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Additional file 1: Table S1. Eligibility criteria for the present systematic review. Table S2. Strategy for database search (up to September 1st, 2019). Table S3. Studies excluded during full-text eligibility assessment with reasons.

Background There is limited data on the beneficial effects of probiotics on the gingival health of patients undergoing treatment with fixed orthodontic appliances. This study aims to compare the effect of probiotic tablets combined with regular oral hygiene versus regular oral hygiene alone on gingival status in these patients. The effect of probiotic intake on plaque formation and salivary microbiome composition will be also assessed. Methods and analysis This is a 3 month single-centre, single blind (clinical and laboratory examiners), parallel group randomised controlled two arm superiority trial. Fifty paediatric patients attending the Postgraduate Orthodontic Clinic at the Hamdan Bin Mohammed College of Dental Medicine (HBMCDM), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai, United Arab Emirates, who meet the eligibility criteria will be recruited. Block randomisation with 1:1 allocation and concealment of allocation will be carried out. The treatment group will receive probiotic tablets containing Streptococcus salivarius M18 and Lactobacillus acidophilus together with regular oral hygiene versus the control group on regular oral hygiene alone. Clinical examination and collection of saliva for microbiome assay will be carried out at baseline and end of study. Self-reporting by patients will be used to document acceptability and adverse effects. Statistically significant decrease in gingival bleeding on probing in the treatment group will be classified as primary outcome of treatment success. Statistically significant reduction in Plaque Index, Gingival Index and shift in the composition of the oral microbiome in favour of beneficial bacteria are secondary outcomes indicative of efficacy of probiotic intake. Ethics and dissemination Ethical approval for the study has been granted by the HBMCDM, MBRU, Institutional Review Board (Reference #: MBRU-IRB-2018–015). Study findings will be disseminated via publication in peer-reviewed journal. Trial registration number ISRCTN95085398

Purpose Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain. Methods Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer. Results All the CC15-MRSA isolates had the multilocus sequence typing profile ST1535, 13–13-1–1-81-11-13, which is a single locus variant of ST15. Of the 6 contigs related to the SCC element, one comprised a recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC element had 5 transposase genes, namely 3 identical paralogs of tnpIS431 and 2 identical paralogs of tnpIS256. Two identical copies of a tnpIS256-based insertion element flank the aacA-aphD gene. Two copies of this insertion element were present with 1 located in the SCC element and another inserted into the sasC gene. A short 3 kb region, which lacks any bacteriophage structural genes and site-specific DNA integrase, was inserted into the hlb gene. The hsdM and the 5’-part of the hsdS gene are replaced by a copy of the hsdM/hsdS paralogs from νSaβ giving rise to a new chimeric paralog of hsdS in νSaα. Conclusion CC15-MRSA shows a novel SCCmecV/SCCfus composite element. Its variant of hsdM/hsdS probably facilitated uptake of foreign mobile genetic elements that promoted emergence of CC15-MRSA. Close surveillance is needed to monitor spread and emergence of further CC15 MRSA strains.

Background/Aims: Accurate and rapid laboratory diagnosis of Clostridium difficile infections (CDI) remains a significant challenge. A two-step algorithm for detection of toxigenic C. difficile in stool based on initial screening for glutamate dehydrogenase assay followed by confirmation by toxin A+B detection using an enzyme immunoassay (EIA) or molecular assay has been proposed. We aimed to evaluate the C. difficile Quik Chek Complete® (QCC-EIA) versus the GeneXpert® C. difficile polymerase chain reaction (PCR) assay in this two-step algorithm. Materials and Methods: Two hundred and ten liquid stool samples obtained between June 2014 and June 2015 from patients suspected of CDI were tested by the QCC-EIA and GeneXpert PCR assay. The GeneXpert assay was used as the reference standard to calculate the QCC-EIA sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Results: Of the 210 stool samples tested, 43 (20.5%) were positive by QCC-EIA, while 31 (14.8%) were positive by GeneXpert assay. The sensitivity and specificity of the QCC-EIA were found to be 100 and 93%, respectively; the PPV and NPV were 72 and 100%, respectively. The binary toxin was detected in 12 (38.7%) and tcdC gene deletion in 3 (9.6%). Conclusions: The low specificity of QCC-EIA makes it less reliable as a confirmatory test for CDI diagnosis. This test may be used as a screening test in a two-step algorithm when combined with a molecular assay or another confirmatory test.

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

To determine the molecular characterization of extended-spectrum beta-lactamases (ESBL) isolates from a tertiary center in Saudi Arabia using multiplex polymerase chain reaction (PCR) technique and assess their antibiotic susceptibility pattern.Prospective study conducted at the Saudi Aramco Dhahran Health Center, Dhahran, Saudi Arabia between April-December 2006. Extended-spectrum beta-lactamases phenotype of isolates identified by automated methods was confirmed using E-test. Multiplex PCR for the detection of blaTEM, blaSHV and blaCTX-M was performed. Susceptibility to a panel of antibiotics was determined.One hundred isolates (Escherichia coli [E.coli] n=84; Klebsiella pneumoniae [K. pneumoniae] n=16) were studied and 71% harbored the blaCTX-M gene. For E.coli isolates 43 (51%) harbored CTX-M+TEM combination and 21 (25%) had CTX-M alone. In contrast, only one K. pneumoniae isolate (6.2%) harbored the CTX-M+TEM combination and 3 (18.8%) isolates had CTX-M only. One E.coli and 7 K. pneumoniae isolates were blaSHV positive. The blaCTX-M gene was found predominantly in urinary isolates (n=63/71; 88.7%). The presence of blaCTX-M was significantly higher in isolates from outpatients compared to inpatient (p0.05). Sensitivity to imipenem was 100% and 78% to nitrofurantoin. Resistance to amoxicillin-sulbactam was significantly higher in blaCTX-M positive isolates (p0.05).The findings indicate a high-level of blaCTX-M positive ESBL isolates circulating in our setting with the dissemination of these in the community. The trend of multidrug resistance profile associated with carriage of blaCTX-M gene is cause for concern.

To investigate the occurrence of human papillomavirus (HPV) infection and the associated risk factors in Bahrain's female population.This study was carried out between March to December 2004, which includes cervical scrapings for Pap smear and HPV-DNA testing using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis, obtained from 100 women attending the Gynecology Clinic at Salmaniya Medical Center and Sheikh Sabah Health Center in the Kingdom of Bahrain. We distributed questionnaires that include the sociodemographic data as well as information on risk factors such as smoking, parity, and the contraceptive used.Eleven women (11%) with normal cytology were HPV-positive. The RFLP analysis detected HPV-types 16, 18, 45, 62 and 53. Positive women were significantly older (43.3 +/- 10.1 years) than negatives (36.5 +/- 9.9 years; p=0.04), however, there was no difference in age of first sexual contact (positive: 18.1 +/- 5.7 years versus negative: 20.6 +/- 4.4 years). Polygamy, smoking and hormonal contraception was not identified as risk factors, but positive women showed higher parity.In this study on HPV infection in Bahrain, the 11% positivity with high risk HPV types, in the presence of normal cytology suggests that in addition to the cervical cancer screening program, offer of HPV testing deserves consideration.

To investigate the effect of pre-exposure antibiotics on cytolethal distending toxin (CDT) production and toxigenic effect of C. jejuni.Sonicates and filtrates were prepared from known cdt+ and cdt- isolates of C. jejuni which had been pre-exposed to varying concentrations (MIC, 1/2 MIC, 1/4 MIC, 1/8 MIC) of erythromycin and ciprofloxacin. The CDT toxigenic effect was examined using INT 407 and HeLa cells.A trend of increased toxigenic effect was observed with pre-exposure to antibiotics. This was more pronounced with erythromycin pre-exposure compared to ciprofloxacin. Although a trend of increasing toxigenic effect with decreasing antibiotic concentration was demonstrable, some differences were observed between isolates. In one isolate the increased toxigenic effect was statistically significant (P0.05) at 1/4 MIC in INT 407 cells and at 1/8 MIC in HeLa cells.This study provides evidence of an association between CDT production by C. jejuni and pre-exposure to antibiotics. Pre-exposure to ciprofloxacin and erythromycin at concentrations below MICs could potentiate CDT activity. Further work is needed to elucidate the mechanism involved. We recommend that these antibiotics be used in the treatment of C. jejuni enteritis only when strongly indicated and with careful monitoring of patients.