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Objective: to determine the frequency of the possible side effects of the COVID -19 inactivated vaccine. Study Design: Cross-sectional survey. Place and Duration of Study: Pakistan Naval Ship Shifa Hospital, Karachi Pakistan from Jan to Apr 2021. Methodology: A total of 305 recipients of inactivated COVID-19 vaccine were asked to fill out a questionnaire themselves or by the health care worker via telephonic conversation. The questionnaire comprised queries regarding general and local side effects that the participants experienced after getting vaccinated for COVID-19. Results: Out of 305 recipients, 270(88.5%) were men, and 35(11.5%) were women. Participants' age ranged from 18-60 years.After the first dose, 83(27.2%) cases [male 63(23.3%) vs. female 20(57.1%)], were reported with side effects, while 75(24.5%)recipients, [male: 54(19.9%) vs. female: 21(58.8%)], had side effects after the second dose. Generalized symptoms were fever,headache, dizziness, and body aches, while local side effects were pain, itching, swelling and rash at the injection site.259(84.9%) recipients reported spontaneous recovery after the first dose. After the second dose, 286(93.8%) recipients recovered spontaneously. The remaining 44(13%) of the recipients' required symptomatic treatment. After the second dose,only 19(6%) recipients needed symptomatic treatment. Conclusion: It is important to document the possible side effects of COVID vaccine so that public awareness and education can be made to minimize public fear of vaccine side effects. Inactivated vaccine for COVID-19 has minimal reported side effects and hence has a good safety profile.

The Enterobacteriaceae family are the most common pathogens associated with hospital and community acquired infections worldwide. These bacteria are treated with broad spectrum antibiotics especially 3rd generation cephalosporins. Over the period of time due widespread and rigorous use of these medications, Enterobacteriaceae has developed antibiotic resistance (AMR). Among all, the most compelling antibiotic resistance mechanism is production of -lactamases enzymes by this microorganism. Over the course of time -lactamase has evolved more than 1300 distinct enzymes. Amongst these most deleterious is extended spectrum beta lactamases (ESBL). ESBL producing Enterbacteriacaeae are responsible for a high number of deaths worldwide. These enzymes are considered challenging as they are difficult to be identified in the laboratory wShich cause delay in diagnosis and administration of appropriate antimicrobial therapy. The coexistence of ESBL with other antibiotic resistance gene is another therapeutic challenge rendering empirical antibiotic treatment ineffective

Objective: To assess and compare the knowledge, attitude and practices of janitorial staff regarding the hospital waste management system in public and private hospitals of Hyderabad. Study Design: Comparative cross-sectional study. Place and Duration of Study: Public and Private Hospitals of Hyderabad, from Oct 2017 to Mar 2018. Methodology: All 47 male and female janitorial staff of private and 47 public hospitals, aged 18 years were given a semistructured questionnaire about knowledge, attitude and practices regarding healthcare waste management. Scoring adequate knowledge, positive attitude and good practices were done to draw the results. Results: Out of the 94 included, 62 were male, and 32 were females. The majority of workers, 52 (55%), had working experience 10 years and between 5-10 years, respectively. In most of the knowledge and attitude-related questions, scoring of adequate knowledge and positive attitude was significantly higher in staff working in private than in the public hospital. In contrast, the scoring of practice-related questions was found to be significantly higher in staff working in a public hospital compared to those working in a private hospital. Conclusion: Knowledge, Attitude and Practices among janitorial staff working in public and private hospitals were not up to the mark and were not following the standard operative procedures while handling the healthcare waste. Hospital administration to formulate and implement refresher comprehensive training programs for the janitorial staff.

Objective: To discover the frequency of vancomycin resistant enterococci (VRE) fecal colonization and subsequent bacteremia in patients with hematological diseases in a bone marrow transplant center. Study Design: Cross-sectional study. Place and Duration of Study: Department of Microbiology, Armed Forces Institute of Pathology (AFIP), in collaboration with Armed Forces Bone Marrow Transplant Center, Rawalpindi, from Jan 2016 to Dec 2019. Methodology: Stool specimens/anal swabs from all enrolled patients were collected aseptically and transported to the laboratory without delay. Blood cultures were collected aseptically from only those enrolled patients who developed signs and symptoms of bacteremia. Stool and blood cultures were processed as per standard microbiological protocols. Enterococci were identified to species level by colony morphology and biochemical tests. Modified Kirby Bauer disc diffusion method and VITEK-2 system (Version-8.01 bio Merieux, France) were used to perform antimicrobial sensitivity of each isolate. Results: A total number of 246 patients were studied. Among them, 67 (27%) patients had fecal colonization by vancomycin resistant enterococci. We report a statistically significant association of recent hospitalization, prolonged exposure to antimicrobial therapy, chemotherapy exposure and use of indwelling devices during the hospital stay with vancomycin resistant enterococci colonization. Vancomycin resistant enterococci bacteremia was detected in 57 (23%) patients. Among these 57 patients, 53 (93%) were vancomycin resistant enterococci colonizers. Vancomycin resistant enterococci colonization was significantly associated with vancomycin resistant enterococci bacteremia. Conclusion: A considerable burden of vancomycin resistant enterococci fecal colonization exists among patients with hematological diseases. vancomycin resistant enterococci colonization poses a considerable risk of vancomycin........

Objective: To evaluate the cytospin slide microscopy method for detection of acid fast bacilli (AFB) in bronchoalveolar lavage (BAL) fluid comparing it with concentrated smear microscopy. Study Design: Cross-sectional validation study. Place and Duration of Study: Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from Dec 2016 to Sep 2018. Methodology: BAL specimens from suspected tuberculosis patients who were sputum smear negative, submitted to AFIP for diagnosis were included in the study. Smears for microscopy were prepared with the modified cytospin method as well as the standard concentrated technique. The prepared smears from both methods were stained with Ziehl–Neelsen (ZN) staining method and examined under 100 × oil immersion lens. TB culture performed on BACTEC MGIT 960 automated culture system (Becton Dickinson, USA) was taken as gold standard for TB diagnosis. The two methods were compared in terms of sensitivity, specificity, positive predictive value and negative predictive value. Results: Out of the 130 samples tested, 62 (47.7%) were positive on culture using MGIT 960 system. The sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy of the modified cytospin method for pulmonary TB diagnosis was found to be 68.3%, 100%, 100%, 77% and 84.6%, respectively. Conclusion: The sensitivity of the modified cytopsin smear method was significantly higher than that of the concentrated method. The study concludes that this is a simpler and more accurate method for BAL fluid microscopy.

Objective: To evaluate the epidemiology of clostridioides difficile infections and colonisation in a tertiary-care setting. Method: The cross-sectional study was conducted at the Combined Military Hospital, Rawalpindi, Pakistan, from June 1, 2017, to October 31, 2019, and comprised adult patients admitted in high-risk units of the hospital for any disease experiencing watery stools after 48 hours of hospital admission and passing more than 3 stools per day with no other recognised aetiology. Stool samples of the participants, diagnosed with antibiotic associated diarrhoea, were submitted forglutamate dehydrogenase antigen assay and clostridioides toxin A/B assay detected by enzyme-linked immunosorbent assay and clostridioides difficile toxin gene detection by polymerase chain reaction. Clostridium difficile-associated diarrhoea was diagnosed by a positive toxin assay or polymerase chain reaction. Data was analysed using SPSS25. Results: Of the 715 subjects, 322(45%) were males and 393(55%) were females. The overall mean age was 56.64±8.57 years, and 488(68.3%) were aged 60 years. The incidence of clostridioides difficile-associated diarrhoea was found in 10(1.4%) patients and was highest in oncology unit 3(4.3%). No positive case was detected from the high dependency unit and the surgical ward. All the10(1.4%) positive cases were on >2 antibiotics with a combination of oral vancomycin and intravenous metronidazole. Mortality rate was significantly higher in the positive cases compared to those with clostridioides difficile colonisation (p

Objective: To evaluate Gene Xpert MTB/RIF and Multiplex PCRfor detection of Mycobacterium tuberculosis and Rifampicin resistance comparing with gold standard MGIT 960. It was cross sectional validation study. Methods: This study had been carried out at Department of Microbiology Armed Forces Institute of Pathology (AFIP), Rawalpindi Pakistan from March 2018 to October 2018.MGIT 960 culture system MTB positive Rifampicin (RIF) resistant and RIF susceptible (negative control) samples were taken. Gene Xpert MTB / RIF assay and Multiplex PCR were applied simultaneously and compared with gold standard MGIT 960. Results: Out of 192 samples evaluated, 84(44%) were culture positive RIF resistant and 108(56%) were culture positive RIF susceptible as negative control. Out of total culture positive RIF resistant, all 84 were found positive for MTB by Gene Xpert MTB /RIF assay and Multiplex PCR method. Gene Xpert MTB/RIF assay detected all 84 RIF culture resistant samples for Rif resistance. Multiplex PCR detected only 44 RIF culture resistant, while remaining 40 did not showed resistance to rpoB gene codon 531 region. Sensitivity, Specificity, PPV and NPV of Gene Xpert MTB/RIF were 100% each respectively. Sensitivity, Specificity, PPV and NPV of Multiplex PCR for detection of RIF resistance were 52%, 100%, 100%, 72% respectively. Conclusion: Molecular detection of MTB and RIF resistant by Gene Xpert MTB/ RIF and Multiplex PCR simultaneously is rapid and cost effective method. Both methods can help clinician to initiate early empirical therapy to patient in resource limited region. Keywords: RIF, Gene Xpert MTB/ RIF, Multiplex PCR.

Introduction In Pakistan, the fourth wave of coronavirus disease 2019 (Covid-19) started around July 2021, which was dominated by the Delta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The vaccination drive to immunize the people of Pakistan against Covid-19 was also going on during this period. There were multiple types of vaccines being administered to the people of Pakistan, as the vaccines had been procured from multiple sources. Some people had apprehensions about different vaccines being administered in the country. The purpose of this study was to compare the clinical characteristics and outcome of the patients vaccinated against Covid-19 with those of the non-vaccinated patients during the fourth wave of Covid-19 in Pakistan Naval Ship (PNS) Shifa Hospital. Methods The cross-sectional descriptive study was performed at PNS Shifa Hospital Karachi, from July to October 2021. All the Covid-19 patients treated in PNS Shifa Hospital during the "fourth Covid-19 wave" were interviewed. Their medical records were accessed, and they were followed up till their discharge from the hospital. The vaccinated and non-vaccinated patients were compared for differences in their age or gender distribution, the severity of illness, comorbidities, and mortality. Results There were 884 participants in the study: 664 (75.11%) men and 220 (24.89%) women. There were 493 patients below 40 years of age, 233 were 40-59 years old, and 158 were aged 60 and above. One hundred and sixty-nine patients had one or more comorbidities, including hypertension, diabetes mellitus, ischemic heart disease, various malignancies, bronchial asthma, and chronic kidney disease. There were 63 (7.13%) obese patients, 28 of whom developed severe disease. Five hundred and four (57%) patients were vaccinated and 380 (47%) were non-vaccinated. Among the vaccinated patients, the effect of Covid-19 was mild in 58.37%, moderate in 36.11%, severe in 0.79%, and critical in 4.37%. Among the non-vaccinated patients, the effect of Covid-19 was mild in 40.26%, moderate in 46.58%, severe in 3.16%, and critical in 10%. The difference in disease severity between the two groups was statistically significant (

Emergence of resistance among Escherichia coli (E.coli) isolates against therapeutic options for UTIs (Urinary tract infections) has led to renewed interest in older antibiotics like Fosfomycin. In this study we evaluated diagnostic accuracy of Rapid Fosfomycin NP test based on glucose metabolism for rapid Fosfomycin susceptibility testing among urinary E.coli isolates.In a cross-sectional validation study conducted in the Microbiology Department, Armed Forces Institute of Pathology, Rawalpindi, Pakistan from 15th March to 15th September 2020, 149 consecutive urine specimens were included as per selection criteria. Rapid Fosfomycin NP test was performed as per protocol of Nordmann P et al on urinary E.coli isolates for detection of Fosfomycin resistance and results were compared with reference modified Kirby-Bauer disk diffusion method.Out of total 149 E.coli isolates from 149 urine specimens, 80 were classified as Fosfomycin susceptible and 69 as Fosfomycin resistant by reference disk diffusion method. Sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy of rapid Fosfomycin NP test was found to be 94.2%, 98.75%, 98.48%, 95.2% and 96.64%, respectively. In our study reliable results were achieved after 2.5 hours of incubation.The rapid Fosfomycin NP test is valid and user-friendly technique which can be performed with minimal technical expertise. It is less time consuming than disk diffusion and Etest strips and easy to perform as compared to agar dilution method. It can be useful as alternative to agar dilution in urinary E.coli isolates which would help in selecting appropriate therapeutic option for UTIs.

Acinetobacter baumannii has emerged as one of the leading causes of multidrug resistant nosocomial infections worldwide. It is able to survive in hospital environment and build up diverse resistance mechanisms making it difficult to treat with current antibiotics. Objective: It was to determine the frequency and patterns of Acinetobacter baumannii in intensive care units (ICU) settings.A cross sectional study was carried out in the Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, from 1st July 2017 to 30th June 2019. A total of 603 non-duplicate clinical specimens were received from intensive care units. Specimens yielding growth of multidrug resistant Acinetobacter baumannii, were evaluated as per standard protocol. The antimicrobial sensitivity testing was performed as per Clinical and Laboratory Standard Institute guidelines (2017-2018).Among Acinetobacter baumannii (310 isolates), 5% were multidrug resistant, 93% extensively drug resistant and 1% pan drug resistant. Percentage of carbapenem resistant strains was 92%. In drugs like tigecycline and polymyxin, resistance was noted as 73% and 1% respectively. High yield of this superbug was mainly obtained from respiratory specimens (43.5%), whereas 24% were detected from wound infections and 29% from other samples. .This study showed a rapidly increasing resistance in Acinetobacter baumannii. Therefore, polymyxin remains the only option in our intensive care units, but its usage as empirical therapy in our setting has led to the emergence of resistance to this drug. Implementing infection control practices, antimicrobial stewardship and restricted use of polymyxin can play a significant role in reducing health care burden.

Polymyxins play a significant role against carbapenem-resistant Enterobacteriaceae (CRE). A total of 121 clinical samples yielded growth of CRE that were included in the study. Rapid Polymyxin NP test was performed on all the isolates as described by Nordmann P et al. and results were compared with broth microdilution method. Majority of the isolates were Klebsiella pneumoniae (70.2%) followed by Escherichia coli (17.4%). A total of 71 isolates were found resistant and 50 as susceptible by broth microdilution. Sensitivity and specificity of rapid polymyxin NP test were found to be 97.2% and 100%, respectively. Our study concluded that rapid polymyxin NP test is reliable and can be used as an alternative to broth microdilution in resource limited settings.

INTRODUCTION: Typhoid remains a major healthcare problem in low and middle-income countries. The emergence of extremely drug-resistant (XDR) typhoid strains from the Indian subcontinent has led to very limited therapeutic options. Azithromycin being the only oral option for XDR typhoid faces a threat of rapid resistance due to its overuse after the COVID-19 pandemic. OBJECTIVE: To evaluate the reliability of azithromycin disc diffusion testing against clinical isolates of typhoidal salmonellae in comparison with E-test minimum inhibitory concentrations (MICs). STUDY DESIGN: This is a cross-sectional validation study. Place and duration of the study: The Department of Microbiology, Pakistan Navy Ship Shifa hospital, Karachi from June 1 to December 31, 2020. METHODOLOGY: Antimicrobial susceptibility was performed by Kirby Bauer disc diffusion method for 60 isolates including Salmonella enterica ser. Typhi and Paratyphi A using Clinical Laboratory Standard Institute (CLSI) guidelines. MICs by the E-test method were determined for Azithromycin only. RESULTS: A significant proportion of the isolates (55%) had high azithromycin MIC in the wild-type distribution range (8-16 µg/ml). Ten (16.6%) isolates showed false resistance, i.e., zone diameter

The aim of this study is to see the frequency, clinical presentation, and therapeutic response of extensively drug-resistant Salmonella enterica serovar Typhi and current susceptibility pattern of typhoidal Salmonella strains in our setup. This study was carried out at the Department of Medical Microbiology and Immunology and Department of Medicine, Pakistan Navy Ship (PNS) Shifa Hospital, Karachi, from January 1 to December 31, 2018. All the blood culture samples of patients (indoor and outdoor) with suspicion of enteric fever were processed. Isolates were cultured and identified using standard microbiological procedures. The antimicrobial sensitivity against the typhoidal Salmonellae was determined using Kirby-Bauer disc diffusion method as per the guidelines of Clinical and Laboratory Standards Institute (2018) and all the extensively drug-resistant (XDR) isolates were confirmed by Vitek 2 system. Clinical presentation and response to treatment of patients were followed. A total of 292 typhoidal Salmonella isolates were cultured. Resistance to ciprofloxacin against both Salmonella Typhi and Salmonella Paratyphi A was found to be very high (91%). Percentage of multidrug-resistant (MDR) isolates in Salmonella Typhi was 76% (182 isolates) and in Salmonella Paratyphi it was 34% (18 isolates). XDR isolates in Salmonella Typhi were significant that is 48% (115 isolates). Only 10 cases were given azithromycin who responded to treatment in mean 4.3 days. Out of 115 cases of XDR Salmonella Typhi, 103 patients were given parenteral meropenem and clinical response was seen in mean 5 days. The emergence and rapid spread of extensively drug-resistant Salmonella Typhi is alarming and highlights the significance of strict antimicrobial susceptibility surveillance programs with antimicrobial stewardship.

Objective To evaluate performance of thin layer agar (TLA) 7H11 method for detection of ofloxacin (OFX) and kanamycin (KM) resistance in smear positive clinical specimens of patients with tuberculosis comparing the results with gold standard MGIT 960 system. Study design Cross-sectional validation study. Place and duration of study Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from April to September 2017. Methodology Acid fast bacilli (AFB) smear positive specimens submitted at the study place, were inoculated on TLA 7H11 agar. Growth was examined along with susceptibility of OFX and KM and compared with gold standard MGIT 960 system. Results One hundred and sixty specimens were evaluated. Sensitivity and specificity of TLA for OFX was found to be 100% and 99.3%, respectively; and PPV and NPV was found to be 90.9% and 100%, respectively. Overall diagnostic accuracy was 99.38%. Sensitivity and specificity of TLA for KM was found to be 80% and 100%, respectively. PPV and NPV was found to be 100% and 99.36%, respectively. Overall diagnostic accuracy was 99.38%. Conclusion Thin layer agar is reliable, easy to perform and cost effective technique not only for rapid detection of MTB but also for drug susceptibility (DST) of second line anti TB agents. It is a suitable alternative to culture on LJ medium and can also be alternative to MGIT 960 system in resource-poor settings.

Introduction:Tuberculosis is an infectious disease with a high prevalence of about 9 million cases occurring annually. Ziehl Neelsen microscopy is the most widely used technique to detect Acid Fast Bacilli, but it is less sensitive. However, fluorescent microscopy is more helpful with simple diagnostic criteria. Gene Xpert®MTB/RIF assay is a rapid molecular assay that enables diagnosis of Tuberculosis with simultaneous detection of rifampicin resistance. Owing to this fact, we aimed at evaluating the diagnostic accuracy of Ziehl Neelsen microscopy, fluorescent microscopy and Xpert MTB/RIF keeping MTB culture (Mycobacterial Growth Indicator Tube) as a gold standard for the diagnosis of tuberculosis.Methodology:This study was carried out at a tertiary care hospital of Rawalpindi in the year 2016. Patients aged 18 to 70 years irrespective of gender with suspected TB based on history, clinical and radiological examination were included in the study. Respiratory clinical specimens including sputum, Broncho-Alveolar Lavage (BAL), and endobronchial washings were collected. Specimens were processed by MGIT (MTB culture), ZN microscopy, fluorescent microscopy and Gene Xpert MTB/RIF assay.Results:A total of 352 respiratory specimens were tested among which 160 (45%) samples were positive by culture. Out of culture positive samples, 158 samples (98.7%) were GeneXpert TB positive while 2 were negative. While only 49 (30.6%) were positive on ZN microscopy and 89 (55%) were positive on fluorescent microscopy. Out of the culture negative samples, 2 were positive with ZN microscopy, one was positive with fluorescent microscopy and 3 were positive on Gene Xpert. Sensitivity, specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV) and diagnostic accuracy of ZN Smear microscopy was 39%, 99.5%, 96%, 63% and 14.5% respectively. Sensitivity, specificity, PPV, NPV and diagnostic accuracy of fluorescent smear microscopy was 55% and 99.5%, 98%, 72% and 79% respectively. Sensitivity, specificity, PPV, NPV and diagnostic accuracy of Gene XPERT was 98% and 99%, 98%, 99% and 98% respectively.Conclusion:In countries like Pakistan where Tuberculosis is endemic, the diagnostic accuracy with highest sensitivity and specificity was Gene Xpert Polymerase Chain Reaction (PCR) MTB/RIF assay which can help in well-timed diagnosis of the disease.

Acute respiratory illness caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) involved the whole globe within no time. Various studies published globally have shown variable severity of disease and mortality. The objective of our study was to describe clinical and epidemiological characteristics of the disease in our setup.in this descriptive case series, individuals with signs and symptoms of Coronavirus disease-19 (COVID-19) and asymptomatic patients with history of close contact to confirmed COVID-19 patients were considered for SARS-CoV-2 Polymerase chain reaction (PCR) assay. Epidemiological and clinical features of only PCR positive cases were recorded. Data regarding hospitalization status, exposure to known COVID-19 patients, clinical feature and clinical outcome of patients was collected and interpreted.A total of 266 patients were found to be SARS-CoV 2 PCR positive which were included in the study. Mean age of patients was 39.45±31.9 years and majority of the patients in our study were male, i.e., 238 (89.5%). Most common clinical features among COVID-19 symptomatic patients were fever and dry cough followed by myalgias and sore throat. Eighteen (7%) out of 266 died in our setup. Time duration of viral shedding after initial positive PCR varied between 11 days to up to more than 55 days.Coronavirus disease-19 (COVID-19) can present with wide range of clinical spectrum and disease can be life threatening. Severity of disease, requirement of ICU care and mortality were directly related to age of the patient and underlying comorbidities. Rigorous precautionary measures are of utmost importance particularly in this high-risk population.

Objective To evaluate a direct antibiotic susceptibility testing method for blood culture.. Methods The cross-sectional comparative study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from December 2016 to October 2017. Direct antimicrobial susceptibility testing was performed from positive blood culture bottles. Bacterial identification was done by using API 10S. Different antimicrobial panels were employed for Gram-negative rods (GNRs), gram-positive cocci (like suspected Staphylococci and Enterococci). Results were compared with conventional disk diffusion testing and very major, major and minor errors were calculated. Result agreement and kappa coefficient scores were generated for categorical agreement. SPSS 24 was used for data analysis. Results Of the 101 bacterial isolates, 82(81.2%) were Gram negative rods and 19(18.8%) were Grampositive cocci. Among 781 bacteria-antibiotic comparisons, the number of very major errors was 3(0.4%), major errors were 7(0.9%) and minor errors were 12(1.5%), while, 759(97.2%) comparisons yielded the same results. The kappa coefficient was 0.946, showing almost perfect agreement. Direct identification of Gram negative rods was successful in 53(64.6%) cases. Conclusions Direct susceptibility testing of blood culture produced reliable results for majority of the antimicrobials.

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.

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.

A 61 year male, admitted in Combined Military Hospital Rawlpindi on 12th March 2017, operated for diverticulitis became colonized with Staphylococcus haemolyticus. Patient suffered repeated septic episodes caused by the same organism during his stay in hospital. The strain was identified as methicillin resistant Staphylococcus haemolyticus (MRSH) also resistant to Linezolid by analytical profile index for Staphylococcus (API Staph) and VITEK 2 Gram positive cocci panel. The isolate was cultured from blood cultures, Central Venous Catheter (CVC) tip and skin swabs. Patient was successfully treated with injectable vancomycin and skin decolonization was acheived with chlorhexidine bath after which no episode of MRSH infection occurred. Patient had an uneventful recovery and was discharged on 21st June. His follow up visit showed clinical improvement.

Invasive salmonellosis caused by Salmonella typhi and Salmonella paratyphi is a serious life-threatening complication in immunocompromised patients. Since blood cultures have only 40-80% sensitivity, very limited diagnostic modalities are left. Here, authors present a case of a 24-year-old pregnant lady who develops a unilateral breast abscess harbouring Salmonella typhi. The isolate was Extremely Drug Resistant (XDR), that is resistant to first line drugs, ciprofloxacin and ceftriaxone. She was successfully treated with combination of injection meropenem and tablet azithromycin and continued for 14 days. To the best of authors knowledge, this was the first reported case of Salmonella enterica serovar Typhi in a pregnant lady from Pakistan.

Background: Effective control of tuberculosis is achieved by early diagnosis and drug susceptibility testing for initiation of appropriate treatment. The performance of crystal violet decolorization assay (CVDA) for susceptibility testing of Mycobacterium tuberculosis to isoniazid (INH) and rifampicin (RIF) was compared in a multicenter study. Methods: Seventy-two M. tuberculosis isolates were tested in two phases by CVDA. Results: In Phase I, the specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and agreement for INH were 100%, respectively. Specificity, sensitivity, PPV, NPV, and agreement for RIF were 98.2%, 100%, 94.1%, 100%, and 98.6%, respectively. In Phase II, specificity, sensitivity, PPV, NPV, and agreement were 98%, 100%, 95.4%, 100%, and 98.6% for INH, respectively. Specificity, sensitivity, PPV, NPV, and agreement for RIF were 96.3%, 88.2%, 88.2%, 96.3%, and 94.4%, respectively. Results in the study were obtained on average 10.9 ± 3.1 days in Phase I and 9.8 ± 2.2 days in Phase II. Conclusion: CVDA can be performed for drug susceptibility testing in developed and developing countries. In addition, further studies with larger sample size are needed for evaluation of this method. Fil: Coban, Ahmet Yilmaz. Akdeniz Üniversitesi; Turquía Fil: Alakbarova, Gumral. Medical Microbiology Laboratory. Thalassemia Center; Azerbaiyán Fil: Satti, Luqman. Armed Forces Institute of Pathology; Pakistán Fil: Tayyab, Nadia. Armed Forces Institute of Pathology; Pakistán Fil: Zaman, Gohar. Armed Forces Institute of Pathology; Pakistán Fil: Morcillo, Nora Susana. Provincia de Buenos Aires. Ministerio de Salud. Hospital "Dr. Antonio A. Cetrángolo"; Argentina Fil: Imperiale, Belén Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; Argentina Fil: Wainmayer, Ingrid. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina Fil: Símboli, Norberto Fabián. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; Argentina

Objective To assess the utility of galactomannan and beta-D-glucan assays in the diagnosis of invasive aspergillosis in clinically suspected cases, and to compare their diagnostic potential to determine whether a combination of the two may result in an early and specific diagnosis. Methods The descriptive cross-sectional case-control study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from April 1, 2017, to March 31, 2018, and comprised serum samples from clinically suspected invasive aspergillosis patients and healthy controls. The sera were tested for galactomannan and beta-D-glucan detection. Proven, probable and possible categories of invasive aspergillosis according to European Organisation for Research and Treatment of Cancer / Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group criteria. Galactomannan antigen was detected using a one-stage immunoenzymatic sandwich microplate assay. Beta-D-Glucan antigen was detected using a protease zymogen-based colorimetric assay. Sensitivity and positive / negative likelihood ratio of both the cases and the controls were calculated and compared. Results Of the 178 subjects, 119(67%) were cases and 59(33%) were controls. Beta-D-glucan assay was more sensitive than galactomannan assay (91.6% versus 80.67%) whereas galactomannan assay was more specific than beta-D-glucan assay (86.44% versus 76.27%) in the diagnosis of invasive aspergillosis. The sensitivities of both assays decreased with decreasing probability of invasive aspergillosis, i.e., maximum sensitivities of both beta-D-glucan and galactomannan assays were for proven cases (100% versus 87.5%), followed by probable cases (89.29% versus 85.71%), and possible cases (91.57% versus 78.31%). Conclusions Both beta-D-glucan and galactomannan assays seemed to play an encouraging role in the diagnosis of invasive aspergillosis in high-risk clinically suspected cases, with the former assay being more sensitive and the latter assay being more specific.

Introduction. Infective endocarditis (IE) is an important clinical condition with significant morbidity and mortality among the affected population. A single etiological agent is identifiable in more than 90 % of the cases, however, polymicrobial endocarditis (PE) is a rare find, with a poor clinical outcome. Here we report a case of native valve dual pathogen endocarditis caused by Burkholderia cepacia and Aspergillus flavus in an immunocompetent individual. It is among unique occurrences of simultaneous bacterial and fungal etiology in IE. Case presentation. A 30-year-old male was admitted to a cardiology institute with complaints of low grade intermittent fever and progressive shortness of breath for last two months. He was a known case of rheumatic heart disease and had suffered an episode of IE three years ago. On the basis of clinical presentation and the results of radiological investigations, a diagnosis of infective endocarditis was made. Paired blood samples for culture and sensitivity, sampled before the commencement of antimicrobial therapy, yielded growth of Burkholderia cepacia which was highly drug resistant. Sensitivity results-directed therapy consisting of tablet Trimethoprim–Sulfamethoxazole, two double-strength tablets 12 hourly, and Meropenem, 1 g IV every 8 h, was commenced. Despite mild relief of fever intensity, overall clinical condition did not improve and double valve replacement therapy was carried out. Excised valves were sent for microbiological analysis. Burkholderia cepacia was grown on tissue culture with a similar antibiogram to that previously reported from the blood culture of this patient. Direct microscopy of section of valvular tissue with 10 % KOH revealed abundant fungal hyphae. Patient serum galactomannan antigen assay was also positive. Histopathological examination of vegetations also revealed hyphae typical of species of the genus Aspergillus. The patient was successfully treated with meropenem, trimethoprim–sulfamethoxazole and voriconazole. Conclusion. The hallmark of successful treatment in this case was exact identification of pathogens, antibiogram-directed therapy and good liaison between laboratory experts and treating clinicians.

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.

Journal of Hospital Infection - In Press.Proof corrected by the author Available online since vendredi 22 decembre 2017

Objective To determine the pattern of blood stream infections and their antibiotic susceptibility profile with infectivity predictors in a neonatal setting. Methods The descriptive cross-sectional study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from December 1, 2016,to April 30, 2018, and comprised blood culture samples received in Bactec/BactAlert paediatric bottles from neonates aged 0-30 days admitted in the neonatal intensive care unit. The samples were processed as per the standard guidelines. Antibiotic susceptibility was checked as per guidelines of the Clinical and Laboratory Institute. VITEK 2 system was used for rapid identification and minimum inhibitory concentrations of the drugs. SPSS 24 was used for data analysis. Results Out of 640 samples, 172(27%) were culture-positive. Among them, 98(57%) were gramnegative rods, 50(29%) gram-positive cocci and 24(14%) were fungi. Of the 172 pathogens identified, Klebsiella pneumoniae was 39(22.7%) followed by Candida species 24(14%) and methicillin-resistant Coagulase-negative staphylococci 20(11.6%). Of Klebsiella pneumoniae isolates, 26(58%) were extended spectrum -lactamase producers. Among Acinetobacterbaumanii, 11(58%) were extensively drug resistant and Carbapenem-resistant strains were 20(91%). Also, 4(8%) isolates of Enterococcus faecium were vancomycin-resistant. Conclusions Majority of the isolates causing blood stream infections in neonatal intensive care unit were multi drug resistant, posing a therapeutic challenge for the neo natologists .

Summary 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.

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

Background: Third generation cephalosporins are still most commonly used antibiotics empirically in our setup leading to emergence of resistance in this group. In this environment of increasing resistance, empirical use of this group of antibiotics would be a futile effort. Therefore, this study was conducted to evaluate the in vitro efficacy of fourth generation cephalosporin cefepime against multi-drug resistant isolates of Pseudomonas aeruginosa from various clinical specimens in our setup.