Aamer Ikram

Non-dermatophyte moulds as pathogens of onychomycosis.

OBJECTIVE To determine the role and pattern of non-dermatophyte moulds as causative agents of onychomycosis. STUDY DESIGN Case series. PLACE AND DURATION OF STUDY Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from November 2009 to July 2010. METHODOLOGY Nail clippings and nail scrapings were obtained from abnormal looking nails with treatment and detection failure for onychomycosis. Microscopic (40% potassium hydroxide mounts) examination and culture on Sabourauds dextrose agar (SDA), SDA containing chloramphenicol, and SDA containing actidione and chloramphenicol were used for species identification. RESULTS Non-dermatophyte moulds were isolated from 32 out of the total 47 culture positive cases (68%). Alternaria alternata was the commonest species (46%). Dermatophytes were isolated from only 7 patients (15%) belonging to genus Trichophyton. Yeasts were isolated in 8 (17%). There was no fungal growth in 53% of cases. CONCLUSION The non-dermatophytes should be considered important in evaluating the culture negative cases for dermatophytes as well as those cases ending up in treatment failure after empirical treatment for dermatophyte infections.

Bacterial biofilm-based catheter-associated urinary tract infections: Causative pathogens and antibiotic resistance

HighlightsBiofilm based catheter associated urinary tract infection is now an emerging problem.Biofilm production is greatly influenced by male gender, increased duration of catheterization and by use of latex catheter.E.coli is the most common isolate of CAUTI but Enterobacter cloacae exhibit highest biofilm production.High antibiotic resistance observe in biofilm producing strains due to slow penetration, resistant phenotype and altered micro environment.Good infection control policies and antibiotic stewardship are needs of hour. Background: We sought to determine the incidence of bacterial biofilm‐based catheter‐associated urinary tract infections, identify variables affecting biofilm formation, and identify etiologic bacterial pathogens and antibiotic‐resistance patterns associated with biofilm‐based catheter‐associated urinary tract infections (CAUTIs) in our setup. Methods: Patients who developed at least 2 symptoms of urinary tract infection after at least 2 days of indwelling urinary catheters were included. Urine was collected aseptically from catheter tubing and processed per standard microbiologic practices. Bacterial pathogens were identified on the basis of gram staining, colony morphology, and biochemical reactions. The detection of the biofilm was done using the tube adherence method. Drug susceptibility testing was done using the Kirby‐Bauer disc diffusion method. Findings: Biofilm was detected in 73.4% isolates, whereas 26.6% of isolates were nonbiofilm producers. Mean duration of catheterization after which biofilm was detected was 5.01 ± 1.31 days. A latex catheter was used in 69.5% of patients, whereas a silicone catheter was used in 30.4% of patients. Escherichia coli was found to be the most common pathogen isolated (52.3%), whereas Enterobacter cloacae exhibited the highest biofilm production (87.5%) among isolated pathogens. Among biofilm producers, the highest resistance was observed with ampicillin (100%). Fosfomycin exhibited the lowest resistance (17.2%). Significant association with biofilm was detected for gender, duration of catheterization, and type of catheter. Conclusion: Biofilm‐based CAUTI is an emerging problem. E coli was the most frequent isolate. High antibiotic resistance was observed in biofilm‐producing strains. Using the variables affecting biofilm formation, tailored intervention strategies can be implemented to reduce biofilm‐based CAUTIs.

Field evaluation of the direct detection of multidrug resistant Mycobacterium tuberculosis by nitrate reductase assay on 7H11 agar

In this study we evaluated the performance of colorimetric nitrate reductase assay (NRA) on Middlebrook 7H11 agar instead of Lowenstein-Jensen medium for detection of isoniazid (INH) and rifampin (RIF) resistance directly on 114 smear positive sputum specimens and compared the results with direct proportion method on LJ medium. The results of both methods were in 100% agreement for detection of RIF resistance while agreement for INH was 96.4%. The average turnaround time for NRA was 18.6 days and majority of the specimens gave positive results within 21 days. Thus direct NRA testing on smear positive sputum specimens by using 7H11 agar could be used as a fast, reliable and inexpensive method in resource starved settings.

Surveillance of device-associated infections in intensive care units of a tertiary care hospital

Journal of Hospital Infection - In Press.Proof corrected by the author Available online since mercredi 9 novembre 2016

A preliminary insight of correlation between human fecal microbial diversity and blood lipid profile.

Abstract The study aimed to evaluate the effect of human gut-derived lactic acid bacteria and yeast on cholesterol levels. Fecal samples from five healthy volunteers were examined for the level and diversity of dominant microbiota. Pichia kudriavzevii (QAUPK01, QAUPK02, QAUPK03, QAUPK04 and QAUPK05) and Candida tropicalis (QAUCT06) were identified by phenotypic methods and DNA sequencing and tested for in vitro cholesterol assimilation ability. Significant correlations (p < 0.05) between fecal microbial diversity, volunteers’ age, body mass index (BMI) and serum lipid profile were established. From biochemical tests, eight strains of lactic acid bacteria (M1.1, M1.2, M2.1, M3.1, M3.2, M4.1, M5.1 and M5.2) were identified but no bsh activity was found in them. However, all yeast strains were able to assimilate cholesterol and maximum assimilation ability was shown by QAUPK03 (83.6%) and QAUPK05 (85.2%) after 72 h of growth at 37 °C.

Rapid Direct Testing of Susceptibility of Mycobacterium tuberculosis to Isoniazid and Rifampin on Nutrient and Blood Agar in Resource-Starved Settings

ABSTRACT In this study, we evaluated the performance of blood agar (by macroscopic growth) and nutrient agar (by a microcolony detection method) for drug susceptibility testing of Mycobacterium tuberculosis against rifampin (RIF) and isoniazid (INH), using 67 smear-positive sputum specimens. The direct proportion method on Lowenstein-Jensen (LJ) medium was used as the “gold standard.” Compared with LJ medium, results for both media were in 100% agreement for RIF, while for INH the agreement levels for blood agar and nutrient agar were 98% and 95%, respectively. Within 2 weeks, 100% of specimens yielded results on blood agar, while 96.8% of specimens yielded results on nutrient agar. Our study showed that blood agar and nutrient agar can be used as alternative media for direct susceptibility testing of RIF and INH, especially in resource-poor settings.

Evaluation Of Nitrate Reductase Assay For Early Detection Of Multi And Extensively Drug Resistance Tuberculosis In Our Setup

OBJECTIVE To evaluate the performance of nitrate reductase assay on smear positive pulmonary specimens for detection of multi and extensively drug resistant tuberculosis simultaneously. STUDY DESIGN Cross-sectional analytical study. PLACE AND DURATION OF STUDY Microbiology Department, Armed Forces Institute of Pathology, Rawalpindi from June to December 2016. METHODOLOGY Smear positive pulmonary samples were processed both by nitrate reductase method on Lowenstein Jenson medium and also inoculated on gold standard Bactec MGIT 960 TB system. All the specimens were first digested and decontaminated according to standard protocol before inoculation. RESULTS Out of total 76 samples, three did not give color and, therefore, were excluded from the final data analysis. Among the remaining 73 samples, mycobacterial index was: 28 specimens were having 1+ (1-9 bacilli/100 fields), 26 samples were 2+ (1-9 bacilli/ field), and 19 samples were having 3+ index (>9 bacilli/field). The respective sensitivity and specificity were 84% and 100% for isoniazid (INH); 82% and 100% for rifampin (RIF); 67% and 100% for amikacin (AK); and both 100% for ofloxacin (OFX). Overall agreement in case of INH, RIF, AK, and OFX was 94.5%, 97.2%, 98.6% and100%, respectively. Overall average agreement was 97.5%. CONCLUSION Nitrate reductase assay is a reliable, low cost and accurate method that can be used for early for diagnosis of multi and extensively drug resistant tuberculosis.

Spectrum of Superficial and Deep Fungal Isolates in Northern Pakistan

Fungi are an important cause of superficial and deep infections in our population. Lack of expertise in proper identification and inadequate diagnostic facilities often lead to underreporting of these infections and thus underestimation of true disease burden. This study was conducted at Department of Microbiology, Armed Forces Institute of Pathology Rawalpindi, Pakistan, from January 2011 through December 2013. Samples included specimen collected from superficial and deep tissues, respiratory tract specimen, blood, bone marrow and other body fluids. Skin (35.1%) and nail (10.2%) samples were the most common specimens from superficial body sites. Tissue specimens from various body organs and bronchoalveolar lavage fluid were the predominant specimens received for investigation of deep seated fungal infections, contributing 34.9% and 5.9% of the total specimens respectively. Yeasts were isolated from 75(22.6%) samples; different species of Candida accounted for majority of the isolates. Growth of molds was detected in 257(77.4%) samples with Aspergillus spp. accounting for 149 (44.9%) of the isolates. Among dermatophytes, Trichophyton interdigitale 13(3.9%) was the most common isolate. Moulds other than dermatophytes were also isolated from skin, hair and nail samples and Alternaria alternata (4.8%) was the most common non-dermatophyte isolated from these sites. Fungal infections and their spectrum varies considerably in different geographical locations and in all cases not responding to antibiotics and high risk groups, a possibility of fungal cause should be sought.

Antimicrobial Sensitivity Pattern of Clinical Isolates of Mycobacterium Tuberculosis: A-Retrospective Study from a Reference Laboratory in Pakistan

Objective: To determine the sensitivity pattern of first line anti-tuberculosis drugs against clinical isolates of Mycobacterium tuberculosis (MTB) in our settings. Place and duration: Department of Microbiology, Armed Forces Institute of Pathology Rawalpindi, Pakistan, from January 2010 through December 2012. Materials & Methods: Samples received during the study period were processed on MGIT 960 system for MTB culture and drug susceptibility testing (DST) was performed for first line antituberculosis drugs, namely rifampicin (RIF), isoniazid (INH), streptomycin (STR) and ethambutol (ETH). MTB ATCC 25177 was used as control strain. Results: A total of 4050 samples were tested on MGIT 960 System, out of which 689(17%) were culture positive. Out of these culture positive cases, 303(44%) were pansensitive, 52(7.5%) pan-resistant, 84(12.2%) sensitive to one drug only, 171(24.8%) resistant to one drug only and 49(7.1%) were resistant to 2 drugs other than MDR. 132(19.16%) cases were multidrug resistant (MDR). Conclusion: Resistance to first line anti-tuberculosis drugs is alarming. Our results highlight the importance of drug susceptibility testing of MTB isolates against first line anti-tuberculosis drugs in an endemic country, so as to properly manage tuberculosis patients.

Direct Susceptibility Testing On Mgit 960 Tb System: A Rapid Method For Detection Of Drug Resistant Tuberculosis

OBJECTIVE To evaluate direct drug susceptibility testing on MGIT 960 system for detection of multidrug resistant tuberculosis from smear positive pulmonary specimens. STUDY DESIGN Cross-sectional analytical study. PLACE AND DURATION OF STUDY Microbiology Department, Armed Forces Institute of Pathology, Rawalpindi, from July 2016 to September 2017. METHODOLOGY Smear positive specimens were pretreated according to guidelines and then tested on MGIT 960 TB system for direct drug susceptibility testing (DST) of isoniazid and rifampin. Samples were also processed by gold standard indirect method, which comprises culture and then DST from positive growth by MGIT 960 TB system. RESULTS Out of 108 specimens, 95 (88%) DST results were reportable. Out of 95 reportable specimens, 17 isolates were resistant to both isoniazid (INH) and rifampin (RIF) by direct DST. The sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy for INH were 92%, 93%, 82%, 97% and 92.6%, respectively; and 95%, 96%, 86.3%, 98.6% and 95.7%, respectively for RIF. Average time to report DST by indirect method was 23.6 ±3.9 days, while it was 11.4 ±2.7 days for the direct method. CONCLUSION Direct susceptibility testing on MGIT 960 system showed very good agreement when compared with indirect method. Time saving is crucial factor in initiation of early effective therapy, especially in drug resistant cases. Further studies on large scale are required for more accurate evaluation of this method.