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Introduction: The increasing frequency and antibiotic resistance among extended-spectrum β-lactamases (ESBLs)-producing bacteria are posing a serious threat. This study sought to investigate the frequency and antibiotic susceptibility of ESBL-producing E. coli and K. pneumoniae at a tertiary care hospital. Methodology: Data were collected from samples sent to the microbiology laboratory between 2006 and 2010 at King Khalid University Hospital, Riyadh. ESBLs were confirmed using Etest strips of cefotaxime/cefotaxime + clavulanic acid, ceftazidime/ceftazidime + clavulanic acid, and cefepime/cefepime + clavulanate. Results: Out of 17,105 samples, 1,076 (6.3%) ESBL-producing isolates of E. coli (808) and K. pneumoniae (268) were confirmed. Among these, 680 (63.2%) isolates were found in urine samples, followed by 287 (26.7%) in superficial swabs, deep wounds swabs, tissues and sterile body fluids, 71 (6.6%) in respiratory, and 38 (3.5%) in blood samples. The overall frequency rates of ESBL E. coli and K. pneumoniae were 6.6% and 5.5%, respectively. The frequency of ESBL-producing E. coli and K. pneumoniae increased significantly during the study period. E. coli resistance against cotrimoxazole was 71.1%, followed by ciprofloxacin (68.2%) and gentamicin (47%). Similarly, 62.7% of K. pneumoniae isolates were resistant to gentamicin, 59.5% to cotrimoxazole, and 49.8% to ciprofloxacin. There was no statistically significant change in antimicrobial resistance over the study period. Conclusions: Although the frequency rates of ESBL-producing E. coli and K. pneumoniae increased, no change in the anti-microbial susceptibility was observed over the study period.

Objectives: To assess the performance of Xpert MTB/RIF, an automated molecular test for Mycobacterium tuberculosis (MTB) and resistance to rifampin (RIF), against smear microscopy and culture method for diagnosis of MTB infection. Methods: This is a retrospective analysis of 103 respiratory and 137 non-respiratory patient specimens suspected of tuberculosis at King Khalid University Hospital, Riyadh, Kingdom of Saudi Arabia performed between April 2014 and March 2015. Each sample underwent smear microscopy, mycobacterial culture, and GeneXpert MTB/RIF test. Results: Fifteen out of 103 respiratory samples were smear and culture positive, whereas 9 out of 137 non-respiratory samples were smear positive. Out of 9 smear positive specimens, 8 were also culture positive. All 15 culture positive respiratory samples were detected by Xpert MTB/RIF (sensitivity and positive predictive value [PPV]=100%). Similarly, all 8 culture positive non-respiratory specimens were identified by Xpert MTB/RIF (sensitivity 100%; PPV 88.8%). The Xpert MTB/RIF detected only one false positive result in 88 smear negative respiratory specimens (specificity 98.9%; negative predictive value [NPV]= 100%). All 125 smear negative non-respiratory specimens tested negative by culture and Xpert MTB/RIF (sensitivity, specificity, PPV, NPV= 100%). Conclusion: The performance of Xpert MTB/RIF was comparable to the gold standard culture method for identification of MTB in both respiratory and non-respiratory clinical specimens. Saudi Med J 2016; Vol. 37 (12): 1404-1407 doi: 10.15537/smj.2016.12.15506

Objectives Early detection of Mycobacterial tuberculosis infection (MTB) is pivotal for the treatment of tuberculosis (TB). Background This study was performed to evaluate the performance of BD ProbeTec ET direct detection assay (DTB) against the gold standard culture technique for confirmation of MTB infection. Methods A total of 266 consecutive and non-duplicate clinical specimens for detection of MTB were included in this study. There were 118 respiratory and 148 non-respiratory samples. All samples were tested by microscopy for acid-fast bacillus (AFB), MTB culture and biochemical identification with simultaneous testing by DTB. Results A total of 88 samples (33%) were culture-positive for MTB including 39/118 respiratory, 29/99 fluid and 20/49 tissue samples. DTB sensitivity for respiratory samples was 97% and specificity was 96% with a positive predictive value (PPV) of 93% and negative predictive value (NPV) of 99%. Sensitivity of DTB in fluid samples was 80%, specificity 88%, PPV 69% and NPV 93% whereas sensitivity of DTB for tissue samples was 25%, specificity 90%, PPV 63% and NPV 63%. Of the 50 (56.8%) smear-positive samples, DTB sensitivity was 100% for respiratory, 85% for fluid and 100% for tissue samples. Conclusion DTB performed within acceptable limits for the rapid detection of MTB in respiratory samples compared to fluid and tissue specimens.

BACKGROUND AND OBJECTIVES: A new test (Dr. KSU H1N1 RT-PCR kit) was recently developed to provide a less expensive alternative to real-time reverse transcriptase-polymerase chain reaction (RT-PCR). We report the findings of a validation study designed to assess the diagnostic accuracy, including sensitivity and specificity, of the new kit, as compared to real-time RT-PCR. DESIGN AND SETTING: Cross-sectional validation study conducted from 18-22 November 2009 at a primary care clinic for H1N1 at a tertiary care teaching hospital in Riyadh. PATIENTS AND METHODS: Nasopharyngeal swab samples and data on socio-demographic characteristics and symptoms were collected from 186 patients. Swab samples were sent to the laboratory for testing with both real-time RT-PCR and the new Dr. KSU H1N1 RT-PCR kit. We measured the sensitivity and specificity of the new test across the entire sample size and investigated how these values were affected by patient socio-demographic characteristics and symptoms. RESULTS: The outcomes of the two tests were highly correlated (kappa=0.85; P

To study the laboratory diagnosis of tuberculosis (TB), and relate the findings to its epidemiology in Central Saudi Arabia.This retrospective study was carried out at the Department of Pathology/Microbiology, King Khalid University Hospital, Riyadh, Kingdom of Saudi Arabia between January 2003 and December 2010. Data were retrieved from the hospital information system on laboratory findings. After adjustment, 9,405 specimens were studied. The specimens were stained by Ziehl-Neelsen (ZN), auramine-rhodamine, and cultured in Bactec alert 960, and Lowenstein-Jensen media. Mycobacterium tuberculosis (M. tuberculosis) complex and non-tuberculous mycobacteria were differentiated by ProbTec system and p-nitrobenzoate medium. The BACTEC MGIT 960 SIRE kit was used for susceptibility testing.A total of 568 (6%) specimens grew M. tuberculosis complex, and 87% were from Saudis with an incidence rate of 55.6/100,000 of TB. Time to positive growth in the Bactec liquid medium was directly related to the acid fast bacilli smear load. Most of the positive patients were from the 18-35 years age group. The percentage of multidrug resistance was 0.7%.Most patients (87%) were Saudis showing an incident rate of 55.6/100,000. An increase of TB cases was noticed in the 18-35 age group. Resistance to isoniazid was 10.6%, 1% to Rifampicin, 2-8% to Ethambutol, and streptomycin was 6%.

To evaluate the role of the rapid influenza diagnostic test (RIDT) and clinical decision in the diagnosis of H1N1.In November 2009, 290 suspected influenza patients were examined for H1N1 during an outbreak in Riyadh, Saudi Arabia. Nasopharyngeal swabs were analyzed using Directigen EZ Flu A+B kit. Monoclonal anti-human influenza A/B and reverse transcription- polymerase chain reaction (RT-PCR) were used. Positive and negative controls were used in each run of specimens. Validity indices were calculated for RIDT and clinical diagnostic criteria.The sensitivity and specificity of RIDT were 40.5% (95% confidence interval [CI]: 33.0-48.5), and 94.5% (95% CI: 88.6-97.6). The sensitivity of clinical decision was 66.3% (95% CI: 58.4-73.4), and the specificity was 65.4% (95% CI: 56.3-73.4). The sensitivity of clinical decision was higher in early presenters (79.2%; 95% CI: 57.3-92.1). The RIDT sensitivity was higher in younger patients (48.4%; 95% CI: 35.7-61.3). The positive predictive value (PPV) was 90.4% (95% CI: 80.7-95.7) for RIDT, and 71.1% (95% CI: 63.1-78.0) for clinical decision. The PPV for RIDT was greater for older (94.7%; 95% CI: 80.9-99.1) and late (90.7%; 95% CI: 76.9-97.0) presenters. The adjusted odds ratio for clinical decision was significant for cough, headache, and fatigue.The RIDT can be useful in epidemics and high prevalence areas, whereas clinical decision, and RT-PCR complement the diagnosis of H1N1 in any setting.

In this prospective study, we determined phenotypic resistance to erythromycin among gram positive bacteria.BACTERIAL ISOLATES WERE IDENTIFIED BY CONVENTIONAL METHODS AND BY THE MICROSCAN: D-test zone was performed according to the Clinical and Laboratory Standards institutes (CLSI) recommendations to determine inducible resistance to clindamycin on gram positive bacteria isolated from different clinical specimens. Bacterial isolates included : group A streptococci (GAS), group B streptococci (GBS), viridans streptococci, S.pneumoniae, Staphylococcus aureus (S.aureus) (both methicillin susceptible (MSSA) and methicillin resistant (MRSA).A total of 1072 gram positive bacterial isolates were tested. The majority was from swabs collected from outpatient clinics. Erythromycin resistance was 8/23 (35%) for S. pneumoniae, 12/91(13%) for GAS and 17/300(5.7%) for GBS. All GAS and viridans streptococci possessed the efflux phenotype only, 8(8.8% and 1(20%), respectively. For GBS, cMLS(B) was 11(3.7%), 3 (1%) iMLS(B) and 2(0.33%) were of efflux phenotype. All S.pneumoniae strains possessed cMLS(B) phenotype. Seventy five isolates (16.3%) of MSSA were resistant to erythromycin compared to 160(83%) of MRSA. The majority of MSSA, 31/460 (6.7%) had an efflux phenotype while 26/460(5.6%) were of cMLS(B) and 19/460(4%) iMLS(B) phenotypes. Constitutive MLS(B) was the most predominant resistant phenotype, 152/193(78.8%) among MRSA.D-test zone should be considered for routine testing to detect inducible clindamycin resistance among significant gram positive bacteria.

Introduction: Resistance of Salmonella to therapeutic agents currently being used for treatment of Salmonella infections is emerging as a global problem. This study aimed to assess the prevalence of Salmonella serotypes and their susceptibility patterns to commonly used drugs for treatment of Salmonella infections including quinolones. Correlation between nalidixic acid susceptibility of these isolates and their ciprofloxacin minimum inhibitory concentrations was also sought. Methodology; Salmonella isolates (n=213) were collected between January 2007 and May 2009 at King Khalid University Hospital in Riyadh, Saudi Arabia. The isolates were serotyped and their susceptibilities to commonly used first-line anti-Salmonella drugs (ampicillin, ceftriaxone, trimethoprim/sulfamethoxazole, nalidixic acid and ciprofloxacin) were determined using the automated Microscan system, the Kirby-Bauer disk diffusion method, and E-test. Results: The most frequently detected serotype was D1 (37%) followed by the serotypes, B (24%) and C1 (11%). Non-typable Salmonella isolates detected using available conventional Salmonella anti-sera were (11%). Overall resistance rates to nalidixic acid, ampicillin, trimethoprim/sulfamethoxazole and ceftriaxone were 99/213 (46%), 43/213 (20%), 34/213 (16%) and 7/213 (3%), respectively. Of the total isolates, 117 (55%) had a ciprofloxacin MIC of < 0.125 µg/ml and among these 105 (90%) were susceptible to nalidixic acid. The remaining 96 (45%) isolates had a ciprofloxacin MIC of ≥ 0.125 µg/ml and among them, 83 (86.5%) were resistant to nalidixic acid. Conclusions: The majority of Salmonella isolates in this study were non-typhi serotypes. Significantly higher proportions of Salmonellae were resistant to nalidixic acid and ciprofloxacin and a vast majority of nalidixic acid resistant organisms exhibited decreased susceptibility to ciprofloxacin.

Antimicrobial resistance to nine anti-pseudomonal agents (azteronam, ceftazidime, cefepime, piperacillin/tazobactam, imipenem, meropenem, ciprofloxacin, amikacin and gentamicin), the magnitude of multidrug resistance, associated underlying conditions, and mortality among patients with Pseudomonas aeruginosa isolates from King Khalid University Hospital, Riyadh, Saudi Arabia from 2001 to 2005 were determined. The results showed that antimicrobial resistance among P. aeruginosa is gradually increasing for most anti-pseudomonal agents, particularly aztreonam, ceftazidime, piperacillin/tazobactam and imipenem. There were 19 (3%) and 12 (2%) multidrug-resistant (MDR) P. aeruginosa patients in 2004 and 2005, respectively, and MDR P. aeruginosa was more commonly found in non-intensive care unit (ICU) patients. Most MDR isolates were from surgical and diabetic patients. The mortality rate was higher among ICU patients.

Background Rickets can occur due to Vitamin D deficiency or defects in its metabolism. Three rare genetic types of rickets with different alterations of genes have been reported, including: Vitamin D dependent rickets type 1, Vitamin D dependent rickets type 2 or also known as Vitamin D resistant rickets and 25 hydroxylase deficiency rickets. Vitamin D dependent rickets type 1 is inherited in an autosomal recessive pattern, and is caused by mutations in the CYP27B1 gene encoding the 1α-hydroxylase enzyme. We report here a new mutation in CYP27B1, which lead to Vitamin D dependent rickets type 1. Case presentation We report on a 13-month-old Arabic Saudi girl with Vitamin D dependent rickets type 1 presented with multiple fractures and classic features of rickets. A whole exome sequencing identified a novel pathogenic missense mutation (CYP27B1:Homozygous c.1510C > T(p.Q504X)) which results in a protein truncating alteration. Both parents are heterozygous carriers of the mutation. Based on data search in Human Gene Mutation Database, 63 CYP27B1 alterations were reported: only 28.6% are protein truncating (5 nonsense, 13 frameshift insertions/deletions, 0 gross deletions), while 61.9% are non-truncating (38 missense, 1 small in-frame insertions/deletion), and 9.5% are possible protein-truncating (5 splice, 1 regulatory). Conclusion The deleterious effect of this alteration, which was the only mutation detected in the CYP27B1 common gene of Vitamin D dependent rickets type 1 in the proband, and its autosomal recessive inheritance fashion, both support a pathogenic nature of this mutation as the cause of Vitamin D dependent rickets type 1.