Overlapping neurological phenotypes in two extended consanguineous families with novel variants in the CNTNAP1 and ADGRG1 genes.

BACKGROUND: Population diversity is important and rare disease isolates can frequently reveal novel homozygous or biallelic mutations that lead to expanded clinical heterogeneity, with diverse clinical presentations. METHODS: The present study describes two consanguineous families with a total of seven affected individuals suffering from a clinically similar severe syndromic neurological disorder, with abnormal development and central nervous system (CNS) and peripheral nervous system (PNS) abnormalities. Whole exome sequencing (WES) and Sanger sequencing followed by 3D protein modeling was performed to identify the disease-causing gene. RNA was extracted from the fresh blood of both families affected and healthy individuals. RESULTS: The families were clinically assessed in the field in different regions of Khyber Pakhtunkhwa. Magnetic resonance imagining was obtained in the probands and blood was collected for DNA extraction and WES was performed. Sanger sequencing confirmed a homozygous, likely pathogenic mutation (GRCh38: chr17:42684199G>C; (NM_003632.3): c.333G>C);(NP_003623.1): p.(Trp111Cys) in the CNTNAP1 gene in family A, previously associated with Congenital Hypo myelinating Neuropathy 3 (CHN3; OMIM # 618186) and a novel nonsense variant in family B, (GRCh38: chr16: 57654086C>T; NC_000016.10 (NM_001370440.1): c.721C>T); (NP_001357369.1): p.(Gln241Ter) in the ADGRG1 gene previously associated with bilateral frontoparietal polymicrogyria (OMIM # 606854); both families have extended CNS and PNS clinical manifestations. In addition, 3D protein modeling was performed for the missense variant, p.(Trp111Cys), identified in the CNTNAP1, suggesting extensive secondary structure changes that might lead to improper function or downstream signaling. No RNA expression was observed in both families affected and healthy individuals hence showing that these genes are not expressed in blood. CONCLUSIONS: In the present study, two novel biallelic variants in the CNTNAP1 and ADGRG1 genes in two different consanguineous families with a clinical overlap in the phenotype were identified. Thus, the clinical and mutation spectrum is expanded to provide further evidence that CNTNAP1 and ADGRG1 are very important for widespread neurological development.

Health care associated Clostridioides difficile infection and colonization in patients admitted at tertiary care hospital Pakistan.

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.

Antimicrobial susceptibility pattern and genotypic characterisation of quinolone and ceftriaxone resistant genes among Salmonella typhi from various regions of Pakistan.

OBJECTIVE: To determine the current antibiotic resistance patterns and identification of quinolone and ceftriaxone resistant genes among Salmonella enterica subspecies serovar Typhi. METHODS: The prospective study was conducted from September 2018 to March 2019 and comprised samples collected from major hospitals and laboratories in Karachi, Quetta, Lahore, Kharia, Rawalpindi, Islamabad and Peshawar after approval from the institutional ethics review board of Hazara University, Mansehra, Pakistan. Antimicrobial susceptibility of isolates collected from the health facilities was checked using the Kirby Bauer disc diffusion method in line with the Clinical and Laboratory Standards Institute guidelines at the Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, Pakistan. All isolates were subjected for identification of genes responsible for quinolone and ceftriaxone resistance using polymerase chain reaction followed by gel-electrophoresis. RESULTS: Among the 96 isolates, phenotypically, ceftriaxone was found resistant in 31(32.29%) and ciprofloxacin in 95(99%). Genotypically, blaCTX-M-15 (beta lactamase, CTX as its acronym, -M from Munich) gene for ceftriaxone resistance was found in all phenotypically resistant 31(32.29%) isolates, while QnrS (Quinolone resistance, S group), GyrA (DNA gyrase subunit A), and GyrB (DNA gyrase subunit B) genes responsible for ciprofloxacin resistance were found in different frequencies (percentages given in table 2). CONCLUSIONS: The spread of extensively drug-resistant Salmonella enterica subspecies serovar Typhi strain to many big cities calls for urgent preventive measures.

Divergent synthesis and elaboration of structure activity relationship for quinoline derivatives as highly selective NTPDase inhibitor.

Quinoline derivatives have interesting biological profile. In continuation for the comprehensive evaluations of substituted quinoline derivatives against human nucleoside triphosphate diphosphohydrolases (h-NTPDases) a series of substituted quinoline derivatives (2a-g, 3a-f, 4, 5a-c, 6) was synthesized. The inhibitory activities of the synthesized compounds were evaluated against four isoenzymes of human nucleoside triphosphate diphosphohydrolases (h-NTPDases). These quinoline derivatives had IC50 (µM) values in the range of 0.20-1.75, 0.77-2.20, 0.36-5.50 and 0.90-1.82 for NTPDase1, NTPDase2, NTPDase3 and NTPDase8, respectively. The derivative 3f was the most active compound against NTPDase1 (IC50, 0.20 ± 0.02 µM) that also possessed selectivity towards NTPDase1. Similarly, derivative 3b (IC50, 0.77 ± 0.06), 2h (IC50, 0.36 ± 0.01) and 2c (IC50, 0.90 ± 0.08) displayed excellent activity corresponding to NTPDase2, NTPDase3 and NTPdase8. The compound 5c emerged as a selective inhibitor of NTPDase8. The most active compounds were then investigated to determine their mode of inhibition and finally binding interactions of the active compounds were analyzed through molecular docking studies. The obtained results strongly support the quinoline scaffold's potential as potent and selective NTPDase inhibitor.

Comparison evaluation between gene Xpert Mtb/Rif and multiplex PCR for rapid diagnosis of mycobacterium tuberculosis.

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.

Evaluation of rapid polymyxin Nordmann Poirel test for detection of polymyxin resistance in clinical isolates of Enterobacteriaceae.

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.

Evaluation of direct drug susceptibility testing of blood culture isolates comparing it with conventional disk diffusion testing.

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.

Evaluation of galactomannan and beta-d-glucan assays for the diagnosis of invasive aspergillosis in clinically suspected cases.

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.

Catheter related recurrent blood stream infection caused by linezolid-resistant, methicillin resistant Staphylococcus haemolyticus; an emerging super bug.

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.

Pattern of Blood Stream Infections and their antibiotic susceptibility profile in a Neonatal intensive care unit of a tertiary care hospital; a current perspective.

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 .

The genetic cause of neurodevelopmental disorders in 30 consanguineous families.

Objective: This study aims to clinically and genetically assess 30 unrelated consanguineous Pakistani families from various ethnic backgrounds, all exhibiting features of neurodevelopmental disorders (NDDs). Methods: We conducted clinical, genetic, biochemical, and molecular analyses on 30 consanguineous families with NDDs enrolled from various regions of Pakistan. The likely molecular causes of primary microcephaly and NDDs were identified. Detailed clinical investigations and molecular diagnoses were performed using whole exome sequencing (WES) of the proband, followed by Sanger sequencing for validation and segregation in the available family members of the affected families. Results: WES identified likely disease-causing homozygous variants in 30 unrelated consanguineous families. Six families presented newly described variants in known NDD-related genes: ABAT (c.1439 T > G; p.Phe480Cys) [OMIM613163], SLC12A6 (c.2865_2865insT; p.Glu955Asnfs*5) [OMIM 218000], SHANK3 (c.1305-3_1,305-2delTT; p.Gln29-_Gly305del) [OMIM 606232], BCKDK (c.356_356insC; p.Gly119Alafs*24) [OMIM 614923], DDHD2 (c.2065G > T; p.Asp689Tyr) [OMIM 615033], ERCC2 (c.1255G > A; p.Glu419Lys) [OMIM 610756]. Additionally, 12 families had previously reported disease-causing variants associated with different types of NDDs: ATRX (c.109C > T; p.Arg37*) [OMIM 309580], GPR56 [ADGRG1] (c.1423C > T; p.Arg475*) [OMIM 606854], NAGLU (c.1694G > A; p.Arg565Gln) [OMIM 252920], DOLK (c.3G > A; p.Met1Ile) [OMIM 610768], GPT2 (c.815C > T; p.Ser272Leu) [OMIM 616281], DYNC1I2 (c.607 + 1G > A; p.?) [OMIM 618492], FBXL3 (c.885delT; p.Leu295Phefs25*) [OMIM 606220], LINGO1 (c.869G > A; p.Arg290His) [OMIM 618103], and ASPM (c.3978G > A; Trp1326*, c.9557C > G; p.Ser3186*, c.6994C > T; p.Arg2332*) [OMIM 608716]. All the identified variants showed segregation compatible with autosomal recessive inheritance. Conclusion: In the present study, we observed a high frequency of ASPM variants in the genetic analysis of 30 consanguineous families exhibiting features of NDDs, particularly those associated with autosomal recessive primary microcephaly. These findings contribute to studies on genotype-phenotype correlation, genetic counseling for families, and a deeper understanding of human brain function and development.

Prevalence and Association of Transfusion-Transmissible Infections with Age of Blood Donors: A Regional Transfusion Centre Study in Northern Pakistan.

OBJECTIVE: To evaluate the prevalence and association of Transfusion-Transmissible Infections (TTIs) with age of blood donors in a regional transfusion centre located in Northern Pakistan. STUDY DESIGN: Descriptive study. Place and Duration of the Study: Armed Forces Institute of Transfusion, Rawalpindi, Pakistan, from January 2017 to December 2021. METHODOLOGY: All blood donors who qualified institutional blood donation criteria were initially screened for HBsAg, Anti-HCV Ab, HIV antigen-antibody combination and syphilis by an automated chemiluminescent microparticle immunoassay analyzer (Architect Plus i 2000 SR, Abbott Diagnostics, Abbott Park, IL). Initially, all seronegative donor blood samples were subjected to nucleic acid amplification test (NAAT). All TTI-positive donors were immediately informed and counselled to consult the medical physicians for further treatment. Descriptive statistics and significance of association were determined. RESULTS: The prevalence of TTIs among blood donors was calculated to be 3.33% among 308,767 donors. HCV (1.4%) was the most prevalent TTI followed by syphilis (0.9%), HBV (0.68%) and HIV (0.26%), respectively. TTIs were most prevalent in the 26 to 35-year-old group, accounting for 5,143 (50.0%) positive donors (p<0.05). CONCLUSION: The prevalence of TTIs among blood donors was found to be 3.33%. HCV was the most common TTI, followed by syphilis, HBV, and HIV. The 26 to 35 year-old group had a significantly high prevalence of TTIs. KEY WORDS: Transfusion-transmissible infections, Hepatitis B virus, Hepatitis C virus, Human immunodeficiency virus, Treponema pallidum, Syphilis, Automated chemiluminescent microparticle immunoassay analyzer, Nucleic acid amplification test.

Synthesis of Thieno[3,2-d]pyrimidine Derivatives through Sequential SN Ar and Suzuki Reactions as Selective h-NTPDase Inhibitors.

In this study various of thieno[3,2-d]pyrimidine derivatives have been synthesized by treating different secondary amines through aromatic nucleophilic substitution reaction (SN Ar) followed by Suzuki reaction with aryl and heteroaryl boronic acids. A bis-Suzuki coupling was also performed to generate bis-aryl thienopyrimidine derivatives. The synthesized compounds were screened for the hydrolytic activity of h-NTPdase1, h-NTPdase2, h-NTPdase3, and h-NTPdase8. The compound N-benzyl-N-methyl-7-phenylthieno[3,2-d]pyrimidin-4-amine 3 j selectively inhibits the activity of h-NTPdase1 with IC50 value of 0.62±0.02 µM whereas, the compound 4 d was the most potent inhibitor of h-NTPdase2 with sub-micromolar IC50 value of 0.33±0.09 µM. Similarly, compounds 4 c and 3 b were found to be selective inhibitors for isozymes h-NTPdase3 (IC50 =0.13±0.06 µM) and h-NTPdase8 (IC50 =0.32±0.10 µM), respectively. The molecular docking study of the compounds with the highest potency and selectivity revealed the interactions with the important amino acid residues.

Loss-of-function variant in the LRR domain of SLITRK2 implicated in a neurodevelopmental disorder.

Background: Neurodevelopmental disorders are characterized by different combinations of intellectual disability (ID), communication and social skills deficits, and delays in achieving motor or language milestones. SLITRK2 is a postsynaptic cell-adhesion molecule that promotes neurite outgrowth and excitatory synapse development. Methods and Results: In the present study, we investigated a single patient segregating Neurodevelopmental disorder. SLITRK2 associated significant neuropsychological issues inherited in a rare X-linked fashion have recently been reported. Whole-exome sequencing and data analysis revealed a novel nonsense variant [c.789T>A; p.(Cys263*); NM_032539.5; NP_115928.1] in exon 5 of the SLITRK2 gene (MIM# 300561). Three-dimensional protein modeling revealed substantial changes in the mutated SLITRK2 protein, which might lead to nonsense-medicated decay. Conclusion: This study confirms the role of SLITRK2 in neuronal development and highlights the importance of including the SLITRK2 gene in the screening of individuals presenting neurodevelopmental disorders.

Salmonella Typhi from Northwest Pakistan: Molecular Strain Typing and Drug Resistance Signature.

Objective: To determine the molecular strain typing and drug resistance pattern of Salmonella enterica serovar Typhi prevalent in Northwest Pakistan. Methodology: A total of 2,138 blood samples of suspected typhoid patients from Northwest Pakistan were collected followed by identification of Salmonella Typhi through biochemical, serological, and species-specific fliC-d gene amplification. These isolates were typed by variable-number tandem repeat (VNTR) profiling and investigated for drug resistance. Results: The overall prevalence of Salmonella Typhi was found to be 8.8% (n = 189). Thirty different VNTR strain types of Salmonella Typhi were detected and the most prevalent strain types were T1 and T4, whereas T27 was less prevalent strain. Among the 189 isolates 175 (92.5%) isolates were multidrug resistant, whereas 12 (5.8%) isolates were extensively drug resistant. Resistance to imipenem in Salmonella Typhi was not observed. Most of the isolates have genes encoding for resistance to fluoroquinolones, including gyrA (n = 164), gyrB (n = 160), parC (n = 164), parE (n = 160), ac(6')-ib-cr (n = 163), qnrS (n = 15), and qnrB (n = 3). Similarly, chloramphinicol (cat; n = 147), azithromycin (msrA; n = 3), and co-trimoxazole (dfrA7; n = 145) resistance genes were detected among Salmonella Typhi isolates. Conclusion: In this study, T1 and T4 type Salmonella Typhi strains were predominantly prevalent in Northwest Pakistan. Antibiotic resistance among Salmonella Typhi isolates were observed. Findings of the study would be helpful to devise an appropriate antibiotic policy to control the emergence of drug-resistant Salmonella Typhi in Pakistan.

Frequency And Clinical Spectrum Of Multidrug Resistant Acinetobacter Baumannii As A Significant Nosocomial Pathogen In Intensive Care Unit Patients.

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.

Evaluation of Thin Layer Agar 7H11 for Direct Susceptibility Testing of Mycobacterium Tuberculosis Complex against Second Line Anti Tuberculosis Drugs on Smear Positive Specimens.

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.

Multiplex PCR for Rapid Diagnosis of Drug Resistant Mycobacterium Tuberculosis.

OBJECTIVE: To evaluate a multiplex PCR for rapid diagnosis of drug resistant mycobacterium tuberculosis (MTB) strain. STUDY DESIGN: Cross-sectional observational study. PLACE AND DURATION OF STUDY: Department of Microbiology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from January to September 2018. METHODOLOGY: Over a period of 8 months, a total of 84 cultured positive samples were included in the study using nonprobability sampling techniques. MTB isolates were phenotypically characterised using MGIT 960 system for antituberculosis agents including rifampicin (RIF), isoniazid (INH), ethambutol (EMB) and Streptomycin. The DNA was extracted using Gentra system DNA extraction kit. The multiplex PCR was optimised for genetic characterisation of MTB samples for rpo B (rifampicin), kat G (isoniazid) and emb B (ethambutol) gene. The gel electrophoresis was performed to observe comparative banding pattern of amplified gene products. RESULTS: For detecting drug resistance, the specificity and sensitivity of multiplex PCR in isolates was 100% and 100% for rifampicin, 100% and 71% for isoniazid, and 100% and 60% for ethambutol, respectively. When compared to phenotypically resistance results, the positive predictive value (PPV) was 100% each and the negative predictive value (NPV) was calculated to be 100%, 74% and 71% for RIF, INH and EMB, respectively. CONCLUSION: Multiplex PCR is a useful gadget for quick determination of drug-resistant TB in specimens, hence permitting an initial therapeutic approach. However, for accurate management of patients, phenotypic method should be used to confirm results.

Cerebral Abscess caused by Novel Species: Streptococcus Pluranimalium.

Streptococcus pluranimalium, a gram-positive aerobic coccus, has been isolated primarily from several farm animals. The pathogenicity of this species is not well characterised either in animals or humans. As per the literature, cases of S. pluranimalium infection in humans have been reported only a handful of times. We report the case of cerebral abscess caused by S. pluranimalium in a patient who presented with weakness and confusion. The diagnosis of cerebral abscess was made on imaging supported by microbiological culture. Burr hole procedure for abscess drainage followed by an antibiotic regimen based on culture and sensitivity results contributed to a successful outcome. The bacteria were identified by analytical profile index for Streptococci (API Strep) and VITEK 2 gram-positive cocci panel. The case was successfully treated with vancomycin.

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.