A case oriented study: Whole genome sequencing (WGS) on a wild urease negative Proteus mirabilis isolated from deep surgical site infection (SSI) at El Hussein University Hospital, Al Azhar University Cairo, Egypt

Background: Proteus mirabilias  ( P. mirabilis) strains are motile Gram negativerods that colonize the humangastrointestinal tract and could be a source of nosocomial infections especially in immune compromised cancer patients. Proteus mirabilis is identified by its urease production as a major bacterial virulence especially in urinary tract infections. Aim: This study aimed to characterize a case of a urease negative P. mirabilis isolated from a cancer patient suffering from deep surgical site infection.  Methods: Conventional biochemical tests performed on swarming bacterial growth cultures were characteristic of P. mirabilis except for urease production. Identification was confirmed by Vitek-2 compact system and Vitek- MS. Dienes test proved the isolate is antigenically different from other urease positive P. mirabilis. Whole genome sequencing (WGS) identified this P. mirabilis strain with the seven encoding urease genes ureABCDEFG as well as their positive regulator gene UreR. Results: Mutations were found within amino acid sequences of UreB, UreE, UreF and UreG and UreR. Antibiotic sensitivity as well as WGS identified resistance genes to multiple classes of antibiotics.  Conclusion: This is the first report of a wildly existed urease negative P. mirabilis due to mutations in the urease gene cluster (UreABC) as well as the regulator UreR. Questions are raised towards the urease enzyme as a key virulence factor to P. mirabilis. Other virulence factors that allow this species to cause other severe infections should be considered. The rate of isolation of urease negative P. mirabilis should be monitored and assessed in the future

Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014.

INTRODUCTION: Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region. METHODS: Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1-3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death. RESULTS: At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens-influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease. CONCLUSIONS: Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest

Self-reported antibiotic stewardship and infection control measures from 57 intensive care units: An international ID-IRI survey

We explored the self-reported antibiotic stewardship (AS), and infection prevention and control (IPC) activities in intensive care units (ICUs) of different income settings. A cross-sectional study was conducted using an online questionnaire to collect data about IPC and AS measures in participating ICUs. The study participants were Infectious Diseases-International Research Initiative (IDI-IR) members, committed as per their institutional agreement form. We analyzed responses from 57 ICUs in 24 countries (Lower-middle income (LMI), n = 13; Upper-middle income (UMI), n = 33; High-income (HI), n = 11). This represented (similar to 5%) of centers represented in the ID-IRI. Surveillance programs were implemented in (76.9%-90.9%) of ICUs with fewer contact precaution measures in LMI ones (p = 0.02); (LMI:69.2%, UMI:97%, HI:100%). Participation in regional antimicrobial resistance programs was more significantly applied in HI (p = 0.02) (LMI:38.4%,UMI:81.8%,HI:72.2%). AS programs are implemented in 77.2% of institutions with AS champions in 66.7%. Infectious diseases physicians and microbiologists are members of many AS teams (59%&50%) respectively. Unqualified healthcare professionals(42.1%), and deficient incentives(28.1%) are the main barriers to implementing AS. We underscore the existing differences in IPC and AS programs' implementation, team composition, and faced barriers. Continuous collaboration and sharing best practices on APM is needed. The role of regional and international organizations should be encouraged. Global support for capacity building of healthcare practitioners is warranted. (C) 2022 Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences

Multinational prospective cohort study of rates and risk factors for ventilator-associated pneumonia over 24 years in 42 countries of Asia, Africa, Eastern Europe, Latin America, and the Middle East: Findings of the International Nosocomial Infection Control Consortium (INICC)

Objective: Rates of ventilator-associated pneumonia (VAP) in low- and middle-income countries (LMIC) are several times above those of high-income countries. The objective of this study was to identify risk factors (RFs) for VAP cases in ICUs of LMICs. Design: Prospective cohort study. Setting: This study was conducted across 743 ICUs of 282 hospitals in 144 cities in 42 Asian, African, European, Latin American, and Middle Eastern countries. Participants: The study included patients admitted to ICUs across 24 years. Results: In total, 289,643 patients were followed during 1,951,405 patient days and acquired 8,236 VAPs. We analyzed 10 independent variables. Multiple logistic regression identified the following independent VAP RFs: male sex (adjusted odds ratio [aOR], 1.22; 95% confidence interval [CI], 1.16-1.28; P <.0001); longer length of stay (LOS), which increased the risk 7% per day (aOR, 1.07; 95% CI, 1.07-1.08; P <.0001); mechanical ventilation (MV) utilization ratio (aOR, 1.27; 95% CI, 1.23-1.31; P <.0001); continuous positive airway pressure (CPAP), which was associated with the highest risk (aOR, 13.38; 95% CI, 11.57-15.48; P <.0001)Revisión por pare

Geographical Variability in the Likelihood of Bloodstream Infections Due to Gram-Negative Bacteria: Correlation with Proximity to the Equator and Health Care Expenditure (vol 9, e114548, 2014)

Hosp Univ Austral, Div Infect Dis Prevent & Infect Control Serv, Buenos Aires, DF, ArgentinaHosp Univ Austral, Microbiol Lab, Buenos Aires, DF, ArgentinaMonash Hlth, Monash Infect Dis, Clayton, Vic, AustraliaWollongong Hosp, Wollongong, NSW, AustraliaUniversidade Federal de São Paulo, Div Infect Dis, Lab Especial Microbiol Clin, São Paulo, BrazilHosp Israelita Albert Einstein, São Paulo, BrazilVirginia Commonwealth Univ, Med Ctr, Richmond, VA USAHosp Rim & Hipertensao, São Paulo, BrazilHosp Santa Casa Porto Alegre, Porto Alegre, RS, BrazilHosp Conceicao, Porto Alegre, RS, BrazilHosp Walter Cantidio, Fortaleza, Ceara, BrazilHosp Diadema, São Paulo, BrazilHosp Espanhol, Salvador, BA, BrazilHosp Clin Goiania, Goiania, Go, BrazilMt Sinai Hosp, Toronto, ON M5G 1X5, CanadaUniv Alberta, Div Infect Dis, Edmonton, AB, CanadaCairo Univ Kasr Ainy, Dar Al Fouad Hosp, Fac Med, Dept Clin Pathol, Cairo, EgyptHygeia Gen Hosp, Athens, GreeceUniv Tubingen Hosp, Internal Med, Div Infect Dis, Tubingen, GermanyTokyo Metropolitan Tama Med Ctr, Dept Infect Prevent, Tokyo, JapanAmphia Hosp Breda, Lab Microbiol & Infect Control, Breda, NetherlandsThammasat Univ Hosp, Div Infect Dis, Pathum Thani, ThailandSt John Hosp & Med Ctr, Infect Prevent & Control Dept, Grosse Pointe Woods, MI USAUniv Hosp Bern, Dept Infect Dis, CH-3010 Bern, SwitzerlandUniv Bern, Bern, SwitzerlandBarnes Jewish Hosp, St Louis, MO 63110 USAUniversidade Federal de São Paulo, Div Infect Dis, Lab Especial Microbiol Clin, São Paulo, BrazilWeb of Scienc

International Nosocomial Infection Control Consortium report, datasummary of 50 countries for 2010-2015 : Device-associated module

Q3Artículo original1495-1504Background: We report the results of International Nosocomial Infection Control Consortium (INICC) sur-veillance study from January 2010-December 2015 in 703 intensive care units (ICUs) in Latin America,Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific.Methods:During the 6-year study period, using Centers for Disease Control and Prevention National Health-care Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI), we collected prospective data from 861,284 patients hospitalized in INICC hospital ICUs for an aggregateof 3,506,562 days.Results:Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAIrates were higher in the INICC ICUs: in the INICC medical-surgical ICUs, the pooled rate of central line-associated bloodstream infection, 4.1 per 1,000 central line-days, was nearly 5-fold higher than the 0.8per 1,000 central line-days reported from comparable US ICUs, the overall rate of ventilator-associatedpneumonia was also higher, 13.1 versus 0.9 per 1,000 ventilator-days, as was the rate of catheter-associated urinary tract infection, 5.07 versus 1.7 per 1,000 catheter-days. From blood cultures samples,frequencies of resistance ofPseudomonasisolates to amikacin (29.87% vs 10%) and to imipenem (44.3%vs 26.1%), and ofKlebsiella pneumoniaeisolates to ceftazidime (73.2% vs 28.8%) and to imipenem (43.27%vs 12.8%) were also higher in the INICC ICUs compared with CDC-NHSN ICUs.Conclusions:Although DA-HAIs in INICC ICU patients continue to be higher than the rates reported inCDC-NSHN ICUs representing the developed world, we have observed a significant trend toward the re-duction of DA-HAI rates in INICC ICUs as shown in each international report. It is INICC’s main goal tocontinue facilitating education, training, and basic and cost-effective tools and resources, such as stan-dardized forms and an online platform, to tackle this problem effectively and systematically

Prevalence of Human rhinovirus infection in young children with acute wheezing

Introduction: Recurrent wheezing is one of the leading causes of chronic illness in childhood. We aimed to evaluate the prevalence of Human Rhinovirus (HRV) infection in the acute attack of wheezy chest which began after a respiratory illness. Methodology: The study was conducted on 200 children aged 2 months to 5 years presenting to the emergency department with an acute wheezy episode either for the first time or recurrent wheeze defined as >2 reports of wheezing in the first 3 years of life. All subjects were subjected to a complete history and clinical examination. Chest X-ray was done to all subjects. Nasopharyngeal and oropharyngeal swabs were obtained from all subjects and the presence of HRV was determined by PCR examination. Results: By PCR method, 163 patients (81.5%) were positive for viral infection. Due to viral co-infection, 49.5% (99 cases) were +ve for Respiratory Syncytial virus followed by HRV 43.5% (87 cases). Conclusion: HRV was the second common viral infection in children with wheezes. Its prevalence was more in winter with higher incidence of recurrence. Compared to the other respiratory viruses, it had the higher mortality 43.7%. Keywords: Asthma, Rhinovirus infection, Wheeze

Diagnostic role of FilmArray Pneumonia Panel compared to routine microbiological methods to identify pneumonia pathogens

Background: Lower respiratory tract infections can be caused by an array of pathogens. Rapid and accurate identification of these organisms is essential for selection of the appropriate antimicrobial regimen. Objectives: Identify microbiology of lower respiratory tract samples by the syndromic multiplex BioFire FilmArray Pneumonia Panel (FAPP) and correlate with the findings by routine microbiological methods. Methods: This study was conducted on 118 non-repetitive respiratory samples, collected through March 2020 to February 2021 for isolation and identification of respiratory pathogens. Results: The FAPP yielded an overall positivity rate of (85/118; 72%). Compared to routine culture; the FAPP were concordantly positive for 37/118 (31.4%) of specimens, and discordant for 39/118 specimens (33%) with 92.5% of positive percentage of agreement. The commonest bacterial pathogens detected by the two methods were Klebsiella pneumoniae, Pseudomonas aeruginosa. Of note, Acinetobacter and other bacterial pathogens were frequently detected by FAPP and not by culture, indicating colonization or contamination (false-positive results). False-negative FAPP results were Candida and bacterial pathogens not included in the FAPP panel, as Morganella. At the semi-quantification level, the concordance rate was 93.9% as out of forty- nine bacterial cultures with significant growth, 46 showed a higher semi-quantification of more than 105 copies of DNA/ml by FAPP and (27/46; 58.7%) showed total agreement with target pathogens isolated by the culture too. Conclusion: BioFire FilmArray Pneumonia Panel (FAPP) was sensitive and detected more potential pneumonia pathogens than culture methods, but it should be interpreted cautiously. Semi- quantification of FAPP helped to understand pathogen significance and correlate with true pathogen

Phenotypic and Genotypic Features of Klebsiella pneumoniae Harboring Carbapenemases in Egypt: OXA-48-Like Carbapenemases as an Investigated Model

This study aimed at the characterization of carbapenem-resistant Klebsiella pneumoniae isolates focusing on typing of the blaOXA-48-like genes. Additionally, the correlation between the resistance pattern and biofilm formation capacity of the carbapenem-resistant K. pneumoniae isolates was studied. The collected isolates were assessed for their antimicrobial resistance and carbapenemases production by a modified Hodge test and inhibitor-based tests. The carbapenemases encoding genes (blaKPC, blaNDM, blaVIM, blaIMP, and blaOXA-48-like) were detected by PCR. Isolates harboring blaOXA-48-like genes were genotyped by Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR) and plasmid profile analysis. The discriminatory power of the three typing methods (antibiogram, ERIC-PCR, and plasmid profile analysis) was compared by calculation of Simpson&rsquo;s Diversity Index (SDI). The transferability of blaOXA-48 gene was tested by chemical transformation. The biofilm formation capacity and the prevalence of the genes encoding the fimbrial adhesins (fimH-1 and mrkD) were investigated. The isolates showed remarkable resistance to &beta;-lactams and non-&beta;-lactams antimicrobials. The coexistence of the investigated carbapenemases encoding genes was prevalent except for only 15 isolates. The plasmid profile analysis had the highest discriminatory power (SDI = 0.98) in comparison with ERIC-PCR (SDI = 0.89) and antibiogram (SDI = 0.78). The transferability of blaOXA-48 gene was unsuccessful. All isolates were biofilm formers with the absence of a significant correlation between the biofilm formation capacity and resistance profile. The genes fimH-1 and mrkD were prevalent among the isolates. The prevalence of carbapenemases encoding genes, especially blaOXA-48-like genes in Egyptian healthcare settings, is worrisome and necessitates further strict dissemination control measures

Diagnosis of human brucellosis in Egypt by PCR

Background: Brucellosis is a significant health problem in Egypt.Methodology: To establish a PCR technique for diagnosis of active brucellosis in our institutions, DNA extraction was done using a commercial kit, and a laboratory extraction procedure. PCR amplification was done using 2 sets of primers: B4/B5 and JPF/JPR. Extraction of Brucella DNA using the commercial kit failed; therefore, this technique was discontinued. The laboratory extraction method was successful and more economic.Results: The technique showed high sensitivity, specificity, and accuracy. The PCR positivity increased significantly (P=0.001) with increasing the positive standard tube agglutination titer and showed 100% positivity in patients with positive blood culture.Conclusions: An accurate and sensitive PCR technique was established. Based on the results, the PCR method is recommended as an alternative to culture for the diagnosis of brucellosis. A large-scale study to evaluate this PCR technique to screen for brucellosis in Egypt is needed