducting a nationwide epidemiological survey on tinea capitis regardless of age is suggested. The isolation of many non-dermatophyte molds in the current study may shade questions about the perception that tinea capitis is caused by dermatophytes only. Therefore, studies on their potential pathogenic role on skin and skin-related (nail and the scalp) infections appear to be an active field of research.

Non-Dermatophyte Mold Dominated Onychomycosis in Patients Attending a Rank Higher Specialized Dermatology Clinic in Addis Ababa, Ethiopia

Background

Onychomycosis is a common refractory fungal infection associated with significant morbidity. The objective of this study was to determine the prevalence of onychomycosis, and the diversity and species composition of fungal etiological agents.

Materials and Methods

A clinic-based, prospective, non-randomized cross-sectional study was carried out between October 2018 and June 2019 at Rank Higher Specialized Dermatology Clinic, Addis Ababa, Ethiopia. Nail scrapings were collected aseptically from 200 patients clinically identified with nail disorders of fungal origin by dermatologists. Fungal etiological agents were identified microscopically and by culture method following standard procedures.

Results

Among 200 nail scrapings, 161 (80.5%) samples were found out to be culture positive. Of these, 135 (83.9%) samples yielded single colonies while 26 (16.1%) mixed colonies gave a total of 190 isolates. Among the isolates, 25.8% were dermatophytes while 61.1% were non- dermatophytes molds, and 13.1% were yeasts. Females were more likely to present dystrophic nails than men. Patients in the middle age group were more affected. Trichophyton interdigitale, Aspergillus spp, and Candida albicans were the dominant species.

Conclusion

The prevalence rate of onychomycosis in the present study was high. The isolation rate of non-dermatophyte molds was higher than dermatophytes and yeasts. Trichophyton interdigitale, Aspergillus spp, and Candida albicans were the dominant etiological agents. Females and patients in the middle age group were more affected. An increase in the prevalence of non-dermatophyte molds in nail infections dictates further investigation demonstrating how this group of fungi causes onychomycosis.

Bacterial and Fungal Profile, Antibiotic Susceptibility Patterns of Bacterial Pathogens and Associated Risk Factors of Urinary Tract Infection Among Symptomatic Pediatrics Patients Attending St. Paul’s Hospital Millennium Medical College: A Cross-Sectional Study

Background

Urinary tract infection is a common infection in pediatrics. Understanding the common etiology of urinary tract infections, their antimicrobial susceptibility pattern, and associated risk factors in a particular setting can provide evidence for the appropriate treatment of the cases.

Purpose

The current study is aimed to determine the common etiology and prevalence of uropathogens associated with urinary tract infection, as well as the antibiotic susceptibility profile of bacterial isolates, and to identify risk factors associated with urinary tract infection among pediatric patients.

Materials and Methods

The study was conducted at St. Paul Hospital Millennium Medical College between October 2019 and July 2020. Urine was collected aseptically from patients, inoculated onto culture media, and incubated at 37 °C for 18–48 hours. Bacteria and yeast were identified following standard procedures. Antibiotic susceptibility testing of bacterial pathogens was carried out by the Kirby Bauer disc diffusion method. Descriptive statistics and logistical regressions were used to estimate the crude ratio with a 95% confidence interval. P-value < 0.05 was considered significant.

Results

Significant bacterial/fungal growth was observed in 65 samples giving a prevalence of 28.6% of which 75.4% (49/65) and 24.6% (16/65) were bacterial and fungal pathogens, respectively. About 79.6% of bacterial etiology were Escherichia coli and Klebsiella pneumoniae. The highest resistance was observed against ampicillin (100%), cefazolin (92.1%), and trimethoprim-sulfamethoxazole (84.1%), both of which are commonly used for empirical treatment in Ethiopia. Length of hospital stay (P=0.01) and catheterization (P=0.04) were statistically associated with urinary tract infection.

Conclusion

The high prevalence of urinary tract infection was observed in our study. Enterobacteriaceae were the major cause of urinary tract infection. Length of hospital stay and catheterization were significantly associated with urinary tract infection. Both Gram-negative and Gram-positive bacteria were extremely resistant to ampicillin and trimethoprim-sulfamethoxazole.

Catheter-associated urinary tract infections in adult intensive care units at a selected tertiary hospital, Addis Ababa, Ethiopia

Background

Catheter-associated urinary tract infection is the leading cause of hospital-acquired infections. They remain the second most common healthcare-associated infection in critically sick patients.

Objective

To determine the prevalence of catheter-associated urinary tract infection, the spectrum of etiological agents, antibiotic sensitivity profile of bacterial pathogens among adult patients admitted to intensive care units.

Materials and methods

Patients admitted to the intensive care unit of hospitals in Addis Ababa who were on urethral indwelling catheters for >48 hours from October 2020 to September 2021 were included in the study. Urine specimens were aseptically collected and processed as per standard protocols. Microorganisms were isolated, identified, and subjected to antibiotic susceptibility testing.

Results

In all 220 pateints included in the study development of significant bacteriuria/candiduria was not affected by sex, age, and prior antibiotic therapy. However, the length of stay in the intensive care unit was significantly associated with bacteriuria /candiduria (P-value < 0.001). The overall prevalence of bacteriuria/candiduria was 51.4% among which 21.0%, 19.1%, and 11.4% were bacteriuria, candiduria, and polymicrobial infections, respectively. About 138 organisms were recovered of which 79 (57.25%) were bacteria and 59 (42.75%) were yeast isolates. Acinetobacter species, Pseudomonas species, Klebsiella species E. coli, and Enterococcus species were the dominant bacterial isolates. Candida. albicans, Candida. krusei and Candida. tropicalis were the commonest yeasts. Many gram-negative bacterial isolates were resistant to ceftriaxone 36(94.7%), ampicillin 21(91.3%) followed by cefotaxime34(89.5%), amikacin (16.0%), nitrofurantoin (17.4%), meropenem (20.0%) and imipenem (20.0%). Out of 79 bacterial pathogens, 52(65.8%) were multiple antibiotic resistant of which 37(71.0%) were Gram-negative bacteria and 15(29%%) were Gram-positive bacteria. About 13(86.7%) isolates of Acinetobacter, all isolates of Klebsiella species (100%) and E. coli (100%) were multiple antibiotic-resistant. Out Of 18,10(55.56%), isolates of Enterococcus were multiple antibiotic-resistant.

Conclusions

A very high prevalence of bacteriuria/ candiduria was demonstrated in this study. This warrants the establishment of multidimensional infection control approach on catheter associated urinary tract infection in ICU. In addition to high prevalence of candiduria, recovery of non-albicans candida species almost in equal proportion with candida albicans in the present study was an important finding as non-albicans candida species distinct to C. albicans are intrinsically resistant to the commonly used azole antifungal drugs in Ethiopia. The prevalence of rate MDR bacteria in our ICU particularly of E. coli, Klebsiella spp, Pseudomonas and Acetobacter spp was very high. In order to combat this problem, proper antibiotic policies should be formulated.

Phenotypic characterization of carbapenem non-susceptible gram-negative bacilli isolated from clinical specimens

Background

Multidrug resistant, extremely drug-resistant, pan-drug resistant, carbapenem-resistant, and carbapenemase-producing gram-negative bacteria are becoming more common in health care settings and are posing a growing threat to public health.

Objective

The study was aimed to detect and phenotypically characterize carbapenem no- susceptible gram-negative bacilli at the Ethiopian Public Health Institute.

Materials and methods

A prospective cross-sectional study was conducted from June 30, 2019, to May 30, 2020, at the national reference laboratory of the Ethiopian Public Health Institute. Clinical samples were collected, inoculated, and incubated for each sample in accordance with standard protocol. Antimicrobial susceptibility testing was conducted using Kirby-Bauer disk diffusion method. Identification was done using the traditional biochemical method. Multidrug-resistant and extensively drug-resistant isolates were classified using a standardized definition established by the European Centre for Disease Prevention and Control and the United States Centers for Disease Prevention and Control. Gram-negative organisms with reduced susceptibility to carbapenem antibiotics were considered candidate carbapenemase producers and subjected to modified carbapenem inactivation and simplified carbapenem inactivation methods. Meropenem with EDTA was used to differentiate metallo-β-lactamase (MBL) from serine carbapenemase. Meropenem (MRP)/meropenem + phenylboronic acid (MBO) were used to differentiate Klebsiella pneumoniae carbapenemase (KPC) from other serine carbapenemase producing gram-negative organisms.

Results

A total of 1,337 clinical specimens were analyzed, of which 429 gram-negative bacterial isolates were recovered. Out of 429 isolates, 319, 74, and 36 were Enterobacterales, Acinetobacter species, and Pseudomonas aeruginosa respectively. In our study, the prevalence of multidrug-resistant, extensively drug-resistant, carbapenemase-producing, and carbapenem nonsusceptible gram-negative bacilli were 45.2%, 7.7%, 5.4%, and 15.4% respectively. Out of 429 isolates, 66 demonstrated reduced susceptibility to the antibiotics meropenem and imipenem. These isolates were tested for carbapenemase production of which 34.8% (23/66) were carbapenemase producers. Out of 23 carbapenemase positive gram-negative bacteria, ten (10) and thirteen (13) were metallo-beta-lactamase and serine carbapenemase respectively. Three of 13 serine carbapenemase positive organisms were Klebsiella pneumoniae carbapenemase.

Conclusion

This study revealed an alarming level of antimicrobial resistance (AMR), with a high prevalence of multidrug-resistant (MDR) and extremely drug-resistant, carbapenemase-producing gram-negative bacteria, particularly among intensive care unit patients at the health facility level. These findings point to a scenario in which clinical management of infected patients becomes increasingly difficult and necessitates the use of “last-resort” antimicrobials likely exacerbating the magnitude of the global AMR crisis. This mandates robust AMR monitoring and an infection prevention and control program.

Bacterial and fungal profile, drug resistance pattern and associated factors of isolates recovered from blood samples of patients referred to Ethiopian Public Health Institute: cross-sectional study

Background

Blood stream infections are serious infections that usually induce prolongation of hospital stay, morbidity and mortality in several countries including Ethiopia. The aim of this study was to determine bacterial and fungal profile, their drug resistance patterns, and risk factors associated with blood stream infections.

Methods

A cross sectional study design was conducted from February 23 to June 23, 2020 at Ethiopian public health. A structured questionnaire was used to collect data on socio-demographic factors and clinical conditions. Blood specimens were analyzed using standard microbiological techniques. Antimicrobial susceptibility tests were performed using Kirby–Bauer disc diffusion technique and Vitek compact 2. Simple and multiple logistic regressions were used to assess the potential risk factors.

Results

A total of 175 pathogens isolated from 346 blood specimens. Of these, 60% Gram-negative bacteria, 30.86% Gram-positive bacteria and 9.14% fungal isolates were identified. Burkholderia cepacia and Coagulase negative staphylococcus were the predominant pathogen among Gram-negative and Gram-positive bacteria respectively. Among fungus, Candida krusei (56.25%) was the most predominant isolate. The highest proportions of antibacterial resistance were observed among 3rd generation cephalosporin and penicillin. Most fungal isolates expressed resistance to fluconazole. Sex (P = 0.007), age (P < 0.001) and use of invasive medical devices (P = 0.003) were identified as risk factors for bacterial blood stream infections.

Conclusion

The study showed high prevalence of blood stream infection was due to B. cepacia and non-C. albicans spp. This finding alarming ongoing investigation of blood stream infection is important for recognizing future potential preventive strategies including environmental hygiene and management of comorbid medical diseases to reduce the problem.

Profiling of potential pulmonary fungal pathogens and the prevalence of the association between pulmonary tuberculosis and potential fungal pathogens in presumptive tuberculosis patients referred to Saint Peter's Specialized Tuberculosis Referral Hospital, Addis Ababa, Ethiopia

Objective

The burden of pulmonary fungal infection is increasing and often misdiagnosed as pulmonary tuberculosis in developing countries where the prevalence of pulmonary tuberculosis is high. |Therefore, the purpose of this study is to determine the spectrum of potential pulmonary fungal pathogens and the prevalence of the association between pulmonary tuberculosis and potential fungal pathogens.

Materials and methods

A cross-sectional study was conducted between October 2018 and May 2019. Sputum was collected from 636 study participants. Part of the sputum was inoculated onto Brain Heart Infusion agar, and fungi were identified following standard microbiological procedures. The remaining part of the sample was used for the investigation of pulmonary tuberculosis.

Results

Among 636 sputum samples, 75.9% (483) and 25.6% (163) were positive for potential fungal pathogens and pulmonary tuberculosis, respectively. The prevalence of the association between pulmonary tuberculosis and potential fungal pathogens was 20.0%. Of fungal isolates, 81.4% were yeasts. The remaining 128 (18.6%) isolates were molds. The isolation rate of fungi was higher in males (51.6%) than in females (48.4%). There was no statistically significant association between the prevalence of potential pulmonary fungal pathogens and sex (p = 0.239). Patients in the age group of 35 to 44 and above were slightly more affected than younger age groups. The association between potential fungal pathogens and age was not statistically significant (p = 0.50).

Conclusion

High prevalence of potential pulmonary fungal pathogens and the association of tuberculosis and potential fungal pathogens recorded in this study will enforce health personnel to pay due attention to these conditions and arise the interest of researchers to conduct further work on the burden of the association between tuberculosis and potential fungal pathogens. Our study also revealed the need to employ conventional microbiology tests along with clinical and radiological evidence since clinical manifestations and radiological pictures of tuberculosis mimic that of pulmonary fungal infection.

Evaluation of antibacterial and acute oral toxicity of Impatiens tinctoria A. Rich root extracts

The high prevalence of morbidity and mortality from bacterial infections, together with the growing threat of antibacterial resistance, necessitated the development of alternative new drugs from traditional medicine. In Ethiopia, Impatiens tinctoria A. Rich has been traditionally used for the treatment of fungal infections such as ringworms that cause tinea pedis and it have also different medical values. Scientific information on its biological activity against a broad range of bacteria and safety data is scant, compared to its folklore data. In this study, we evaluated antibacterial activities and acute oral toxicity of aqueous, ethanol and ethyl acetate root extracts of Impatiens tinctoria A. Rich. Aqueous, ethanol and ethyl acetate extracts of the plant were evaluated using agar hole diffusion and agar dilution methods. Biological activities of the plant extracts were expressed as a zone of inhibition diameter, minimum inhibitory concentration (mg/ml), and minimum bactericidal concentration (mg/ml). The safety studies were performed by oral acute toxicity study according to the organization of economic cooperation and development test Guidelines 420.Gram-positive bacteria were more susceptible to the extracts compared to gram-negative bacteria, especially against S. aureus and S. epidermidis, which are commonly found in the skin. Ethyl acetate extract was more potent than ethanol and aqueous extracts. The 50% lethal dose (LD50) of tested mice was above 9600 mg/kg. This study provides a scientific basis for the antibacterial activity of the root extracts of I. tinctoria A. Rich, where, the ethyl acetate extract showed the most promising activity. Therefore, the antibacterial potential and practical non-toxicity of the study plant extracts suggested the possibility of using it for the development of antimicrobial drugs by further studying the plant in different directions.

Distribution of Candida albicans and non-albicans Candida species isolated in different clinical samples and their in vitro antifungal suscetibity profile in Ethiopia

Background

The spectrum of yeasts and their antifungal susceptibility profile are poorly known and treatment of fungal disease has remained empirical. The aim of this study is to determine the spectrum and antifungal susceptibility profile of yeasts particularly of Candida species.

Methods

A descriptive study on the composition of Candida species and antifungal susceptibility profile were conducted from January 2018 to September 2018. Clinical samples collected from different sites were cultured on Sabouraud dextrose agar and incubated for an appropriate time. Identification of yeast isolates and their antifungal susceptibility profile were determined by the VITEK 2 compact system. Descriptive statistics such as frequency and percentage of Candida species were calculated using SPSS version 20.

Results

Of 209 yeasts recovered, 104(49.8%), 90 (43.1%), 15(7.2%) were C. albicans, non albicans Candida species, and other yeasts, respectively. Among non albicans Candida species, Candida krusei was the commonest isolate. Of other yeast groups, 66.7% was represented by Cryptococcus laurentii. Regardless of Candida species identified, 85.6, 3.9, and 10.5% of the isolates were susceptible, intermediate, and resistant to fluconazole, respectively. C krusei was 100% resistant to the drug. Voriconazole demonstrated the greatest antifungal activity against Candida isolates in which 99.4% of Candida isolates were susceptible. The susceptibility and the resistance rate of Candida isolate to both caspofungin and micafungin were the same being 96 and 4% respectively. However, micafungin was more potent than caspofungin. The susceptibility, resistant, and intermediate rates of yeasts against flucytosine were, 86.2, 6.6, and 7.2%, respectively.

Conclusions

The present study demonstrated the distribution of Candida species in different clinical specimens where the isolation rate of non-albicans Candida species was comparable to Candida albicans. The high resistance rate of C. krusei to fluconazole and flucytosine may demonstrate that the treatment of candidiasis empirically is questionable.

High Prevalence of Multi-Drug Resistance and Extended Spectrum Beta Lactamase Production in Non-Fermenting Gram-Negative Bacilli in Ethiopia

Background

Emergence of resistance to multiple antimicrobial agents in Non-Fermenting Gram-Negative Bacilli is a major problem to public health, as it limits drug treatment options against infections. The aim of this study was to determine the prevalence of multi-drug resistance and extended spectrum beta lactamase production in Non-Fermenting Gram-Negative Bacilli.

Materials and methods

Different clinical samples were collected and processed following standard procedures. Each sample was then inoculated onto culture media. Identification, drug susceptibility testing, and extended spectrum beta lactamase production of the isolates were carried out by using the VITEK 2 compact system.

Results

Among 996 clinical samples, 135 samples yielded Non-Fermenting Gram-Negative Bacilli of which Pseudomonas and Acinetobacter species were the commonest isolates. The overall drug resistance rates of Non-Fermenting Gram-Negative Bacilli were above 80% against ampicillin (89.6%), cefuroxime axetil (88.9%), nitrofurantoin (85.9%), cefalotin (84.4%), cefoxitin (83.7%), cefazolin (83.0%), and cefuroxime (83.0%). Tobramycin with a resistance rate of 19.3% was the most active antimicrobial agent. Out of 135 isolates, 81.5% were multi-drug resistant of which 13.3% were extensively drug resistant and 10.4% were pandrug resistant. Extended spectrum beta lactamase production was detected in 48.9% of the isolates.

Conclusions

The spectrum of bacterial species isolated was diverse. The isolates demonstrated high level of drug resistance in different classes of antibiotics. The magnitude of multi-drug resistance and the level of extended spectrum beta lactamase production were high. Hence, further studies on multi-drug resistant and extended spectrum beta lactamase producing Non-Fermenting Gram-Negative Bacilli both in the community and in hospital setting are essential.

Multidrug-resistant profile and prevalence of extended spectrum β-lactamase and carbapenemase production in fermentative Gram-negative bacilli recovered from patients and specimens referred to National Reference Laboratory, Addis Ababa, Ethiopia

Background

The emergence of multidrug-resistance (MDR), production of extended-spectrum β-lactamases, and carbapenemase in members of fermentative gram-negative bacilli are a serious threat to public health.

Objective

The aim of this study was to determine the burden of multi-drug resistance, the production of extended-spectrum β-lactamases (ESBLs), and carbapenemase in fermentative Gram-negative bacilli in Ethiopian Public Health Institute.

Materials and methods

A cross-sectional study was carried out from December 2017 to June 2018. Different clinical samples were collected, inoculated, and incubated according to standard protocols related to each sample. Bacterial identification was performed by using the VITEK^R 2 compact system using the GN^R card. Antimicrobial susceptibility testing was carried out by the Kirby-Bauer disc diffusion method. Production of ESBL and carbapenemase were confirmed by combination disc and modified Hodge Test method respectively.

Results

A total of 238 fermentative Gram-negative bacilli were recovered during the study period, among which E.coli were the predominant isolates followed by K. pneumoniae. The highest percentage of antibiotic resistance was noted against ampicillin (100%) followed by trimethoprim/sulfamethoxazole (81.9%). The isolates showed better sensitivity towards carbapenem drugs. Out of 238 isolates, 94.5% were MDR and of which 8.8% and 0.8% were extensively and pan drug resistant, respectively. Nearly 67% and 2% of isolates were producers of ESBL and carbapenemase, respectively. The isolation rates of MDR, ESBL, and carbapenemase producing stains of the isolates were ≥70% in intensive care unit while the isolation rates in other wards were ≤25%.

Conclusions

The findings of this study revealed that the burden of MDR and ESBL was high and carbapenemase producing isolates were also identified which is concerning. This situation warrants a consistent surveillance of antimicrobial resistance of fermentative Gram-negative bacilli and implementation of an efficient infection control program.

Prevalence of tuberculosis, multidrug resistant tuberculosis and associated risk factors among smear negative presumptive pulmonary tuberculosis patients in Addis Ababa, Ethiopia

Background

The diagnoses of active smear negative PTB, remains difficult. As a result, treatment is often carried out empirically relaying on clinical criteria. The distribution and magnitude of smear negative PTB, smear negative MDR-TB and associated factors in the same day diagnosis strategy are not clearly known in the study area. Therefore, this study aimed to determine the prevalence of TB, MDR-TB and associated risk factors among presumptive smear negative pulmonary tuberculosis patients in Addis Ababa, Ethiopia.

Methods

Analytic cross sectional study design was used. A total of 418 smear negative presumptive pulmonary TB patients were enrolled from selected health facilities since August 01, 2017 to January 5, 2018. Sputum samples were examined by Ziehl Neelsen microscopy, Xpert MTB/RIF assay and Culture. Drug susceptibility testing was performed by line probe assay and BACTEC MGIT 960 system. These laboratory tests were performed in Ethiopian Public Health Institute, National TB Reference Laboratory. Data was analyzed by SPSS Ver.20.

Results

From the total of 418 enrolled patients, 27 (6.5%) were Xpert MTB/ RIF and 26 (6.4%) were culture confirmed smear negative PTB patients. The positivity rate among male and female was 10.2 and 3.5% (p = 0.005) respectively. From 26 culture positive isolates 3 (11.54%) were MDR TB; from MDR-TB confirmed isolates 2/23 (8.7%) were among new and 1/3 (33.3%) was among retreatment smear negative presumptive pulmonary TB patients. All Rifampicin resistant smear negative pulmonary TB isolates by Xpert MTB/ RIF assay were found to be MDR TB and 7/26 (26.9%) isolates were INH mono resistant. History of migration found to be a potential factor for developing smear negative pulmonary TB.

Conclusion

In this study a significant proportion of smear negative pulmonary TB was diagnosed. Furthermore, a high smear negative multi drug resistant (MDR) TB and other mono drug resistant TB prevalence was confirmed. Due to the limitations of smear microscopy which is used as a primary diagnostic tool, these TB strains are missed to be diagnosed and transmission continues in the community.

Prevalence, Risk Factors, and Spectrum of Fungi in Patients with Onychomycosis in Addis Ababa, Ethiopia: A Prospective Study

BACKGROUND

Onychomycosis is a common refractory infection deleteriously affecting quality of life via social stigma and upsetting day-to-day activities.

OBJECTIVE

To study the prevalence of onychomycosis, spectrum of fungal etiological agents, and associated risk factors.

METHODS

A prospective nonrandomized study on the prevalence of onychomycosis was carried out from September 2017 to April 2018 at a dermatology center in Addis Ababa. Nail scrapings were collected from 303 patients clinically identified with nail disorders of fungal origin by dermatologists. Fungal etiological agents were identified microscopically and by culture method following standard procedures.

RESULTS

The prevalence of onychomycosis was 60.4%. Fungi neither were detected nor showed visible fungal growth in 39.6% of the cases. Females were more likely to present dystrophic nails than men. Patients in the middle age group were more affected. The isolation rates of dermatophytes, yeasts, and nondermatophyte molds were 44.7%, 33.3%, and 32.3%, respectively. Trichophyton rubrum, Scytalidium dimidiatum, and Candida albicans were the dominant species of dermatophytes, nondermatophyte molds, and yeasts, respectively. There was no statistically significant association between onychomycosis and risk factors.

CONCLUSIONS

The prevalence rate of onychomycosis in the present study was high. The isolation rate of nondermatophyte molds was comparable with that of dermatophytes. Further studies on the prevalence of onychomycosis, fungal etiological agents, and changes in species distribution of the etiological agents of nail infection in Ethiopia are important.

Dermatophytosis: Prevalence of Dermatophytes and Non-Dermatophyte Fungi from Patients Attending Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia

BACKGROUND

Dermatophytosis is a disease of major public health problem around the globe causing a considerable morbidity.

OBJECTIVE

To study the prevalence of dermatophytosis and the spectrum of fungi implicated in causing the infection.

METHODS

Nail, skin, and scalp scrapings were collected from 318 patients and were used for microscopy and culture study. Fungal pathogens were identified by studying the macroscopic and microscopic characteristics of their colonies.

RESULT

Tinea capitis was the predominant clinical manifestation consisting of 48.1% of the cases. Among 153 patients with tinea capitis, 73.2% were in the age group of 1-14 years. Of 318 study participants, 213 (67.98%) were found to be positive for dermatophytosis microbiologically. Out of 164 fungal isolates, 86 were dermatophytes and 78 were non-dermatophyte fungi. Among 86 dermatophytes, T. violaceum represented 38.4% of dermatophyte isolates and 89.7% of the isolates were recovered from tinea capitis. Of 76 non-dermatophyte molds, Aspergillus spp., Scytalidium dimidiatum, and Cladosporium spp. were the most common isolates, respectively.

CONCLUSIONS

Failure to detect or isolate fungal pathogens in a large number of clinical samples revealed the limitation of clinical diagnosis in differentiating dermatophytosis from other skin infections demonstrating that clinical diagnosis should be coupled with laboratory methods. Recovery of large number of non-dermatophyte fungi along with dermatophytes in our study showed that non-dermatophyte fungi are emerging as important causes of dermatophytosis, warranting the implementation of intensive epidemiological studies of dermatophytosis across the country.

Prevalence and Antimicrobial Susceptibility of Bacterial Uropathogens Isolated from Pediatric Patients at Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia

BACKGROUND

Urinary tract infection (UTI) is considered as the most common bacterial infection seen among the pediatric patients.

OBJECTIVE

This study was carried out in order to determine the prevalence of urinary tract infection in pediatric patients, identify bacterial uropathogens responsible for the infection, and study the antibiotic sensitivity patterns of bacterial isolates.

MATERIALS AND METHODS

A cross-sectional study designed and conducted from January to April 2014. Clean-voided midstream urine specimens were obtained from 384 pediatric patients less than or equal to 15 years in sterile universal bottles. Urine collected from each patient was inoculated onto CLED and blood agar plates using a calibrated inoculating loop with a capacity of 0.001 ml. Inoculated plates were incubated for 24-48 hours at 37°C at inverted position aerobically. Bacterial isolates were indentified and characterized by Gram stain and by using an array of standard routine biochemical tests. The antimicrobial susceptibility test was carried out by using the Kirby-Bauer disc diffusion method. Frequency distribution tables were used to describe the findings. Logistical regression was also used to estimate crude odds ratio (COR) with 95% confidence interval (CI) of positive responses to the different variables, and P values less than 0.05 were taken as statistically significant.

RESULT

In this study, a total of 384 patients (199 males and 185 females) aged less than or equal to 15 years from whom urine samples were collected were enrolled. Of these patients, 61 (15.9%) had significant bacteriuria. Of the 185 females, 36 (19.5%) came up with positive cultures, while 25 (12.6%) of the 199 males had significant bacteriuria, and the largest number of study subjects were below the age of 3 years, and the largest positive culture was obtained from this age group, accounting for 35 (57.4%.) out of 61 positive cultures. Bacterial species belonging to six genera were isolated and identified from 61 positive cultures, and the genera were Escherichia, Klebsiella, Staphylococcus, Proteus, Acinetobacter, and Enterococcus. E. coli was isolated in 28 cases (49.5 %), followed by Klebsiella spp. in 17 cases (27.9%), Staphylococcus spp. in 5 patients (8.2%.) (S. aureus in one and coagulase-negative staphylococci in 4 cases), Enterococcus in 7 cases (11.5%), Proteus spp. in 3 cases (4.9%), and Acinetobacter in one case (1.6%). Of the bacterial isolates, E. coli was found out to be the most common pathogen followed by Klebsiella spp. Furthermore, E. coli and Klebsiella spp. were the most common pathogens in female patients accounting for 71.4% and 64.7%, respectively. Regarding susceptibility tests, E. coli and Klebsiella spp. were not 100% susceptible to any of the 11 antibiotics tested. Acinetobacter spp. had 100% resistance to three antibiotics: gentamicin (GN), trimethoprim-sulfamethoxazole (SXM), and augmentin (AMP). But they were 100% susceptible to ciprofloxacin (CIP), cefuroxime (CXM), norfloxacin (NOR), and ceftazidime (CAZ). On the contrary, Proteus spp. was 100% sensitive to all drugs except to nitrofurantoin. Species of Enterococcus had resistance of 71.4% to chloramphenicol (C) and 85.7% to both SXM and erythromycin. S. aureus was 100% susceptible to almost all drugs, while coagulase-negative staphylococci were not as susceptible as S. aureus. Multidrug resistance to two or more drugs was observed in 73.7% of the bacterial isolates.

CONCLUSION

This study determined the prevalence of urinary tract infection in pediatric patients and highlighted the major bacterial uropathogens involved in UTI for the first time in the country. Furthermore, bacterial pathogen species and their frequency was consistent with the usually reported pattern, with E. coli being the most common organism isolated in cases of urinary tract infections followed by Klebsiella spp. Most of the bacterial isolates were multidrug resistant, and it is therefore suggested that appropriate antimicrobials should be administered to reduce the risk of multidrug resistant organisms developing and avert ineffectiveness of antibiotics. This condition indicates that antibiotic selection should be based on knowledge of the local prevalence of bacterial organisms and antibiotic sensitivities rather than empirical treatment. The present study indicated that ciprofloxacin (CIP), ceftazidime (CAZ), cefotaxime (CTX), cefuroxime (CXM), clindamycin (DA), and ceftriaxone (CRO) were the best antibiotics for the treatment of Gram-negative and Gram-positive bacterial uropathogens, respectively, in the study area relatively.

Vulvovaginal candidiasis: species distribution of Candida and their antifungal susceptibility pattern

BACKGROUND

Vulvovaginal candidiasis is a global issue of concern due to its association with economic costs, sexually transmitted infections, and ascending genital tract infection. The aim of this study was to determine species distribution and antifungal susceptibility pattern of Candida species causing vulvovaginal candidiasis.

METHODS

A cross sectional study was conducted from November 2015 to December 2016 at the Family Guidance Association of Ethiopia. Vaginal swabs collected from study subjects that were clinically diagnosed with vulvovaginal candidiasis were cultured. Yeast identification and antifungal susceptibility testing were determined by the automated VITEK 2 compact system. The association of vulvovaginal candidiasis with possible risk factors was assessed and analyzed using SPSS version 20.

RESULTS

The overall prevalence of vulvovaginal candidiasis was 41.4%. The association of vulvovaginal candidiasis was statistically significant with previous genital tract infection (p = 0.004), number of life-time male sex partners (p = .037), and number of male sex partners in 12 month (p = 0.001). Of 87 Candida isolates recovered, 58.6% were C. albicans while 41.4% were non-albicans Candida species. The highest overall drug resistance rate of Candida species was observed against fluconazole (17.2%), followed by flycytosine (5.7%). All Candida isolates were 100% susceptible to voriconazole, caspofungin, and micafungin. C. albicans, was 100% susceptible to all drugs tested except fluconazole and flycytosine with a resistance rate of 2% each drug. C. krusei, was 100 and 33.3% resistant to fluconazole and flycytosine, respectively.

CONCLUSIONS

High prevalence rate of vulvovaginal candidiasis and observation of high prevalence rate of non-albicans Candida species in the present study substantiate, the importance of conducting continuous epidemiological surveys to measure changes in species distribution from C. albicans to non-albicans Candida species in Ethiopia. Although, fluconazole still appeared to be active against all isolates of C. albicans and non-albicans Candida species high resistance rate of C. krusei against the drug may demonstrate a search for alternative antifungal drugs when treating vulvovaginal candidiasis caused by C. krusei.

Species distribution and antibiotic susceptibility profile of bacterial uropathogens among patients complaining urinary tract infections

BACKGROUND

Urinary tract infection is the second most common type of infection and the problem is further compounded by the emergence of drug resistance in bacterial uropathogens. The aim of this study was to determine the spectrum of bacterial uropathogens and their drug resistant pattern.

METHODS

A single institutional cross-sectional study was carried out at Arsho Advanced Medical laboratory from September 2015 to May 2016. A total of 712 urine samples were collected, inoculated onto primary isolation culture media, incubated at 37 °C for 18-24 h, and significant bacteriuria was determined. Identification and the antimicrobial susceptibility testing of bacteria were determined by using the automated VITEK 2 compact system.

RESULTS

Out of 712 urine samples processed, 256 (36%) yielded significant bacteriuria of which 208 (81.25%) were obtained from female and 48 (18.75%) from male patients. Age group of 25-44 were more affected with the infection. Of 256 bacterial isolates recovered, Escherichia coli, was the dominant bacterium. Ampicillin and trimethoprim/sulfamethoxazole were the least effective drugs while piperacillin/tazobactam was the most effective drug against Gram-negative bacteria. Erythromycin was the least effective drug while vancomycin was the most active drug against Gram-positive bacteria.

CONCLUSIONS

Observation of many bacterial species causing UTI in this study warrants, a continuous epidemiological survey of UTI in health institutions across the country. High level of drug resistance to the commonly prescribed drugs necessitates a search for other options.

Fungal keratitis in patients with corneal ulcer attending Minilik II Memorial Hospital, Addis Ababa, Ethiopia

BACKGROUND

Fungal keratitis is an important cause of corneal blindness all over the world. Although there are several reports on fungal keratitis from developing and developed countries, fungal keratitis in Ethiopia is poorly known. The aim of this study was to determine the prevalence of fungal keratitis and spectrum of fungi implicated in causing the infection.

METHODS

The present study was a single institutional cross-sectional study carried out in Minilik II Memorial Hospital eye clinic, Addis Ababa, Ethiopia from September 2014 to August 2015. Corneal scraping was obtained under aseptic condition with sterile 21 gauge needle by an ophthalmologist from patients suspected of microbial keratitis. Each scraping was inoculated onto Sabouraud Dextrose Agar in C-shaped streaks and incubated at 25 °C aerobically for four weeks. Cultures of mycelia fungi were identified by examining macroscopic and microscopic characteristics of their colonies. Yeasts were identified by employing biochemical and assimilation test procedures and using CHROMagar Candida culture. All data were coded, double entered and analyzed using SPSS version 20.

RESULT

Out of 153 cases of microbial keratitis, fungi were recovered from 69 patients giving fungal keratitis prevalence of 45.1. Patients from rural areas were significantly affected than patients in urban regions (P = 0.005). Age groups of 25-34 (P = 0.017) and 15-24 years (P = 0.008) were significantly affected. Fungal keratitis was significantly associated with farmers (P = 0.0001), daily laborers (P = 0.0001), unemployed (P = 0001) and students (P = 0.004). Fungal keratitis was statistically associated with trauma (P = 0.006), and diabetes (P = 0.024). Seventy six fungal isolates were recovered, of which molds accounted 63 (82.9 %) of the total isolates. Fusarium and Aspergillus species were the two predominant molds accounting 27.6 and 25 % of the total isolates respectively. Yeast isolates accounted only 17.1 %.

CONCLUSION

High prevalence of fungal keratitis recorded in the present study, highlights the need for nationwide study on fungal keratitis and precise identification of the causative fungi and institution of appropriate treatment strategy.

Prevalence and antimicrobial susceptibility pattern of methicillin resistant Staphylococcus aureus isolated from clinical samples at Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia

Background

Staphylococcus aureus particularly MRSA strains are one of the major causes of community and hospital acquired bacterial infections. They are also becoming increasingly multi-drug resistant and have recently developed resistance to vancomycin, which has been used successfully to treat MRSA for many years. In-vitro determination of drug resistance patterns of S. aureus is critical for the selection of effective drugs for the treatment of staphylococci infections.

The main aim of this study was to determine the prevalence of methicillin resistant S. aureus strains from different clinical specimens from patients referred for routine culture and sensitivity testing.

Method

A cross sectional study was conducted among 1360 participants at Yekatit 12 Hospital Medical College in Ethiopia from September 2013 to April 2014. Clinical samples from various anatomical sites of study participants were cultured on blood agar and mannitol salt agar and identified to be S. aureus by using catalase, coagulase and DNAse tests. S. aureus isolates then were screened for MRSA using 30 μg cefoxitin disc and other 11 antimicrobial drugs by disc diffusion procedure, and agar dilution and E tests for vancomycin. All S. aureus isolates examined for beta-lactamase production by employing nitrocefin. Data were analyzed using SPSS version 20 software and logistic regressions were applied to assess any association between dependent and independent variables.

Results

Of 1360 clinical specimens analyzed S. aureus was recovered from (194, 14.3 %). Rate of isolation of S. aureus with regard to clinical specimens was the highest in pus (118, 55.4 %).No S. aureus was isolated from CSF and urethral discharge. Out of 194 S. aureus isolates, (34, 17.5 %) were found out to be MRSA and the remaining (160, 82.5 %) were MSSA. Ninety eight (50.5 %) S. aureus were multi drug resistant and the highest isolates were resistant to penicillin (187, 96.4 %) and least resistant for clindamycin (23, 11.9 %) and vancomycin (10, 5.1 %). MRSA strains were 100 % resistant to penicillin G, erythromycin, trimethoprim-sulfamethoxazole and least resistant to vancomycin (10, 29.4 %). Out of 194 S. aureus isolates (153, 79.0 %) were beta-lactamase producers.

Conclusion

In this study S. aureus isolates exhibited very high degree of resistance to different antibiotics. The isolates were also multidrug resistant to several combinations of the tested antibiotics. The emergence of vancomycin resistant S. aureus highlights the value of prudent prescribing of antibiotics and avoiding their irrational use.

Effect of 1.5% sodium hydroxide final concentration on recovery rate of Mycobacterial Species and decontamination of other Bacterial and Fungal contaminants on sputum

BACKGROUND

Digestion and decontamination of non-sterile clinical specimens such as sputum are an essential step in the isolation of mycobacteria. Masking of mycobacteria in Mycobacterial growth indicator tube (MGIT) 960 liquid culture system by fungi and bacteria other than mycobacteria is a major problem.

OBJECTIVE

To assess the effect of 1.5% sodium hydroxide final concentration on recovery rate of mycobacterial species and decontamination of other bacterial and fungal contaminants from sputum sample.

METHODOLOGY

Laboratory based cross sectional study with convenient sampling technique was carried out on subjects referred to the National Tuberculosis Reference Laboratory of Ethiopian Public Health Institute from November 2015 to February 2016. Single morning sputum was collected from each patient and analyzed.

RESULTS

A total of 264 subjects were enrolled in the study. The mean age of participant was 31 (SD 20.14 - 41.42) years old. The majority (61%) were male. Increasing the final concentration of NaOH from 1% to 1.5% reduced the contamination rate from 22.4% to 6.8% (P<0.001) without affecting mycobacterial recovery (P=1.00). A total of 26 different species of microbial contaminants were identified as being associated with BACTEC MGIT 960 culture system.

CONCLUSION

Results presented in this study demonstrated that the use of a final concentration of 1.5% NaOH with NALC method aids in reducing culture contamination rate for decontaminating sputum samples referred for tuberculosis culture diagnosis. Among the identified microbial contaminants, the most predominant was coagulase negative Staphylococcus species.

Fomitiporia tenuis and Fomitiporia aethiopica (Basidiomycetes, Hymenochaetales), two undescribed species from the Ethiopian highlands: taxonomy and phylogeny

Fomitiporia tenuis sp. nov. and Fomitiporia aethiopica sp. nov. from the Ethiopian highlands are described. Both are characterized by a resupinate habit, globose, dextrinoid basidiospores, cystidioles, and respectively scarcity or absence of hymenial setae. Fomitiporia pseudopunctata and F. robusta are reported also in the same area. The preliminary phylogenetic relationships of F. tenuis, F. aethiopica and F. pseudopunctata are inferred from parsimony analysis based on partial nuclear ribosomal large subunit (nrLSU). A preliminary key to the poroid Hymenochaetales with dextrinoid basidiospores (Fomitiporia, Phellinus s.l., Pseudoinonotus) is proposed.