Irfan Ali Mirza

Prevalence of faecal carriage of Enterobacteriaceae with NDM-1 carbapenemase at military hospitals in Pakistan, and evaluation of two chromogenic media

OBJECTIVES To determine the prevalence and antimicrobial susceptibility of carbapenemase-producing Enterobacteriaceae among hospitalized patients and outpatients attending two military hospitals in Rawalpindi, Pakistan, and to compare the performance of two chromogenic culture media for the isolation of these organisms. METHODS Stool samples from 200 distinct patients were cultured on MacConkey agar and subsequently on two chromogenic media-Colorex KPC and a prototype chromogenic medium, ID Carba-designed for the isolation of carbapenemase-producing Enterobacteriaceae. All Gram-negative isolates growing on either chromogenic medium were investigated for carbapenemases by phenotypic and molecular methods. Producers were subjected to susceptibility testing with 40 antimicrobials by VITEK 2 or agar dilution. RESULTS In total, 64 NDM-1-positive isolates of Enterobacteriaceae, belonging to seven distinct species, were recovered from 37 (18.5%) of the stool samples. No other carbapenemase types were confirmed. Nineteen positive samples were identified among 70 from inpatients (prevalence 27.1%) and there were 18 positive samples among 130 from outpatients (prevalence 13.8%). Fifty-six isolates (87.5%) harbouring the NDM-1 enzyme were recovered on ID Carba compared with 41 isolates (64.1%) on Colorex KPC (P = 0.012). Multidrug resistance was prevalent, but no pan-resistant isolates were found, with most isolates susceptible in vitro to colistin (97%), mecillinam (95%), fosfomycin (94%), tigecycline (89%) and nitrofurantoin (78%). CONCLUSIONS This study shows a high prevalence of multidrug-resistant Enterobacteriaceae with the NDM-1 enzyme in Rawalpindi. The new chromogenic medium, ID Carba, was more sensitive than Colorex KPC and has potential as a screening medium for isolation of Enterobacteriaceae harbouring the NDM-1 enzyme.

Prevalence and molecular characterization of Enterobacteriaceae producing NDM-1 carbapenemase at a military hospital in Pakistan and evaluation of two chromogenic media

The aim of this study was to assess the frequency and genotypic diversity of carbapenemase-producing Enterobacteriaceae (CPE) in stool samples from patients attending a military hospital in Pakistan. Further aims included the identification of factors that might predispose to faecal carriage and evaluation of 2 chromogenic culture media: Brilliance CRE and chromID CARBA. Of 175 patients, 32 (18.3%) had faecal carriage of CPE and all produced NDM-1 carbapenemase. All of these 32 patients were detected using chromID CARBA compared with 20 patients (62.5%) detected using Brilliance CRE (P = 0.0015). Duration of hospitalization and treatment with co-amoxyclav were statistically associated with a higher likelihood of carriage of CPE (P ≤ 0.05). The majority of NDM-1-producing Enterobacteriaceae co-produced CTX-M-1 group extended spectrum β-lactamase, and one third produced armA-type methylase. NDM-1 carbapenemase was most commonly found amongst commensal types of Escherichia coli, especially phylogenetic group B1.

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.

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.

Pattern of Bacterial Pathogens and Their Antimicrobial Susceptibility from Blood Culture Specimens in a Tertiary Care Setting

The objective of this paper is to find out the pattern of bacterial pathogens and their antimicrobial susceptibility from blood culture specimens received from a tertiary care referral setting. This cross-sectional observational study was carried out at the Department of Microbiology, Armed Forces Institute of Pathology, from July 2011 through June 2012. Blood culture specimens were dealt with brain heart infusion broth based manual method and automated BACTEC system. The specimens yielding positive growth were further analyzed and antimicrobial susceptibility carried out as per CLSI recommendations. Out of 2921 blood culture specimens, 465 (16%) yielded growth. Out of these, 245 (53%) isolates were Gram positive, 209 (45%) Gram negatives while 11 (2%) were yeast. Among Gram positive isolates, 208 (85%) were Staphylococcus spp. and among these 158 (76%) were methicillin resistant. Amongst Gram negative group, 115 (55%) isolates were members of enterobacteriaceae family and E. coli was the leading pathogen, while 94 (45%) were non-fermenters (NF). Among these, Acinetobacter spp. and Pseudomonas aeruginosa were common pathogens. In vitro antimicrobial susceptibility of staphylococci revealed that 100% isolates were susceptible to vancomycin and linezolid. The organisms of family enterobacteriaceae revealed better susceptibility to amikacin (68.7%) and imipenem (64.3%). The NF group showed better in vitro susceptibility to tazobactam/piperacillin (65%). Gram positive organisms were predominantly causing blood stream infections. Vancomycin and linezolid in case of Gram positive and amikacin and tazobactam/piperacillin against Gram negative organisms revealed better in vitro efficacy.