Genotypes and prevalence of carbapenemase-producing Enterobacteriaceae and Pseudomonas aeruginosa in a hospital in Saudi Arabia.

BACKGROUND: The molecular epidemiology of resistance of carbapenem-resistant Enterobacteriaceae (CRE) and Pseudomonas aeruginosa are important in the study of multidrug-resistant bacteria. We evaluate the prevalence of the different mechanisms of CRE in a hospital in Saudi Arabia. METHODS: Carbapenem non-susceptible isolates of Enterobacteriaceae and Pseudomonas aeruginosa were tested by real-time PCR for the detection of genes responsible for beta-lactam resistance. RESULTS: There were a total of 200 isolates with carbapenem non-susceptibility and these were Klebsiella pneumoniae (n=96, 48%), Escherichia coli (n=51, 25.5%) and Pseudomonas aeruginosa (n=45, 22.5%). The detected carbapenemases were oxacillinase-48 (OXA-48) (n=83, 41.5%), New Delhi metallo-ß-lactamase (NDM) (n=19, 2.5%) and both NDM and OXA-48 (n=5, 2.5%). The other carbapenemases were imipenemase (n=1, 0.5%), Verona integrin encoded metallo-ß-lactamase (n=6, 3%) and Klebsiella pneumoniae carbapenemase (n=1, 0.5%), but none were detected in 86 isolates (43%). CONCLUSION: The most common carbapenemases were OXA-48 and a significant percentage had no detectable genes. These data will help in the selection of new antimicrobial therapies.

Antimicrobial resistance of gram-negative bacteria: A six-year longitudinal study in a hospital in Saudi Arabia.

INTRODUCTION: Increasing prevalence of antimicrobial resistance is a major concern especially in light of lack of new antimicrobial agents. Here, we present antibiotic resistance pattern of gram-negative bacteria (GNB) over six years (2013-2018) in a hospital in Saudi Arabia. MATERIALS AND METHODS: The study included a report of the cumulative antibiogram of GNB. Interpretation of the antibacterial susceptibility tests was based on the Clinical and Laboratory Standards Institute guidelines and VITEK® 2 system. RESULTS: There was a total of 32,890 GNB isolates and the most common were: Escherichia coli (69.8%), Klebsiella pneumoniae (17.2%) and Pseudomonas aeruginosa (12.8%). Antimicrobial susceptibility of P. aeruginosa and E. coli did not change overtime, however, susceptibility to ceftazidime decreased from 92% to 85% in P. aeuroginosa. Yearly antimicrobial susceptibility did not change significantly overtime for K. pneumoniae. ESBL isolates among K. peumoniae and E. coli was about 26% and 20%, respectively (p=0.0068). For ESBL E. coli, the least effective antibiotics were ciprofloxacin (26%) and trimethoprim-sulfamethoxazole (34%). For ESBL K. pneumoniae, gentamicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and nitrofurantoin had poor activity. For K. pneumoniae, both ciprofloxacin (90%) and trimethoprim-sulfamethoxazole (86%) had better coverage than for E. coli. K. pneumoniae showed less susceptibility to nitrofurantoin than E. coli (20% vs. 92%). CONCLUSION: Antibiotic resistance among P. aeruginosa and E. coli did not change overtime (2013-2018) and the rate of ESBL-producing E. coli and K. pneumoniae was high. Thus, continued surveillance is needed.

The impact of the coexistence of mycobacterium avium with mycobacterium tuberculosis on the result of GeneXpert and MGIT susceptibility test.

Rapid tests to diagnose tuberculosis relies on molecular detection of the M. tuberculosis. GeneXpert MTB/RIF test identifies M. tuberculosis and rifampicin resistance. We present a case of simultaneous coinfection with M. tuberculosis and M. avium. M. tuberculosis was detected in the sputum by PCR GeneXpert method. Unrecognized coexistence of M. tuberculosis and M. avium modified the results of drug susceptibility tests making the primary identification of M. tuberculosis as multi-drug resistant strain. We performed in vitro experiments to investigate the effect of the coexistence of M. avium with M. tuberculosis on the results of GeneXpert method, and drug susceptibility test.

Clostridioides (Clostridium) difficile-associated disease: Epidemiology among patients in a general hospital in Saudi Arabia.

BACKGROUND: Clostridioides (Clostridium) difficile infection (CDI) is an important health care-associated infection with variable incidence and prevalence across the globe. There are limited data from Saudi Arabia on the epidemiology of C. difficile-associated diarrhea (CDAD). In this study, we present the epidemiology and incidence of CDAD in a hospital in Saudi Arabia. METHODS: This study included all stool samples from 2001 to 2018 that were tested for C. difficile. C. difficile toxins were detected by enzyme-linked immunosorbent assay in 2001-2012 and the diagnosis was based on PCR testing (2013-2018). RESULTS: There was a total of 577 distinctive episodes of CDAD representing 5.2% of 10,995 tested stool samples with an annual positivity rate of 0.9%-11.8%. Of all CDAD cases, there were 230 (39.9%) community associated-CDAD, 105 (18.2%) community onset-health care facility associated disease, and 242 (42%) health care facility onset health care facility-associated disease (HCFO-HCFAD). There was a trend of increasing percentage of community onset-health care facility associated disease cases from 17% in 2001 to 20% in 2018 of all cases, and a trend towards less cases of community associated-CDAD from 85% to 50% over time. However, the percentages of HCFO-HCFAD percentages remained relatively stable. The rate of HCFO-HCFAD per 1,000 patient-days increased from 0.009 to 0.22 from 2001 to 2018, respectively. CONCLUSIONS: The rate of CDAD was 5.15% among all tested samples and that there is a large proportion of community associated-CDAD. The findings parallel the data from developed countries and deserve further studies in the risk factors for community-associated CDAD.

Overview of hepatitis C infection, molecular biology, and new treatment.

The World Health Organization estimates that 71 million people worldwide have chronic hepatitis C viral infection. A major challenge is overall lack of public awareness of hepatitis C, particularly among infected people of their infection status. Chronic hepatitis C infection is associated with advanced liver disease, is the main cause of hepatocellular carcinoma and causes many extra-hepatic manifestations. The existence of seven viral genotypes complicates targeting of treatment. Recent years have seen the approval of many direct acting antivirals targeted at hepatitis C virus non-structural proteins. These have revolutionized therapy as they allow achievement of extremely high sustained virologic responses. Of great significance is the development of pan-genotypic drug combinations, including the NS3/4A-NS5A inhibitor combinations sofosbuvir-velpatasvir and glecaprevir-pibrentasvir. However, resistance-associated mutations can result in failure of these treatments in a small number of patients. This, combined with the high costs of treatment, highlights the importance of continued research into effective anti-hepatitis C therapies, for example aimed at viral entry. Recent developments include identification of the potential of low-cost anti-histamines for repurposing as inhibitors of hepatitis C viral entry. In this review we focus on molecular biology of hepatitis C virus, and the new developments in hepatitis C treatment.

Influenza vaccine acceptance by healthcare workers in Saudi Arabia: A questionnaire-based analysis.

The aim of this study was to gauge the reasons for accepting or declining influenza vaccine in healthcare staff in Saudi Arabia. A questionnaire was administered to healthcare workers in Saudi Arabia. In all, 633 respondents who provided gender, nationality and profession were included. Reasons for vaccine uptake or refusal were assessed according to profession and educational level. Uptake of vaccine was lower in the period from 2010 to 2014 (3-13.3%) compared to pre-2010 figures (20.7%), rising to 44.1% in 2015. Comparing data for 'never having been vaccinated' to 'being vaccinated in 2015', there was no significant difference in distribution between nurses (9.27% v 38.8%), physicians (13.9% v 56.0%) and laboratory technicians (15.9% v 33.5%) (p= 0.08). The top reason for vaccination was protection of self and family, while the top reason for refusal was not considering the vaccine to be necessary. Education level had no significant effect on the likelihood of being vaccinated. Improvement of healthcare worker vaccination levels in Saudi Arabia might be achieved by addressing staff concerns on vaccine safety and efficacy, emphasizing the potential dangers of influenza and capitalizing on the staff's focus on protecting themselves and their families.

Microbiology of Elizabethkingia spp. isolates in hospitalized patients.

An increasing number of infections due to Elisabethkingia spp. have been observed and reported in recent years. Here we report the microbiological aspects of 13 cases with positive cultures for Elizabethkingia spp. from 1998 to 2017. Elizabethkingia isolates were identified using the Vitek 2 Compact 60 (AES software) Gram-Negative Identification test (GNI) card (bioMerieux. Marcy-l'Etoile, France). The MICs were determined using Vitek 2 and interpreted according to CLSI guidelines based on the interpretive MIC breakpoints for Acinetobacter spp. Vitek 2 susceptibility results were confirmed using the manual E-test and the colistin result was confirmed using the broth dilution method. Twelve cases were observed between 2010 and 2017 with four cases in 2017. Of the 2017 samples, three out of four isolates were obtained outside the intensive care units compared to one out of eight samples between 2010 and 2016. There was variable susceptibility to trimethoprim/sulfamethoxazole (58.3%), ciprofloxacin (41.7%), piperacillin/tazobactam and gentamicin (16.6% each), and all were resistant to colistin. There is a high rate of drug resistance and further studies to identify the source of the infection are needed to build up a profile of Elizabethkingia spp. to inform public health policy in this context.

The effectiveness of antibacterial curtains in comparison with standard privacy curtains against transmission of microorganisms in a hospital setting.

Studies have shown a correlation between a cleaner patient environment and lower infection rates and reduced risk of transmission. Privacy curtains are potentially important sites of bacterial contamination in hospitals. Privacy curtains integrated with antimicrobial properties have been shown to increase the time to first contamination compared with standard privacy curtains. In this study, we examined the difference in bacterial colonization of different curtains. We experimentally contaminated antibacterial Fantex protective curtains and compared the bacterial counts to natural contamination of privacy curtains. There was a significant reduction in the CFU/cm2 on antibacterial Fantex protective privacy curtains after 24 hours of experimental contamination with Pseudomonas aeruginosa, Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus (MRSA) or extended-spectrum-producing organisms (Escherichia coli or Klebsiella pneumoniae), compared to standard privacy curtains. Levels of environmental contamination with S. epidermis, Streptococcus viridians, E. coli, S. haemolyticus, S. aureus, S. capitis, non-fermenting Gram-negative bacteria, and Bacillus species were also significantly less on the Fantex curtains after two months hanging in the emergency department. Healthcare facilities may find that addressing surfaces, including use of antibacterial privacy curtains, is an effective horizontal strategy for addressing healthcare-associated infections across the board.

Comparison of Cepheid® Xpert Flu and Roche RealTime Ready Influenza A/H1N1 Detection Set for detection of influenza A/H1N1.

OBJECTIVE: To compare two influenza polymerase chain reaction (PCR) methods. METHODS: A total of 749 suspected MERS-CoV patients presenting at Johns Hopkins Aramco Healthcare, Saudi Arabia, each submitted a clinical sample for influenza A reflex testing using the on-site Cepheid® Xpert Flu assay and at the Ministry of Health laboratory by the Roche PCR assay. RESULTS: There was 92.12% overall agreement between the two methods. Specificity of the Cepheid® Xpert Flu was 95.8% for H1N1 and 94.4% for total influenza A. Cepheid® Xpert Flu sensitivity for influenza A was 100% for younger patients (0-19-year age group) but significantly lower both for older patients (68.2% for 60-79-year and 50% for ≥80-year age groups) and overall for males compared to females (72.6% and 94.0%, respectively). CONCLUSIONS: Specificity of the Cepheid® Xpert Flu test was high; however, sensitivity for total influenza A was lower particularly in males and older patients.

Influenza A(H1N1)pdm09 epidemiology in the Eastern Province of Saudi Arabia.

OBJECTIVES: The influenza A(H1N1)pdm09 virus caused a worldwide pandemic in 2009-2010 and has since remained in seasonal circulation. This study was conducted to determine any variations in the influenza A(H1N1)pdm09 status according to sex, age group, sample type, or location within the Eastern Province of the Kingdom of Saudi Arabia. METHODS: Samples from 749 patients with suspected Middle East respiratory coronavirus who presented to Johns Hopkins Aramco Healthcare facilities in the Eastern Province of Saudi Arabia were tested reflexively for influenza A/H1N1 2009 by the Ministry of Health using the RealTime ready Influenza A/H1N1 Detection Set for real-time PCR. The sample types included nasopharyngeal swabs (n=677), expectorated deep cough sputum (n=32), induced sputum (n=17), and tracheal aspirates (n=23). RESULTS: The incidence of influenza A(H1N1)pdm09 was higher among younger patients; 27.94% of patients in the 0-19-year age group tested positive compared to only 3.51% of patients in the ≥80-year age group. The incidence of influenza A(H1N1)pdm09 was higher in Ras Tanura city compared to other locations in the Eastern Province. CONCLUSIONS: Younger individuals in the Eastern Province of the Kingdom of Saudi Arabia had a relatively higher risk of influenza A(H1N1)pdm09 infection. Additionally, an outbreak of influenza A(H1N1)pdm09 may have occurred in Ras Tanura city between April 2015 and February 2016.

Wavelet-based information filtering for fault diagnosis of electric drive systems in electric ships.

Electric machines and drives have enjoyed extensive applications in the field of electric vehicles (e.g., electric ships, boats, cars, and underwater vessels) due to their ease of scalability and wide range of operating conditions. This stems from their ability to generate the desired torque and power levels for propulsion under various external load conditions. However, as with the most electrical systems, the electric drives are prone to component failures that can degrade their performance, reduce the efficiency, and require expensive maintenance. Therefore, for safe and reliable operation of electric vehicles, there is a need for automated early diagnostics of critical failures such as broken rotor bars and electrical phase failures. In this regard, this paper presents a fault diagnosis methodology for electric drives in electric ships. This methodology utilizes the two-dimensional, i.e. scale-shift, wavelet transform of the sensor data to filter optimal information-rich regions which can enhance the diagnosis accuracy as well as reduce the computational complexity of the classifier. The methodology was tested on sensor data generated from an experimentally validated simulation model of electric drives under various cruising speed conditions. The results in comparison with other existing techniques show a high correct classification rate with low false alarm and miss detection rates.

Fusarium Infection in a Kidney Transplant Recipient Successfully Treated with Voriconazole.

Fusarium infections in solid-organ transplant recipients are rare and carry high mortality. We report a case of a kidney transplant recipient who developed infection with Fusarium species. The patient received treatment with oral voriconazole for five months with good response.

Variation in MRSA identification results from different generations of Xpert MRSA real-time PCR testing kits from nasal swabs.

GeneXpert MRSA kits (Cepheid) are based on a multiplex, real-time PCR method for methicillin-resistant Staphylococcus aureus (MRSA) detection, with primers to detect each SCCmec type and the chromosomal orfX-SCCmec junction. Modifications in recent kit versions were proposed to help overcome false-positive issues in earlier kit versions. The main objective of this study was to determine whether use of any version of the GeneXpert MRSA multiplex, real-time PCR kits yielded higher than expected MRSA+ results. We also estimated the level of MRSA in our healthcare facility as a proportion of total S. aureus between 2010 and 2015. We examined results from five generations of the kits used between 2008 and 2015. Results were from nasal swab samples from 16,431 patients in the Johns Hopkins Aramco Healthcare facility in Saudi Arabia. The percentage of isolates scored as MRSA+ for the original Xpert MRSA kit was 18.57%, compared to 6.93±1.12% (mean±SD) for the other four kits. The Xpert MRSA-SA Nasal kit yielded 6.48% Invalid results, compared to 0.73±0.28% for the other four kits. The succeeding Xpert MRSA-SA Nasal G3 and Xpert MRSA-SA Nasal Complete G3 kits yielded Invalid results rates of 0.29% and 1.04% respectively. Levels of MRSA-positive isolates as a percentage of total S. aureus-containing samples ranged between 19.81% and 26.74%. In conclusion, the original Xpert MRSA kit yielded higher than expected rates of MRSA+. Issues with over-estimation of MRSA+ and/or numerous Invalid results have been overcome in the most recent modified kits.

A review and comparison of fault detection and diagnosis methods for squirrel-cage induction motors: State of the art.

Preventing induction motors (IMs) from failure and shutdown is important to maintain functionality of many critical loads in industry and commerce. This paper provides a comprehensive review of fault detection and diagnosis (FDD) methods targeting all the four major types of faults in IMs. Popular FDD methods published up to 2010 are briefly introduced, while the focus of the review is laid on the state-of-the-art FDD techniques after 2010, i.e. in 2011-2015 and some in 2016. Different FDD methods are introduced and classified into four categories depending on their application domains, instead of on fault types like in many other reviews, to better reveal hidden connections and similarities of different FDD methods. Detailed comparisons of the reviewed papers after 2010 are given in tables for fast referring. Finally, a dedicated discussion session is provided, which presents recent developments, trends and remaining difficulties regarding to FDD of IMs, to inspire novel research ideas and new research possibilities.

Modified use of real-time PCR detection of group B Streptococcus in pregnancy.

The CDC recommends antenatal screening of vaginal/rectal samples for Streptococcus agalactiae at 35-37 weeks' gestation, with intra-partum antibiotic prophylaxis for positive cases. We tested a modified use of the Cepheid Xpert GBS real-time PCR kit on enrichment cultures from 554 vaginal/rectal swabs compared to the current subculturing gold standard method. Swabs were inoculated on polymyxin nalidixic acid agar plates, and Todd-Hewitt enrichment broth cultures were examined daily for growth. Todd-Hewitt broth culture was also used for Xpert GBS. There was 92.06 % agreement between the subculture and PCR methods. Sensitivity of Xpert GBS was 100 %, specificity was 89.40 %, positive predictive value was 75.96 % and negative predictive value was 100 %. Colonization incidence was higher with younger (≤24 years) or older (≥35 years) maternal age. Modified use of the Cepheid Xpert GBS would assist rapid diagnosis of S. agalactiae colonization and facilitate timely and appropriate assignment to intra-partum antibiotic prophylaxis.

Misinterpretation of Gram Stain from the Stationary Growth Phase of Positive Blood Cultures for Brucella and Acinetobacter Species.

INTRODUCTION: Acinetobacter baumannii and Brucella species are Gram-negative organisms that are vulnerable to misinterpretation as Gram-positive or Gram-variable in blood cultures. OBJECTIVE: We assess the random errors in gram stain interpretation to reduce the likelihood of such errors and therefore patient harm. METHODOLOGY: Aerobic and anaerobic blood cultures from two patients in an acute care facility in Saudi Arabia were subjected to preliminary Gram-staining. In case 1, VITEK-2 Anaerobe Identification, repeat Gram staining from a blood agar plate, Remel BactiDrop™ Oxidase test, Urea Agar urease test and real-time PCR were used to confirm presence of Brucella and absence of Coryneform species. In case 2, repeat Gram- staining from the plate and the vials, VITEK-2 Gram-Negative Identification, real-time PCR and subculture on to Columbia agar, blood agar, and MacConkey agar were carried out to identify A. baumannii. RESULTS: In case 1, initially pleomorphic Gram-positive bacteria were identified. Coryneform species were suspected. Tiny growth was observed after 24 h on blood agar plates, and good growth by 48 h. Presence of Brucella species was ultimately confirmed. In case 2, preliminary Gram-stain results suggested giant Gram-positive oval cocci. Further testing over 18-24 h identified A. baumannii. CONCLUSIONS: Oxidase test from the plate and urease test from the culture vial is recommended after apparent identification of pleomorphic Gram-positive bacilli from blood culture, once tiny growth is observed, to distinguish Brucella from Corynebacterium species. If giant Gram-positive oval cocci are indicated by preliminary Gram-staining, it is recommended that the Gram stain be repeated from the plate after 4-6 h, or culture should be tested in Triple Sugar Iron (TSI) medium and the Gram stain repeated after 2-4 h incubation.

A review of candidate therapies for Middle East respiratory syndrome from a molecular perspective.

There have been 2040 laboratory-confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) in 27 countries, with a mortality rate of 34.9 %. There is no specific therapy. The current therapies have mainly been adapted from severe acute respiratory syndrome (SARS-CoV) treatments, including broad-spectrum antibiotics, corticosteroids, interferons, ribavirin, lopinavir-ritonavir or mycophenolate mofetil, and have not been subject to well-organized clinical trials. The development of specific therapies and vaccines is therefore urgently required. We examine existing and potential therapies and vaccines from a molecular perspective. These include viral S protein targeting; inhibitors of host proteases, including TMPRSS2, cathepsin L and furin protease, and of viral M(pro) and the PL(pro) proteases; convalescent plasma; and vaccine candidates. The Medline database was searched using combinations and variations of terms, including 'Middle East respiratory syndrome coronavirus', 'MERS-CoV', 'SARS', 'therapy', 'molecular', 'vaccine', 'prophylactic', 'S protein', 'DPP4', 'heptad repeat', 'protease', 'inhibitor', 'anti-viral', 'broad-spectrum', 'interferon', 'convalescent plasma', 'lopinavir ritonavir', 'antibodies', 'antiviral peptides' and 'live attenuated viruses'. There are many options for the development of MERS-CoV-specific therapies. Currently, MERS-CoV is not considered to have pandemic potential. However, the high mortality rate and potential for mutations that could increase transmissibility give urgency to the search for direct, effective therapies. Well-designed and controlled clinical trials are needed, both for existing therapies and for prospective direct therapies.

Overview of Zika infection, epidemiology, transmission and control measures.

The current Zika virus outbreak in the Americas and the proposed link to increases in microcephaly and neurological disorders have prompted the World Health Organization to declare a Public Health Emergency of International Concern on February 1, 2016. The virus is transmitted by Aedes mosquitoes and potentially by transfusion, perinatal and sexual transmission. The potential for spread into countries where Aedes mosquitoes are endemic is high. Previously, cases tended to be sporadic and associated with mild, non-specific symptoms. Prior outbreaks occurred in Yap Island in Micronesia in 2007, the first time Zika arose outside of Africa and Asia, and in French Polynesia in 2013. A birth data review has confirmed that the latter outbreak was followed by an increase in microcephaly cases. A coordinated international response is needed to address mosquito control; expedite development of diagnostic tests, vaccines and specific treatments for Zika; and address the proposed link to microcephaly and neurological diseases.

Direct identification and susceptibility testing of positive blood cultures using high speed cold centrifugation and Vitek II system.

Compared to routine isolated colony-based methods, direct testing of bacterial pellets from positive blood cultures reduces turnaround time for reporting of antibiotic susceptibility. The aim of this study was to compare the accuracy, and precision, of a rapid method for direct identification and susceptibility testing of blood cultures with the routine method used in our laboratory, using Vitek 2. A total of 60 isolates were evaluated using the candidate and the routine method. The candidate method had 100% accuracy for the identification of Gram negative bacteria, Staphylococcus and Enterococcus, 50% for Streptococcus and 33.3% for Corynebacterium species. Susceptibility testing of Gram negative isolates yielded 98-100% essential agreement. For Staphylococcus and Enterococcus isolates, essential agreement was 100% for 17 antibiotics except for moxifloxacin. Direct testing of blood culture samples with Vitek 2 produced reliable identification and susceptibility results 18-24h sooner for aerobic/anaerobic facultative Gram-negative bacteria and Gram-positive Staphylococcus and Enterococcus strains.

Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS.

Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients. In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2) with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1); 100% ethanol treatment (method 3)), and picking colonies from 90 to 180min subculture plates (method 4). Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations.