Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells.

Current guidelines for COVID-19 management recommend the utilization of various repurposed drugs. Despite ongoing research toward the development of a vaccine against SARS-CoV-2, such a vaccine will not be available in time to contribute to the containment of the ongoing pandemic. Therefore, there is an urgent need to develop a framework for the rapid identification of novel targets for diagnostic and therapeutic interventions. We analyzed publicly available transcriptomic datasets of SARS-CoV infected humans and mammals to identify consistent differentially expressed genes then validated in SARS-CoV-2 infected epithelial cells transcriptomic datasets. Comprehensive toxicogenomic analysis of the identified genes to identify possible interactions with clinically proven drugs was carried out. We identified IFITM3 as an early upregulated gene, and valproic acid was found to enhance its mRNA expression as well as induce its antiviral action. These findings indicate that analysis of publicly available transcriptomic and toxicogenomic data represents a rapid approach for the identification of novel targets and molecules that can modify the action of such targets during the early phases of emerging infections like COVID-19.

SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions.

The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress, and fatality. To address this global crisis, up-to-date information on viral genomics and transcriptomics is crucial for understanding the origins and global dispersion of the virus, providing insights into viral pathogenicity, transmission, and epidemiology, and enabling strategies for therapeutic interventions, drug discovery, and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.

Do probiotics promote oral health during orthodontic treatment with fixed appliances? A systematic review.

BACKGROUND: Treatment with fixed orthodontic appliances has been associated with significant biofilm accumulation, thus putting patients at a higher risk of oral health deterioration. The use of probiotics has been proposed to be useful in the prevention or treatment of oral pathologies such as caries and diseases of periodontal tissues. Our aim was to investigate the effects of probiotic use on inflammation of the gingival tissues and the decalcification of the enamel in patients being treated with fixed orthodontic appliances. METHODS: We searched without restrictions 8 databases and performed hand searching until September 2019. We searched for randomized controlled trials (RCTs) evaluating whether individuals with fixed orthodontic appliances benefit from probiotic treatment in terms of the inflammation of the gingivae and decalcification of the enamel. Following the selection of studies and the extraction of pertinent data, we appraised the risk of bias and the confidence in the observed effects based on established methodologies. RESULTS: From the final qualifying studies, three did not show any statistically significant effect on gingival inflammation after probiotic administration of up to 1 month. Similarly, non-significant differences were noted in another study regarding white spot lesions development (mean administration for 17 months). No adverse effects were reported and the level of evidence was considered moderate. CONCLUSIONS: Supplementation of orthodontic patients with probiotics did not affect the development of inflammation in the gingivae and decalcification in the enamel. Additional RCTs, with longer intervention and follow-up periods, and involving different combinations of probiotic strains are required. TRIAL REGISTRATION: PROSPERO (CRD42018118008).

Clostridioides difficile infection: Incidence and risk factors in a tertiary care facility in Riyadh, Saudi Arabia.

BACKGROUND: Significant increase in rates of Clostridioides difficile associated diarrhea (CDI) has been reported globally but there remains a paucity of data from Saudi Arabia. METHODOLOGY: Prospective hospital-based surveillance for CDI using the Center for Disease Control (CDC) criteria was conducted from June to November 2015 in a tertiary healthcare facility in Riyadh, Saudi Arabia. RESULTS: During the surveillance period, 106 episodes of CDI were identified among 59 patients in 137,230 patient-days. The incidence of CDI was 3.5 per 10,000 patient days. Of the 106 episodes, 58% (n=61) were new cases, 12% (n=13) were recurrent cases and 30% (n=32) were duplicate cases. Majority of the new cases (n/N=43/61; 70%) were healthcare onset, followed by community onset (21%) and 8% were community-onset healthcare associated. No statistically significant change in trend was observed during the surveillance period. The most prevalent CDI risk factor was use of proton pump inhibitor (PPI) (92%) followed by prolonged use of antibiotics (77%). Pareto-analysis indicated that controlling for PPI use, prolong and multiple antibiotic exposure and prolonged hospitalization results in 80% CDI reduction. CONCLUSION: The findings indicate a low incidence of CDI. Multicenter studies are needed to elucidate the burden to CDI in the country.

A single-centre investigator-blinded randomised parallel group clinical trial to investigate the effect of probiotic strains Streptococcus salivarius M18 and Lactobacillus acidophilus on gingival health of paediatric patients undergoing treatment with fixed orthodontic appliances: study protocol.

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.

Investigating a rare methicillin-resistant Staphylococcus aureus strain: first description of genome sequencing and molecular characterization of CC15-MRSA.

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 νSaß 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.

Detection of clostridium difficile antigen and toxin in stool specimens: Comparison of the C. difficile quik chek complete enzyme immunoassay and GeneXpert C. difficile polymerase chain reaction assay.

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.

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.

Molecular epidemiology of vancomycin resistant enterococci in a tertiary care hospital in Saudi Arabia.

AIM: Vancomycin-resistant enterococci (VRE) are a major cause of nosocomial infections with high mortality and morbidity. There is limited data on the molecular characterization of VRE in Saudi Arabia. This study was carried out to investigate the premise that a shift in VRE epidemiology is occurring in our setting. METHODS: Enterococcus species identification and susceptibility testing plus VRE phenotypic confirmation by vancomycin and teicoplanin E-test were carried out. Vancomycin resistance genes were detected by PCR. Strain typing was conducted using PFGE. RESULTS: Among the strains of Enterococcus spp. investigated in this study, 17 (4.5%) were VRE. With the exception of one isolate from rectal swab, all others were clinical specimens with blood being the commonest source (n = 11; 64.7%), followed by urine (n = 3; 17.6%). The 17 VRE isolates were Enterococcus faecium (n/N = 13/17) and Enterococcus gallinarum (n/N = 4/17). Among E. faecium isolates, vanA(+)/vanB(+) (n/N = 8/13; 62%) exhibiting VanB phenotype were predominant. One of the five vanA(+)E. faecium isolates exhibited a VanB phenotype indicative of vanA genotype-VanB phenotype incongruence. E. gallinarum isolates exhibited a Van C phenotype although two were vanA(+)/vanC1(+). PFGE revealed a polyclonal distribution with eight pulsotypes. CONCLUSION: These findings indicate an evolving VRE epidemiology with vanA(+)/vanB(+) isolates and vanA genotype-VanB phenotype incongruence isolates, which were previously described as colonizers, are now causing clinical infection.

Comparison of Molecular and Phenotypic Methods for the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae.

In recent years, there has been a rapid dissemination of carbapenem resistant Enterobacteriaceae (CRE). This study aimed to compare phenotypic and molecular methods for detection and characterization of CRE isolates at a large tertiary care hospital in Saudi Arabia. This study was carried out between January 2011 and November 2013 at the King Khalid University Hospital (KKUH) in Saudi Arabia. Determination of presence of extended-spectrum beta-lactamases (ESBL) and carbapenem resistance was in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines. Phenotypic classification was done by the MASTDISCS(TM) ID inhibitor combination disk method. Genotypic characterization of ESBL and carbapenemase genes was performed by the Check-MDR CT102. Diversilab rep-PCR was used for the determination of clonal relationship. Of the 883 ESBL-positive Enterobacteriaceae detected during the study period, 14 (1.6%) isolates were carbapenem resistant. Both the molecular genotypic characterization and phenotypic testing were in agreement in the detection of all 8 metalo-beta-lactamases (MBL) producing isolates. Of these 8 MBL-producers, 5 were positive for blaNDM gene and 3 were positive for blaVIM gene. Molecular method identified additional blaOXA gene isolates while MASTDISCS(TM) ID detected one AmpC producer isolate. Both methods agreed in identifying 2 carbapenem resistant isolates which were negative for carbapenemase genes. Diversilab rep-PCR analysis of the 9 Klebsiella pneumoniae isolates revealed polyclonal distribution into eight clusters. MASTDISCS(TM) ID is a reliable simple cheap phenotypic method for detection of majority of carbapenemase genes with the exception of the blaOXA gene. We recommend to use such method in the clinical laboratory.

Phenotypic and genotypic characterization of extended-spectrum b-lactamases producing Escherichia coli and Klebsiella pneumoniaein a tertiary care hospital in Riyadh, Saudi Arabia.

BACKGROUND AND OBJECTIVES: Extended-spectrum beta-lactamase (ESBL)-producing pathogens remain a public health concern, with limited data on the molecular characterization of isolates. We aimed to determine the molecular characterization of ESBL-producers circulating in our setting and correlate the molecular types with the minimal inhibitory concentration (MIC) to third-generation cephalosporins. DESIGN AND SETTINGS: Retrospective study conducted during the period from January to June 2013 at King Khalid University hospital, a tertiary-care hospital in Riyadh, Saudi Arabia. MATERIALS AND METHODS: All Escherichia coli and Klebsiella pneumoniae confirmed to be ESBL producers were included. The MICs of ceftriaxone and ceftazidime were determined by the E-test. Molecular characterization of ESBL-genes was performed using the Check-MDR-CT102 DNA microarray. RESULT: Of 77 isolates comprising 50 (65%) E coli and 27 (35%) K pneumoniae, the majority (n=63; 81%) were from urine. Most isolates were blaCTX-M gene positive (n=72/77; 93.5%) comprising blaCTX-M1 (n=62), blaCTX-M9 (n=9) and blaCTX-M25 (n=1). Two or more ESBL genes were present in 45% of isolates with blaSHV predominating in K pneumoniae and blaTEM in E coli. Two isolates were positive for blaOXA-48 carried in combination with blaCTX-M9 and blaTEM in E coli and blaCTX-M1/CTX-M9 in K pneumoniae. Ceftriaxone MIC50 and MIC90 of >=256 micro g/mL were seen in E coli and K pneumoniae harboring blaCTX-M alone or in combination with blaSHV or blaTEM. For ceftazidime the highest MIC50 and MIC90 was seen in K pneumoniae harboring blaCTX-M+blaSHV and E coli with blaCTX-M+blaTEM combinations. CONCLUSION: A preponderance of blaCTX-M suggests dissemination of the gene in our setting. The MIC for ceftriaxone and ceftazidime correlate well with molecular characterization of ESBL-producing Enterobacteriaceae.

Occupational exposure to blood-borne pathogens in a tertiary hospital: benchmarking using patient days.

Incidence and risk factors for occupational exposure to blood-borne pathogens (OEBBPs) in a tertiary hospital in Saudi Arabia was assessed. Reported sharps injuries from 2009 to 2010 were analyzed and benchmarked using patient days. OEBBPs caused by sharps injuries increased from 41 in 2009 to 65 in 2010, with an incidence rate of 4.09/10 000 patient days in 2009 and 5.9/10 000 patient days in 2010. Most episodes (41%) occurred during recapping of hollow bore needles after obtaining blood specimens. The highest incidence was among nursing staff(n/N = 87/106; 82%), and injuries also occurred in housekeeping staff (3.7%). A correlationbetween morning shift and OEBBPs was observed, and the highest number of episodes occurred in the emergency room (21.5%) and renal dialysis unit (16.9%). There was exposure to HCV (n = 13) and HBV (n = 4) but not to HIV (n = 0), and no seroconversions were documented. Education on adherence to universal precaution measures and use of safety engineered devices as well as the introduction of an OEBBP notification hotline are recommended.

National surveillance of antimicrobial resistance among Gram-positive bacteria in Saudi Arabia.

BACKGROUND: Antimicrobial-resistant Gram-positive bacteria are important causes of serious infections. METHODS: Between January and December 2009, we examined clinical Gram-positive isolates from 24 hospitals across Saudi Arabia. RESULTS: Among the 13750 isolates, Staphylococcus aureus (62.3%) was the commonest, followed by non-group A beta-haemolytic streptococci (14.8%), group A beta-haemolytic streptococci (7.1%), coagulase-negative staphylococci (6.6%), pneumococci (6.0%), and enterococci (3.1%). Resistance rates were high among S. aureus (methicillin-resistant S. aureus: 32%), coagulase-negative staphylococci (oxacillin: 63%) and pneumococci (penicillin G: 33%; erythromycin: 26%; ceftriaxone: 11%); low among enterococci (vancomycin: 1%) and among beta-haemolytic streptococci. Resistance rates varied between regions, but comparison was complicated by differences in antibiotics tested. Many relevant antibiotics were tested against few isolates (e.g. ampicillin, vancomycin, and high-level gentamicin versus enterococci) while unhelpful tests were widely performed (e.g. cefotaxime, ceftriaxone, and imipenem versus staphylococci. CONCLUSION: Resistance is widespread in staphylococci and pneumococci, but not enterococci and beta-haemolytic streptococci in Saudi Arabia. Rationalization of antibiotic panels tested is urgently needed.

Implementation of the world health organization hand hygiene improvement strategy in critical care units.

BACKGROUND: To determine hand hygiene compliance before and after an intervention campaign in critical care units, this study was carried out in the Intensive care unit (ICU), Neonatal intensive care unit (NICU), Burns unit (BU) and the Kidney unit of the King Abdul Aziz Specialist Hospital, Taif, Saudi Arabia. The observation using the WHO hand hygiene protocol took place in four phases with phase I, between April 24-May 06 2010 and phase II from May 29-June 09 2010. An educational intervention took place between the Phases I and II. Follow-up Phases III and IV were from 01-15 October 2010 and 15-30 March 2011 respectively. FINDINGS: 1,975 hand hygiene opportunities comprising of 409 in Phase I, 406 in Phase II, 620 in Phase III and 540 Phase IV were observed. Compliance rate was 67% pre-intervention, 81% in phase II, declining to 59% and 65% in phases III and IV. Increased compliance in the ICU from 39% in Phase I to 81% in Phase IV (p < 0.05) was sustained throughout the study. Highest compliance rates were recorded among nurses in all phases. The improved compliance for physicians observed in the post-intervention phase was lost in follow-up phases. Missed opportunities for hand hygiene were before patient contact, after touching patient's surrounding and before aseptic techniques. Team-work and leadership were identified as enhancing factors for compliance. CONCLUSION: The WHO hand hygiene strategy combined with health education, continuous evaluation and team approach resulted in increased compliance but this was not sustained in certain critical care areas.

High prevalence of acquired quinolone-resistance genes among Enterobacteriaceae from Saudi Arabia with CTX-M-15 ß-lactamase.

We examined the prevalence of acquired quinolone resistance determinants among Enterobacteriaceae with extended-spectrum ß-lactamases (ESBLs) in Riyadh, Saudi Arabia. qnrA, qnrB, qnrS, aac(6')-Ib-cr, and qepA genes were sought by polymerase chain reaction (PCR) in 160 nonduplicate, clinical Enterobacteriaceae with ESBLs from Prince Salman Hospital in Riyadh during 2009. MICs were determined for qnr- and aac(6')-Ib-cr-positive isolates. Mutations in gyrA and parC were determined for isolates with qnr. ESBL genes were characterized by PCR and sequencing. Among 99 ESBL-producing Escherichia coli, 73% were ciprofloxacin resistant, as were 74% of 61 ESBL-positive Klebsiella pneumoniae. The aac(6')-1b-cr gene was present in 76 ESBL producers, comprising 34 K. pneumoniae and 42 E. coli, whereas qnrA or qnrB genes were found in 21 isolates, all of them also harbouring aac(6')-1b-cr and bla(CTX-M-15), with the latter encoding what was considerably the dominant ESBL in the collection. The qnr-positive isolates harboured a variety of mutation in gyrA and parC but, even with aac(6')-1b-cr also present, high-level ciprofloxacin resistance (MIC >32 µg/mL) was invariably associated with double mutations in gyrA, affecting both Ser83 and Asp87 along with >1 substitution in parC, affecting Ser80 or Glu84.

Trafficking of methicillin-resistant staphylococci and co-colonization with vancomycin-resistant enterococci.

OBJECTIVES: To determine the trafficking of methicillin-resistant staphylococci between the hospital and community as well as the occurrence of co-colonization with vancomycin-resistant enterococci (VRE). SUBJECTS AND METHODS: From November 2005 to April 2006, methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococcus (MRCoNS)-positive patients at the Salmaniya Medical Complex, Bahrain were assessed for VRE co-colonization. Characterization of vancomycin resistance genotype by PCR was carried out. Close family contacts were screened for MRSA and pulsed-field gel electrophoresis (PFGE) analysis of MRSA isolates from patient-family member pairs was conducted. RESULTS: One hundred and eighty-two patients (93 MRSA; 89 MRCoNS) and 356 family members were enrolled. Seven MRSA and 41 MRCoNS strains were isolated from the family members. PFGE analysis revealed the presence of variants of a single MRSA clone among patients and their relatives. A total of 112 patients (62 MRSA; 50 MRCoNS) provided stool for VRE screening. Of these 13 stool specimens (11.6%) were VRE-positive. All the VRE isolates were from MRSA-positive patients, thus positivity rate among MRSA patients was 20.9% (n/N = 13/62). These were predominantly Enterococcus gallinarum with vanC1 genotype and one strain was Enterococcus faecium (vanB genotype). Two E. gallinarum isolates harbored an additional vanB gene. The majority of VRE isolates were from patients in medical and surgical units (n/N = 10/13; 77%). Male gender, prolonged hospitalization and presence of co-morbidities were significantly associated with MRSA/VRE co-colonization (p < 0.05). CONCLUSION: MRSA/VRE co-colonization with MRSA trafficking between the hospital and community environment is a public health concern occurring in our setting.

Predominance of CTX-M genotype among extended spectrum beta lactamase isolates in a tertiary hospital in Saudi Arabia.

OBJECTIVE: 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. METHODS: 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. RESULTS: 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 (p<0.05). Sensitivity to imipenem was 100% and 78% to nitrofurantoin. Resistance to amoxicillin-sulbactam was significantly higher in blaCTX-M positive isolates (p<0.05). CONCLUSION: 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.

Probiotics for the treatment of bacterial vaginosis.

BACKGROUND: The dominance of lactobacilli in healthy vaginal microbiota and its depletion in bacterial vaginosis (BV) has given rise to the concept of oral or vaginal instillation of probiotic Lactobacillus strains for the management of this condition. OBJECTIVES: To ascertain the efficacy of probiotics in the treatment of BV. SEARCH STRATEGY: We searched electronic databases irrespective of publication status or language. These included: Cochrane Central Register of Controlled Trials (CENTRAL), the HIV/AIDS and STD Cochrane Review Groups' specialized registers, the Cochrane Complementary Medicine Field's Register of Controlled Trials, MEDLINE (1966 to 2008), EMBASE (1980 to 2007), ISI science citation index (1955 to 2007), CINAHL (Cumulative Index to Nursing & Allied Health Literature (1982 to 2007).We handsearched of specialty journals, conference proceedings and publications list on the website of the International Scientific Association of Probiotics and Prebiotics (http://www.isapp.net/default.asp).For unpublished studies or ongoing trials, we contacted authors from relevant publications, nutraceutical companies and probiotic-related scientific associations. We searched electronic databases on ongoing clinical trials. SELECTION CRITERIA: Randomized controlled trials using probiotics for the treatment of women of any age diagnosed with bacterial vaginosis, regardless of diagnostic method used. The probiotic preparation could be single or "cocktail" of strains, any preparation type/dosage/route of administration. Studies comparing probiotics with placebo, probiotics used in conjunction with conventional antibiotics compared with placebo or probiotics alone compared with conventional antibiotics were eligible for inclusion. DATA COLLECTION AND ANALYSIS: We screened titles and abstracts , obtained full reports of relevant trialsand independently appraised them for eligibility. A data extraction form was used to extract data from the four included studies. For dichotomous outcomes, odds ratios (OR) and 95% confidence intervals (CI) were derived for each study using RevMan (versions 4.2 and 5). We did not perform meta-analysis due to significant differences in the probiotic preparations and trial methodologies. MAIN RESULTS: Analysis suggests beneficial outcome of microbiological cure with the oral metronidazole/probiotic regimen (OR 0.09 (95% CI 0.03 to 0.26)) and the probiotic/estriol preparation (OR 0.02, (95% CI 0.00 to 0.47)). For the probiotic/estriol preparation, the OR and 95% CI for physician-reported resolution of symptoms was OR 0.04 (95% CI 0.00 to 0.56). AUTHORS' CONCLUSIONS: The results do not provide sufficient evidence for or against recommending probiotics for the treatment of BV. The metronidazole/probiotic regimen and probiotic/estriol perparation appear promising but well-designed randomized controlled trials with standardized methodologies and larger patient size are needed.

Extended spectrum beta-lactamases (ESBL) in Escherichia coli and Klebsiella pneumoniae: trends in the hospital and community settings.

BACKGROUND: To assess the prevalence of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella strains in nosocomial and community-acquired infections. METHODOLOGY: The study was conducted at a centralized microbiology laboratory in the Eastern Province of Saudi Arabia. Laboratory records (January 2004 - December 2005) were assessed. Associated resistance to a panel of antibiotics was determined. RESULTS: A total of 6,750 Gram-negative organisms were assessed for ESBL-phenotype. ESBL was detected in 6% (409/6,750) of isolates, the majority of which were E. coli (83%). ESBL producers were significantly higher among isolates from in-patients 15.4% (143/927) versus out-patients (4.5%; 266/5,823); p < 0.05. Old age (older than 60 years) represented a significant risk for having an ESBL-producing pathogen. Urine was the major source of ESBL isolates in in-patients (46.1%) and out-patients (74.4%). The proportion of urinary E. coli isolates which were ESBL producers was significantly higher among in-patients (53/506; 10.4%) compared to out-patients (182/4,074; 4.4%); p<0.05. Old age (older than 60 years) represented a significant risk for having an ESBL-producing pathogen. Urine was the major source of ESBL isolates in in-patients (46.1%) and out-patients (74.4%). The proportion of urinary E. coli isolates which were ESBL producers was significantly higher among in-patients (53/506; 10.4%) compared to out-patients (182/4,074; 4.4%); p<0.05. Among in-patients, 60% of the ESBL associated infections were nosocomial. All were sensitive to imipenem but high levels of resistance to gentamicin, amikacin, amoxicillin-clavulanic acid and ciprofloxacin was shown. CONCLUSION: The findings document evidence of the spread of multiresistant ESBL-producers into the community. This has significant implications for patient management, and indicates the need for increased surveillance and molecular characterization of these isolates.