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Naegleria fowleri amebae are thermophilic, free-living, and found in soil and fresh water, such as lakes, rivers, ponds, and untreated swimming pools. The ameba enters the brain through the nose [...]

Background: 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. Methods: 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). Results: 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. Conclusion: 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. [ABSTRACT FROM AUTHOR]

Background: 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. Methods: 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. Results: 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. Conclusion: 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 E- test 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. [ABSTRACT FROM AUTHOR]

Background: 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. Methods: 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. Results: 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. Conclusions: 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. [ABSTRACT FROM AUTHOR]

Objective: To determine cut off value of Interferon Gamma Release Assay (IGRA) among Tuberculosis (TB) suspected patients and to compare median Interferon Gamma Release Assay value for Tuberculosis culture positive and culture negative patients. Study Design: Cross sectional study. Place and Duration of Study: Department of Microbiology, Armed Forces Institute of Pathology, National University of Medical Sciences, from Oct 2015 to Apr 2016. Methodology: The study was conducted on patients with suspected tuberculosis. Quantiferon Tuberculosis Gold that has an important role in the immune response to Tuberculosis was performed by Enzyme Linked Immunosorbent Assay method and specimens were cultured on Mycobacterium Growth Indicator Tube 960 System (MGIT 960 system). Quantiferon Tuberculosis Gold values obtained by Enzyme Linked Immunosorbent Assay method were used to determine the sensitivity and specificity of this test. Results: A total of 240 suspected isolates of tuberculosis during the study period were subjected to culture using MGIT 960 system, as per recommended protocol for the method. These samples were also subjected to Quantiferon TB Gold (QTBG) to measure Interferon Gamma Release Assay release. Sensitivity and specificity of IGRA was determined keeping tuberculosis culture as gold standard for this study. Conclusion: Sensitivity and specificity values showed a significant p-value <0.001 with active tuberculosis. In TB endemic areas like Pakistan, new cutoff value must be kept in mind while interpreting results of IGRA. [ABSTRACT FROM AUTHOR]

Objective: To compare the in vitro disk diffusion method and agar dilution method for sensitivity of Polymyxin B against multi drug resistant Acinetobacter baumannii. Study Design: Comparative cross sectional. Place and Duration of Study: The study was carried out in the department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi from 1st Dec 2016 to 30th Dec 2017. Methodology: Total 253 clinical specimens received from intensive care units with yielded growth of multidrug resistant Acinetobacter baumannii were evaluated for Polymyxin B susceptibility. Both Kirby bauer disk diffusion and agar dilution methods were compared with a reference method, broth microdilution. Results: Among 253 multidrug resistant isolates, 180 (71%) were extensively drug resistant and 221 (87%) were carbapenem resistant. Comparison of the disk diffusion and the MIC method by Agar dilution showed 100% correlation. 251 isolates were sensitive and 2 were resistant to Polymyxin B with MICs and disk zone diameters within the range recommended by the CLSI (2014-17). MIC 50 and MIC 90 of Polymyxin B were found to be 0.5 and 1µg/ml with 99.2% susceptibility. Conclusion: Both disk diffusion and agar dilution can be used together as initial screening methods in low income countries for susceptibility reporting of polymyxins. They are simple, reliable and economical. Also hetero resistance shown by some Acinetobacter baumanii strains can easily be picked up by agar dilution method. [ABSTRACT FROM AUTHOR]

We investigated an outbreak of Serratia marcescens (S. marcescens) in NICU of our hospital and are reporting the characteristics of this outbreak along with interventions leading to its resolution. In the month of September and November 2016, seven neonates were identified with blood cultures positive S. marcescens septicemia. To identify the source of the isolate surface swabs were taken from different environmental sources. All S. marcescens isolates were identified by Vitek automated identification system, API 20 E and their antibiogram pattern and further genotyping was done by pulse field gel electrophoresis. During surveillance, 25 blood cultures of newborns were analyzed, 32 environmental samples along with hand swabs of 10 healthcare workers (HCWs) were taken. Seven neonates had blood culture positive S. marcescens sepsis. Only one environmental source (water flasks) yielded S. marcescens with similar antibiogram suggesting the same strain which was further confirmed by pulse field gel electrophoresis. Timely delivery of culture and sensitivity results, good liaison and effective communication between neonatologist and microbiologist, targeted antimicrobial therapy helped in saving the life of six neonates suffering from S. marcescens septicemia. [ABSTRACT FROM AUTHOR]

Background: Urinary tract infections are one of the most common infections especially in young adults. Due to increase in fluoroquinolones use, empirical therapy in uncomplicated urinary tract infections with this group is now controversial. This study was aimed to see the efficacy of nitrofurantoin, ciprofloxacin and cotimoxazole (trimethoprim-sulphamethaxazol); the three most common drugs which can be used orally. Material & Methods: This descriptive study was carried out at the Department of Microbiology, Combined Military Hospital, Quetta, Pakistan from Januery 2014 to June 2014. A total of 270 urinary isolates (Outdoor 132, indoor 138) were cultured from urine specimens during the study period. Identification of isolates were performed by conventional methods and by using API 10S (Biomerieux, France). All the isolates were tested against nitrofurantoin, ciprofloxacin and cotimoxazole (trimethoprim-sulphamethaxazol) along with other routine antibiotics used for urinary pathogens. Results: Out of total 270 urinary isolates, Escherichia coli was the dominant isolate cultured in 158 (58.51%) cases, followed by Klebsiella pneumonia in 48 (17.77%) and enterococcus spp. In 16 (5.92%) cases. Out of total 132 outdoor isolates, percentages of sensitivities of nitrofurantoin, ciprofloxacin and cotimoxazole were 92.4, 47.1 and 62.1 respectively. In case of total 138 indoor isolates, percentages of sensitivities for these three drugs were 84.0, 34.7 and 28.9 respectively. Conclusion: Nitrofurantoin is very effective against both outdoor and indoor urinary isolates and can be used empirically for uncomplicated urinary tract infections. [ABSTRACT FROM AUTHOR]

Primary amebic meningoencephalitis caused by Naegleria fowleri is a rare but nearly always fatal parasitic infection of the brain. Globally, few survivors have been reported, and the disease has no specific treatment. We report a confirmed case in Pakistan in a 22-year-old man who survived after aggressive therapy.

Objectives: To evaluate the epidemiology of clostridioides difficile infections and colonisation in a tertiary-care setting., Methods: 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 for glutamate 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, while 227(31.7%) 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<0.05)., Conclusions: The incidence of clostridioides difficile-associated diarrhoea was found to be low.

Objective: To compare the efficacy of Gene Xpert mycobacterium tuberculosis-rifampicin and multiplex polymerase chain reacton for the detection of mycobacterium tuberculosis and Rifampicin resistance., Methods: The cross-sectional validation study was conducted at the Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from March to October 2018, and comprised mycobacterium tuberculosis-positive rifampicin-resistant and rifampicin-susceptible samples, with the latter acting as negative controls. Gene Xpert mycobacterium tuberculosis-rifampicin assasy and multiplex polymerase chain reacton were applied simultaneously and compared with gold standard mycobacterium growth indicator tube 960. Data was analysed using SPSS 24., Results: Of the 192 samples, 84(44%) were culture-positive rifampicin-resistant and 108(56%) were culture-positive rifampicin-susceptible. Overall, 84(44%) were found positive. Gene Xpert mycobacterium tuberculosis-rifampicin assay detected all 84(100%) rifampicin-resistant samples, while multiplex polymerase chain reacton detected 44(52.3%) such samples. Sensitivity, specificity, positive predictive value and negative predictive value of Gene Xpert were 100% each respectively, while the corresponding values for multiplex polymerase chain reacton were 52%, 100%, 100% and 72% respectively., Conclusions: Molecular detection of mycobacterium tuberculosis and resistance by Gene Xpert and multiplex polymerase chain reacton simultaneously was found to be a rapid and cost-effective method.

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.

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 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 .

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.

Methicillin-Resistant Coagulase-Negative Staphylococcusposes a challenging situation in healthcare settings. The spread of resistance among such organisms against major drugs is alarming as it limits the treatment options for serious infections. Traditionally, Vancomycin had remained a mainstay of treatment of Methicillin-Resistant Staphylococci. Linezolid introduction into the clinical practice was a major breakthrough since it provided orally administered treatment of Methicillin-Resistant Staphylococci. Widespread use of Linezolid has gradually turned the impending fear of emergence of resistance against this novel drug into a reality. We report first case of Linezolid-Resistant Methicillin-Resistant Staphylococcushemolyticusfrom Pakistan, isolated from a leukemic patient. The organism caused a necrotic lesion on the right forearm at cannulation site of intravenous catheter. Ooze swab yielded the pure growth of Linezolid-Resistant Methicillin-Resistant Staphylococcushemolyticus.

Background: Thrombocytopenia is often seen in the patients of malaria infected with Plasmodium vivax. We studied patients admitted in hospital having coexisting thrombocytopenia and malaria, and recorded the response to anti-malarial therapy., Methods: In this cross-sectional descriptive study, a total of 120 patients admitted in medical ward with Plasmodium vivax malaria and co-existing thrombocytopenia were studied., Results: Out of total 120 slide positive Malaria patients who had low platelet count (<150x10(9) /L), platelet count increased to ≥150x10(9) /L in 73 (60.8%) patients after five days of anti-malarial therapy while in 47 (39.2%) patients thrombocytopenia persisted. After ten days of anti-malarial therapy, platelet count in all the patients recovered to ≥ 150x10(9) L. None of the patients required platelet transfusion., Conclusion: In majority of the patients of Plasmodium vivax malaria having thrombocytopenia, platelet count returns to normal within five to ten days of start of anti-malarial treatment and nlatelet transfusion is not required.