Performance of the BD ProbeTec ET direct detection assay for the analysis of Mycobacterium tuberculosis in respiratory and non-respiratory clinical specimens.

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.

Evaluation of GeneXpert MTB/RIF for detection of Mycobacterium tuberculosis complex and rpo B gene in respiratory and non-respiratory clinical specimens at a tertiary care teaching hospital in Saudi Arabia.

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.

ESBL-producing Escherichia coli and Klebsiella pneumoniae at a tertiary care hospital in Saudi Arabia.

INTRODUCTION: The increasing frequency and antibiotic resistance among extended-spectrum ß-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.

Changing epidemiology of tuberculosis detected by an 8-year retrospective laboratory study in a tertiary teaching hospital in central Saudi Arabia.

OBJECTIVE: To study the laboratory diagnosis of tuberculosis (TB), and relate the findings to its epidemiology in Central Saudi Arabia. METHODS: 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. RESULTS: 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%. CONCLUSION: 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%.

The role of rapid testing and clinical decision in the diagnosis of human influenza A H1N1 infection.

OBJECTIVE: To evaluate the role of the rapid influenza diagnostic test (RIDT) and clinical decision in the diagnosis of H1N1. METHODS: 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. RESULTS: 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. CONCLUSION: 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.

A validation study comparing the sensitivity and specificity of the new Dr. KSU H1N1 RT-PCR kit with real-time RT-PCR for diagnosing influenza A (H1N1).

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<.0001). The sensitivity and specificity of the new test were 99.11% and 83.78%, respectively. The sensitivity of the new test was affected only minimally (96%-100%) by patient characteristics and number of symptoms. On the other hand, the specificity of the new test varied depending on how soon patients were tested after onset of symptoms (100% specificity when swabs were taken on the first day of the symptoms, decreasing to 75% when swabs were taken on or after the third day). The specificity of the new test also increased with increasing body temperature. CONCLUSION: The new test seems to provide a cost-effective alternative to real-time RT-PCR for diagnosing H1N1 influenza. However, further testing may be needed to verify the efficacy of the test in different settings and communities.