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The occurrence and antimicrobial resistance (AMR) of typhoid fever in the WHO Eastern Mediterranean Region (EMR) are poorly characterized. Robust surveillance data are needed to inform strategies for typhoid control and prevention in the region. We conducted a systematic review of typhoid fever occurrence, complications, and AMR patterns in EMR countries. We identified 70 studies published from 1990 to 2021, including a total of 44,541 cases with blood culture confirmed typhoid fever in 12 EMR countries, with 48 (69%) studies and 42,008 cases from Pakistan. Among 56 studies with AMR data, fluroquinolone (68% of 13,013 tested isolates), and multidrug resistance (40% of 15,765 tested isolates) were common. Forty (57%) of the 56 studies were from Pakistan, and all reports of extensively drug resistant Salmonella Typhi (48% of 9,578 tested isolates) were from studies in Pakistan. Our findings support the need for continued efforts to strengthen surveillance and laboratory capacity for blood-culture detection of typhoid fever in the region, including data from an ongoing collaboration among CDC, the American University of Beirut, and the WHO EMR office.

Introduction: The role of bacteria in the pathogenesis of periodontitis, pericoronitis, and periapical infections has been well-established. However, the variation in the severity and prognosis of these lesions could suggest a potential role of other microorganisms, such as viruses and fungi. This study aims to evaluate the presence of adenovirus, human papillomavirus-16, Epstein-Barr virus, Candida, and non-Candida fungi in these infections. Methodology: A cross-sectional study including 120 healthy adult patients presenting with dental infections requiring dental extractions were conducted to assess the prevalence and the relative quantity of viruses and fungi in saliva, infected, and healthy tissues using quantitative polymerase chain reaction tests. Samples were collected, and a categorical scale was used for the prevalence and a continuous scale for the relative quantification. Statistical analyses were performed using Chi-square for the prevalence and Wilcoxon rank test for the relative quantification. Results: Except for the Epstein-Barr virus and Candida, the presence of viruses and fungi was significantly associated with dental infections. Adenovirus showed an association with pericoronitis, while human papilloma virus-16 exhibited an association with periapical infections. Non-Candida fungi, on the other hand, showed a positive association with all infected tissues and saliva as compared to healthy control lesions except for periapical infections. Conclusions: According to this study, viruses and fungi were found to be prevalent in dental infections. However, their associations with those infections vary depending on the types of viruses or fungi involved and the category of dental infections.

The impact of pneumococcal conjugate vaccines (PCVs) on the burden of invasive pneumococcal disease (IPD) and serotype distribution was examined across age groups from data collected by the Lebanese Inter-Hospital Pneumococcal Surveillance Program. Between 2005 and 2020, 593 invasive Streptococcus pneumoniae isolates were collected from 79 hospitals throughout Lebanon. Serotypes and antimicrobial resistance (AMR) profiles were identified, and trends compared over 3 eras: PCV7, post-PCV7/ pre-PCV13, and PCV13 eras. The prevalence of PCV7 serotypes decreased significantly from 43.6% in the PCV7 era to 17.8% during the PCV13 era (p

BackgroundThe coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. Secondary bacterial infections are associated with unfavorable outcomes in respiratory viral infections. This study aimed at determining the prevalence of secondary bacterial infections in COVID-19 patients admitted at a tertiary medical center in Lebanon.MethodologyFrom May till November, 2020, a total of 26 Gram-negative isolates were recovered from 16 patients during the course of their COVID-19 infection with Escherichia coli being the most prevalent. The isolates were assessed for their antimicrobial susceptibility by broth microdilution against 19 antimicrobial agents from different classes. Whole genome sequencing of 13 isolates allowed the mining of antimicrobial resistance (AMR) determinants as well as mobile genetic elements and sequence types (ST). Finally, broth microdilution with three different efflux pump inhibitors [theobromine, conessine and PheArg-β-naphthylamide (PAβN)] was done.ResultsAntimicrobial susceptibility testing showed that out of the 26 Gram-negative isolates, 1 (4%) was extensively drug resistant and 14 (54%) were multi-drug resistant (MDR). Whole genome sequencing results revealed a plethora of AMR determinants among the 13 sequenced isolates. Moreover, the 9 Enterobacterales and 4 Pseudomonas aeruginosa sequenced isolates belonged to 9 and 2 different ST, respectively. Using a variety of efflux pump inhibitors we demonstrated that only PAβN had a significant effect when combined with levofloxacin, and the latter regained its activity against two P. aeruginosa isolates.ConclusionThe identification of carbapenem and colistin resistant Gram-negative bacilli causing secondary bacterial infections in critical patients diagnosed with COVID-19 should be of high concern. Additionally, it is crucial to monitor and track AMR, post-COVID pandemic, in order to better understand the effect of this disease on AMR exacerbation.

BackgroundThe emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon.MethodsWe collected 250 nasopharyngeal swabs from HCWs across Lebanon between December 2021 and January 2022. Data on the date of positive PCR, vaccination status, specific occupation, and hospitalization status of participants were collected. Extracted viral RNA from nasopharyngeal swabs was converted to cDNA, library prepped using the coronaHIT method, followed by whole genome sequencing on the Illumina NextSeq 500 platform.ResultsA total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant.ConclusionThis study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

International audience; This cross-sectional study was conducted to determine the prevalence of Salmonella at different stages of the broiler production chain and layer flocks in addition to their antibiotic resistance profile and molecular patterns. Over a period of 3 years, different sample matrices were collected from Lebanese farms, slaughterhouses and retail markets. Out of 672 Salmonella serotyped, 514 were analysed for antimicrobial resistance and 214 for clonality using Pulsed-field gel electrophoresis (PFGE). The results highlighted an important prevalence of Salmonella, 30% in farms, 35.8% in slaughterhouses and 22.4% at retail level. A large diversity of serotypes was identified with predominance among Salmonella Infantis (32.9%), Salmonella Enteritidis (28.4%) and Salmonella Kentucky (21.4%). High resistance to nalidixic acid was revealed in all the isolates. The most prominent resistance was exhibited in S. Kentucky and S. Infantis. The latter was resistant to tetracycline (99%), streptomycin (88.2%) and remarkable multi-drug resistance (MDR) (89.7%). All S. Kentucky isolates were resistant to ciprofloxacin, MDR (62.4%) and 6% were resistant to extended-spectrum cephalosporin (ESCs). One persistent clone of S. Enteritidis was found common between poultry and humans. Similar genomic profiles were detected between farms, slaughterhouses and retail suggesting the dissemination of identical clones throughout the food chain possibly due to weak barriers preventing such transmission.

Carbapenem resistance in Enterobacteriaceae, Acinetobacter baumannii and Pseudomonas aeruginosa is increasing worldwide, which has led the World Health Organization (WHO) to list these bacteria in the critical priority pathogens group. Infections by such pathogens pose a serious threat to hospitalised patients and are associated with clinical and economic consequences. What worsens the case is the weak pipeline of available antimicrobial agents to treat such infections and the absence of new drugs. The aim of this review was to shed light on all studies tackling carbapenem resistance in Enterobacteriaceae, A. baumannii and P. aeruginosa in the Eastern Mediterranean region, with indication for each country, description of studies timeline, prevalence of carbapenem resistance, and carbapenem resistance-encoding genes detected in these countries.

The emergence of SARS-CoV-2 variants including the Delta and Omicron along with waning of vaccine-induced immunity over time contributed to increased rates of breakthrough infection specifically among healthcare workers (HCWs). SARS-CoV-2 genomic surveillance is an important tool for timely detection and characterization of circulating variants as well as monitoring the emergence of new strains. Our study is the first national SARS-CoV-2 genomic surveillance among HCWs in Lebanon. We collected 250 samples from five hospitals across Lebanon between December 2021 and January 2022. We extracted viral RNA and performed whole genome sequencing using the Illumina NextSeq 500 platform. A total of 133 (57.1%) samples belonging to the Omicron (BA.1.1) sub-lineage were identified, as well as 44 (18.9%) samples belonging to the BA.1 sub-lineage, 28 (12%) belonging to the BA.2 sub-lineage, and only 15 (6.6%) samples belonging to the Delta variant sub-lineage B.1.617.2. These results show that Lebanon followed the global trend in terms of circulating SARS-CoV-2 variants with Delta rapidly replaced by the Omicron variant. This study underscores the importance of continuous genomic surveillance programs in Lebanon for the timely detection and characterization of circulating variants. The latter is critical to guide public health policy making and to timely implement public health interventions.

This is a retrospective medical file review of adult inpatients with Streptococcus pneumoniae infections admitted to a Lebanese hospital between 2006 and 2015. We revisited the clinical scenarios of these infections in view of increasing antibiotic resistance in Lebanon. One hundred and three patients were included; 92% were eligible for pneumococcal vaccination, yet none were vaccinated. Non-invasive pneumococcal disease (non-IPD) represented 64% of these infections. Superinfections caused by antibiotic-resistant bacteria were documented in 17.5% of the patients, with the predominance of ventilator-associated pneumonia (12.6%). Kidney disease and septic shock were positive predictors for mortality [adjusted odds ratio (OR) = 14.96, 95% confidence interval (CI) 2.34–95.45, P = 0.004; OR = 5.09, 95% CI 1.33–19.51, P = 0.02, respectively]. Herein, the differences in clinical success, S. pneumoniae infection-related death, and total mortality were not statistically significant between invasive pneumococcal disease (IPD) and non-IPD subgroups (59.5% vs. 77.3%, P = 0.056; 21.6% vs. 9.1%, P = 0.08; and 35.1% vs. 22.7%, P = 0.174; respectively). Upon comparing antibiotic susceptibility of S. pneumoniae during the first two years of the study (2006–2007) (n = 32 isolates) and the last two (2014–2015) (n = 14 isolates), there was an increasing non-susceptibility to penicillin (34.4%–50.0%, P = 0.25), and a decreasing susceptibility to erythromycin and clindamycin (81.3%–78.6%, P = 0.67 and 90.6%–85.7%, P = 0.65; respectively).

Objectives To investigate the acquired resistome in 18 colistin-resistant Escherichia coli isolated from different poultry farms in Lebanon, analyse Inc plasmids associated with mcr and assess potential transmission to humans. Methods A total of 18 E. coli were recovered from poultry faeces collected from different poultry farms in Lebanon. Broth microdilution (BMD) assay was performed to determine the antimicrobial resistance profiles. WGS was used to identify the genetic determinants behind the resistance in these isolates. Results BMD results showed that all of the 18 isolates were colistin resistant. Furthermore, resistance to trimethoprim/sulfamethoxazole was the most recorded among the isolates and only one isolate was resistant to cefepime. Sequencing results showed that the isolates were distributed into seven different STs and that the most abundant was ST1140. The number of antimicrobial resistant determinants ranged from 4 to 21 among the 18 isolates, with tet(A) and floR being the most frequent. Moreover, a total of 15 different plasmid replicon types were identified. The mcr-1 gene was shown to be predominantly located on IncX4 plasmids. Additionally, two isolates harboured the IncI2-type self-conjugative plasmid. Conclusions The findings show that mcr and other important resistance determinants occur in MDR E. coli isolated poultry farms in Lebanon. The occurrence of mcr on mobile plasmids and the zoonotic potential and clinical relevance of some strains highlight a risk of transmission to humans.

Background and aim: Extended-spectrum beta-lactamases are the main cause of resistance in Enterobacteriaceae to beta lactam antibiotics. The aim of this study was to evaluate the antimicrobial effect of EpiQuercican supplement, combined with different antimicrobial agents, on ESBL-producing isolates and determine the underlying molecular mechanism of resistance in these isolates. Materials and methods: Eleven ESBL producing Enterobacteriaceae isolates were collected from Saudi Arabia hospitals between 2016 and 2017 and disk diffusion test was performed in accordance with Clinical and Laboratory Standards Institute (CLSI) guidelines to determine the susceptibility of the isolates to 5 different antibiotics in the presence of EpiQuercican supplement. Polymerase chain reaction was performed for detection of ESBL genes, and efflux pump inhibitor was used to study the mechanism of resistance in these isolates. Results: The best synergistic effect was obtained when the supplement was combined with carbapenems followed by 4th generation cephalosporins. Either no effect or antagonistic effect was seen with most of the isolates when the supplement was added to the 3rd generation of cephalosporins. Among the tested genes responsible for ESBL production in this study, our results indicated the predominance of TEM genes (73%) followed by CTX-M genes (9%). As for the mechanism of resistance in ESBL isolates, 4 isolates showed to use efflux pumps as their main mechanism of resistance. Conclusion: The EpiQuercican supplement showed some promising results, yet its antibacterial mechanism of action needs to be elucidated further. Keywords: EpiQuercican, Enterobacteriaceae, ESBL

Beards are controversial in the operating room setting because of the possible retention and shedding of pathogens. Surgical site infection poses a significant burden on healthcare systems. All male healthcare workers who entered the operating room were approached to participate in the study. Four facial swab samples were anonymously collected and a hygiene practice questionnaire was administered. Sample A was taken from the upper and lower lips, sample B from cheeks, and samples C and D were collected by 20 and 40 cm shedding below the face. Colony-forming units (CFUs) and minimum inhibitory concentrations (MICs) of meropenem resistance were determined for samples A and B. Random samples from A, B, C, and D, in addition to meropenem-resistant isolates were cultured with chlorohexidine. Sixty-one bearded and 19 nonbearded healthcare workers participated in the study. 98% were positive for bacterial growth with CFU ranging between 30 × 104 and 200 × 106 CFU/mL. Bacterial growth was significantly higher in bearded participants (P.05). Eighteen (27.1%) isolates were resistant to meropenem; of these which 14 (77.8%) were from bearded participants, this was not statistically significant. Chlorohexidine was effective in inhibiting the growth of all strains including the meropenem-resistant isolates. Bearded men in the operating room had a significantly higher facial bacterial load. Larger-scale resistance studies are needed to address facial bacterial resistance among healthcare workers in the operating room. This study aimed to estimate the facial microbial load and identify strains and antimicrobial resistance profiles in bearded versus nonbearded male healthcare workers in the operating room of a tertiary hospital in the Middle East.

To investigate the acquired resistome in 18 colistin-resistantA total of 18BMD results showed that all of the 18 isolates were colistin resistant. Furthermore, resistance to trimethoprim/sulfamethoxazole was the most recorded among the isolates and only one isolate was resistant to cefepime. Sequencing results showed that the isolates were distributed into seven different STs and that the most abundant was ST1140. The number of antimicrobial resistant determinants ranged from 4 to 21 among the 18 isolates, withThe findings show that

ObjectiveWe recently demonstrated that EBV DNA is correlated with proinflammatory responses in mice and in rheumatoid arthritis (RA) patients; hence, we utilized an RA mouse model to examine whether EBV DNA enhances the risk and severity of arthritis and to assess its immunomodulatory effects.MethodsC57BL/6J mice were treated with collagen (arthritis-inducing agent), EBV DNA 6 days before collagen, EBV DNA 15 days after collagen, Staphylococcus epidermidis DNA 6 days before collagen, EBV DNA alone, or water. Mice were then monitored for clinical signs and affected joints/footpads were histologically analysed. The relative concentration of IgG anti- chicken collagen antibodies and serum cytokine levels of IL-17A and IFNϒ were determined by ELISA. The number of cells co-expressing IL-17A and IFNϒ in joint histological sections was determined by immunofluorescence.ResultsThe incidence of arthritis was significantly higher in mice that received EBV DNA prior to collagen compared to mice that only received collagen. Similarly, increased clinical scores, histological scores and paw thicknesses with a decreased gripping strength were observed in groups treated with EBV DNA and collagen. The relative concentration of IgG anti-chicken collagen antibodies was significantly increased in the group that received EBV DNA 6 days prior to collagen in comparison to the collagen receiving group. On the other hand, the highest number of cells co-expressing IFNϒ and IL-17A was observed in joints from mice that received both collagen and EBV DNA.ConclusionEBV DNA increases the incidence and severity of arthritis in a RA mouse model. Targeting mediators triggered by viral DNA may hence be a potential therapeutic avenue.

Background: Foodborne diseases are still a major health issue in Lebanon, although some steps have been taken forward in food safety. To this purpose, PulseNet Lebanon, a foodborne diseases tracking network, was established in 2009, through the collaboration between the Ministry of Public Health (MoPH) and the American University of Beirut (AUB). Materials and Methods: Three papers published regarding the PulseNet project were summarized. Initially, clinical and food samples, collected within the surveillance network scope, were identified by using the respective API for Salmonella and Listeria spp. Salmonella spp. were further serotyped by using the Kauffman and White method. Campylobacter spp. were determined by the 16 S rRNA sequencing method. Antimicrobial susceptibility to a number of antibiotics was determined by using the disk diffusion method for Samonella and Campylobacter spp. Genomic diversity was determined by using pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD). Results: Results indicated that 290 clinical and 49 food isolates were identified as Salmonella. Serotyping revealed the prevalence of ten and seven serotypes in the clinical and food samples, respectively. Fifty-one isolates from chicken ceca and carcass were identified to be Campylobacter spp. Fifty-nine samples were identified to be Listeria monocytogenes. Antimicrobial susceptibility testing revealed a wide range of resistance among the different samples. PFGE showed a variation in pulsotypes among the Salmonella serotypes. PFGE also linked certain outbreaks to their food sources. This method also demonstrated 13 subtypes with 100% similarity among the L. monocytogenes isolates. Finally, the Camplyobcater spp. were grouped into nine clusters with a minimum similarity of 43.5% using RAPD. Conclusion: This summary of results shows the importance of implementing a “farm-to-fork” approach in the surveillance of foodborne disease outbreaks in Lebanon, allowing the detection of pathogens causing foodborne disease outbreaks in a timely fashion.

BackgroundInvasive pneumococcal disease (IPD) remains a global health problem. IPD incidence has significantly decreased by the use of pneumococcal conjugate vaccines (PCV). Nevertheless, non-PCV serotypes remain a matter of concern. Eight Streptococcus pneumoniae serotype 24F isolates, belonging to a non-PCV serotype, were detected through the Lebanese Inter-Hospital Pneumococcal Surveillance Program. The aim of the study is to characterize phenotypic and genomic features of the 24F isolates in Lebanon.MethodsWGS using long reads sequencing (PacBio) was performed to produce complete circular genomes and to determine clonality, antimicrobial resistance and virulence determinants.ResultsThe sequencing results yielded eight closed circular genomes. Three multilocus sequence typing (MLST) types were identified (ST11618, ST14184, ST15253). Both MLST and WGS analyses revealed that these isolates from Lebanon were genetically homogenous belonging to clonal complex CC230 and clustered closely with isolates originating from Canada, United States of America, United Kingdom and Iceland. Their penicillin binding protein profiles correlated with both β-lactam susceptibility patterns and MLST types. Moreover, the isolates harbored the macrolide and tetracycline resistance genes and showed a similar virulence gene profile. To our knowledge, this study represents the first report of complete phenotypic and genomic characterization of the emerging Streptococcus pneumoniae, serotype 24F, in the Middle East and North Africa region.

Antimicrobial resistance (AMR) is a worldwide health concern that continues to escalate. A PubMed literature search identified articles from January 2015–August 2020 reviewing cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria (GNB) in Lebanon, Jordan and Iraq, specifically focused on three main pathogens, namely Acinetobacter spp., Enterobacteriaceae (i.e. Escherichia coli and Klebsiella spp.) and Pseudomonas aeruginosa. Sixty-seven relevant articles published within the past 5 years highlighting trends in AMR in Lebanon, Jordan and Iraq were included. Increased resistance to carbapenems in Acinetobacter spp. isolates was observed in Lebanon, Jordan and Iraq; colistin resistance remained relatively low. Studies on Enterobacteriaceae isolates were more varied, with high rates of carbapenem and cephalosporin resistance and lower levels of colistin resistance in Lebanon. Studies from Iraq found high cephalosporin and colistin resistance along with increased susceptibility to carbapenems. In Jordan, most studies recorded high resistance to cephalosporins along with high susceptibility to carbapenems and colistin. Studies on P. aeruginosa isolates were limited: most isolates in Lebanon were carbapenem-resistant and colistin-susceptible; studies in Iraq showed varying levels of resistance to carbapenems and cephalosporins with high susceptibility to colistin; and studies in Jordan found varying levels of susceptibility to carbapenems, cephalosporins and colistin. The most commonly observed resistance mechanisms in GNB were genetic modifications causing increased expression of antimicrobial-inactivating enzymes and decreased permeability. Overall, this review highlights the concerning rise in AMR and the need for improved understanding of the resistance mechanisms to better inform healthcare providers when recommending treatment for patients in this region.

Introduction: Infections caused by extensively-drug resistant (XDR) and pan-drug resistant (PDR) Klebsiella pneumoniae represent an emerging threat due to the high associated mortality. This study aimed to characterize two carbapenem resistant K. pneumoniae strains from the same patient, the first being PDR (referred to as IMP 1078b) and the second being XDR (referred to IMP 1078s) isolated from the same patient. Methodology: Antimicrobial susceptibility testing was done for the 2 K. pneumoniae isolates, followed by carbapenem/β-lactamase inhibitor combination assay, and fitness cost against cefepime and meropenem. Then, whole-genome sequence analysis was performed to decipher the molecular mechanisms behind the high level of resistance recorded in both isolates. Finally, qRT-PCR was done for β-lactam resistant genes. Results: This is the first report about a K. pneumoniae isolate harboring 47 antimicrobial resistance genes and having type IV pilli (Yersinia) and the fimbrial adherence determinant Stb (Salmonella) as virulence factors. Further analysis on both isolates are discussed within the article. Conclusion: The co-existence of a high number of antimicrobial resistant (AMR) genes and virulence factor genes may lead to a life threatening invasive and untreatable infection.

The beginning of the twenty-first century has been marked by three distinct waves of zoonotic coronavirus outbreaks into the human population. The current pandemic COVID-19 (Coronavirus disease 2019) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With a rapid infection rate, it is a global threat endangering the livelihoods of millions worldwide. Currently, and despite the collaborative efforts of governments, researchers, and the pharmaceutical industries, there are no substantially significant treatment protocols for the disease. To address the need for such an immediate call of action, we leveraged the largest dataset of drug-induced transcriptomic perturbations, public SARS-CoV-2 transcriptomic datasets, and expression profiles from normal lung transcriptomes. Our unbiased systems biology approach not only shed light on previously unexplored molecular details of SARS-CoV-2 infection (e.g., interferon signaling, inflammation and ACE2 co-expression hallmarks in normal and infected lungs) but most importantly prioritized more than 50 repurposable drug candidates (e.g., Corticosteroids, Janus kinase and Bruton kinase inhibitors). Further clinical investigation of these FDA approved candidates as monotherapy or in combination with an antiviral regimen (e.g., Remdesivir) could be promising treatment options against COVID-19.

Background: Countries in the World Health Organization (WHO) Eastern Mediterranean Region (EMR) are predisposed to highly contagious, severe and fatal, emerging infectious diseases (EIDs), and re-emerging infectious diseases (RIDs). This paper reviews the epidemiological situation of EIDs and RIDs of global concern in the EMR between 2001 and 2018. Methods: To do a narrative review, a complete list of studies in the field was we prepared following a systematic search approach. Studies that were purposively reviewed were identified to summarize the epidemiological situation of each targeted disease. A comprehensive search of all published studies on EIDs and RIDs between 2001 and 2018 was carried out through search engines including Medline, Web of Science, Scopus, Google Scholar, and ScienceDirect. Results: Leishmaniasis, hepatitis A virus (HAV) and hepatitis E virus (HEV) are reported from all countries in the region. Chikungunya, Crimean Congo hemorrhagic fever (CCHF), dengue fever, and H5N1 have been increasing in number, frequency, and expanding in their geographic distribution. Middle East respiratory syndrome (MERS), which was reported in this region in 2012 is still a public health concern. There are challenges to control cholera, diphtheria, leishmaniasis, measles, and poliomyelitis in some of the countries. Moreover, Alkhurma hemorrhagic fever (AHF), and Rift Valley fever (RVF) are limited to some countries in the region. Also, there is little information about the real situation of the plague, Q fever, and tularemia. Conclusion: EIDs and RIDs are prevalent in most countries in the region and could further spread within the region. It is crucial to improve regional capacities and capabilities in preventing and responding to disease outbreaks with adequate resources and expertise.

Human rotavirus remains a major cause of gastroenteritis worldwide despite the availability of effective vaccines. In this study, we investigated the genetic diversity of rotaviruses circulating in Lebanon. We genetically characterized the VP4 and VP7 genes encoding the outer capsid proteins of 132 rotavirus-associated gastroenteritis specimens, previously identified in hospitalized children (

Objectives Extended-spectrum β-lactamases (ESBLs) are increasingly detected globally among Escherichia coli and Klebsiella spp. Studies show a link between inappropriate use of antibiotics and resistance. In this study, the profiles of ESBLs in E. coli and Klebsiella spp. isolated from three Lebanese hospitals and their relationship to antibiotic consumption were determined. Methods A total of 300 E. coli and 91 Klebsiella spp. isolates resistant to third- or fourth-generation cephalosporins were collected between May 2011 and December 2012. Antibiotic susceptibility and consumption data were also collected from 2010–2012. Double-disk synergy and Etest ESBL assays were performed, followed by PCR for ESBL genes. Pulsed-field gel electrophoresis (PFGE) was performed for representative isolates. Statistical analysis for consumption and susceptibility data over 3 years was performed. Results Similar to other Lebanese studies, CTX-M-15 was predominant. Among the Klebsiella spp. isolated in hospitals 1 and 2, 43% harboured four different ESBLs. Eight Klebsiella spp. and fourteen E. coli pulsotypes were detected, showing genetic diversity among isolates. A significant correlation was detected between total use of antimicrobial agents and resistance to various antibiotics. A correlation was also detected between use of penicillins and resistance to aztreonam, ceftazidime and ciprofloxacin, and use of third- and fourth-generation cephalosporins and resistance to ceftazidime, cefuroxime, cefoxitin and ciprofloxacin in Klebsiella spp. ( P 0.05). Conclusions This study shows the predominance of CTX-M-15 among cephalosporin-resistant E. coli and Klebsiella spp. in Lebanese hospitals. It also shows that the heightened use of antibiotics could be a driving factor for resistance emergence.

Background The objective of this study was to determine whether patients infected with extended-spectrum beta-lactamase (ESBL)-producing organisms are colonized at multiple body sites. Methods This was a prospective cohort study at a tertiary care center in Beirut, Lebanon. Hospitalized patients with infections caused by ESBL-producing organisms were included. Cultures were obtained from the primary site of infection as well as from other sites (skin, nasopharynx, urine, rectum). Molecular analysis was performed on isolates to determine clonal relatedness. Results One hundred patients were included in the study. Only 22 patients had positive cultures from sites other than the primary site of infection. The most common ESBL gene was CTX-M-15 followed by TEM-1. In 11 of 22 patients, isolates collected from the same patient were 100% genetically related, while in the remaining patients, genomic relatedness ranged from 42.9% to 97.1%. Conclusions Colonization at sites other than the primary site of infection was not common among our patient population infected with ESBL-producing organisms. The dynamics of transmission of these bacterial strains should be studied in further prospective studies to determine the value of routine active surveillance and the need for expanded precautions in infected and colonized patients.

Background Acute respiratory infections (ARI) are the leading cause of death worldwide, especially among children. The majority of these infections in children are of viral etiology. In this study, we evaluated the incidence of viral ARI among children in Lebanon. Patients and methods Children presenting with symptoms of ARI were prospectively recruited between September 2009 to February 2012. Nasopharyngeal aspirates were obtained from patients and screened for 11 respiratory viruses using a multiplex Luminex-based PCR assay. Results Two hundred twenty-one patients were recruited with a median age of 1 year (IQR: 0 - 5). Out of 221 patients, 116 (52.5%) were positive for at least one virus, the majority (103/116; 88.8%) of which were in children under 6-year of age. Overall, 188 viruses were detected. Rhinovirus (RhV) was the most common virus detected in 81 (69.8%) patients followed by coxsackie virus and echovirus (CVEV) which were detected as one target in the panel in 45 (38.8%), and parainfluenza viruses (PIV types: 1, 2, 3, 4) in 24 (20.7%) patients. Coinfection with more than one virus was detected in 49 (42.9%) patients. RhV and CVEV were the most common viruses associated with co-infections and higher risk of rhinorrhea. Conclusions Viral pathogens account for at least half of the ARIs in Lebanon, with a high frequency of co-infections being detected.

Introduction: Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in Lebanon are scarce. This study was undertaken to reveal the spoligotypes of MTB isolates recovered from patients in Lebanon. Methodology: MTB isolates from 49 patients living in Lebanon were recovered and identified. The samples were heat killed and subjected to DNA extraction. Spoligotyping was performed using microbeads from TB-SPOL Kit and the fluorescence intensity was measured using Luminex 200®. Generated patterns were assigned to families using the SITVIT2 international database of the Pasteur Institute of Guadeloupe and compared. Results: The spoligotyping of the 49 MTB isolates revealed that 31 isolates belonged to Lineage 4 (Euro-American, 63.3%), 12 to Lineage 3 (East- African Indian, 24.5%), 3 to Lineage 2 (East Asian, 6%) and 2 were unknown. Over half of the genotypes (16 of 30) harbored SIT127 supposed to belong to the L4.5 sublineage. One isolate belonging to the rare Manu-Ancestor SIT523 was recovered for the first time in Lebanon, being associated with highly virulent extensively drug-resistant (XDR) MTB phenotype. Conclusion: The application of the Spoligotyping Multiplex Luminex® method is an efficient, discriminatory and rapid method to use for first-lane genotyping of MTB isolates. Though humble numbers were tested, this study is one of the first to describe the genomic diversity and epidemiology of MTB isolates of Lebanon, and suggests an increasing prevalence of SIT127 in the country.

Introduction: Most hospitals rely on rapid antigen-detection kits for the diagnosis of rotavirus infection. Several small studies reviewed the sensitivity and specificity of some of these kits. These studies showed discrepancy in results obtained for sensitivity and specificity that varied according to the type of kit used, area of study, and type of test used as standard for diagnosis of rotavirus infection. The objective of the study is to determine the sensitivity and specificity of five commonly used rotavirus immunoassay kits in comparison to RT-PCR as standard. Methodology: Stool samples (N = 1,414) collected from children under 5 years of age hospitalized with gastroenteritis were tested for rotavirus by immunoassay kits and RT-PCR in a prospective hospital-based surveillance study conducted at 7 centers in Lebanon. Concordance and discrepancy between the two methods was used to calculate sensitivity and specificity, using RT-PCR as the “gold standard”. Results: The sensitivity and specificity were respectively 95.08% and 86.62% for the SD Bioline® (Standard Diagnostics, Inc, South Korea) kit calculated on 645 samples, 65.86% and 45.90% for the VIROTECT® (Trinity Biotech, Ireland) kit calculated on 327 samples, 83.9% and 64.2% for the Rota-Strip (C-1001) (Coris Bioconcept, Belgium) calculated on 95 samples, 52.3% and 10.9% for the Acon® (Acon Laboratories, Inc, California, USA) kit calculated on 122 samples, 68.1% and 20% for the VIKIA® Rota-Adéno (Biomerieux, France) kit calculated on 32 samples. Conclusion: A wide discrepancy was detected between the calculated and advertised sensitivity and specificity for most of the kits.

Introduction Infections caused by extended spectrum beta lactamase (ESBL) producing bacteria continue to be a challenge for choosing the appropriate therapy since they may exhibit coresistance to many other classes of antibiotics. The aim of the study was to screen pregnant women for ESBL producing bacteria in Beirut, Lebanon, to examine their phenotypic and genotypic characterization and to study the association between ESBL colonization with adverse neonatal outcomes. Method In this cross-sectional study, vaginal samples from 308 pregnant women at 35–37 weeks of gestation were studied during a one-year period. The samples were plated on MacConkey agar and selective MacConkey agar supplemented with ceftazidime. Phenotypic confirmation of ESBL production was performed by double-disc synergy test and all isolates were screened by PCR for the resistance genes blaSHV, blaTEM, and blaCTX-M. Clonal relatedness of Escherichia coli isolates was investigated by pulsed-field gel electrophoresis. Results In total, 59 women out of 308 (19.1%) were colonized by ESBL producing gram negative bacteria. Two babies born to mothers colonized with ESBL were diagnosed with sepsis. The susceptibility rates of isolates to other antibiotics were 39% to co-trimoxazole, 49.2% to ciprofloxacin, 91.5% to gentamicin, 18.6% to aztreonam and 35.6% to cefepime. Most of isolates were highly sensitive to meropenem and imipenem, with a susceptibility of 93.2%. PCR was performed on all E. coli isolates to detect the most common ESBL producing genes; blaCTX-M was the predominant gene (90.7%), followed by blaTEM (88.4%) and finally blaSHV (44.2%). PFGE analysis of 34 E. coli isolates revealed 22 distinct clusters showing more than 85% similarity. Conclusion In conclusion, this study showed that Lebanon has a high prevalence of ESBL carriage in pregnant women. Further studies that include a continuous screening of pregnant women and follow up of their newborn clinical status should be conducted to foresee the risk of transmission.

Acinetobacter baumannii has become increasingly resistant to leading antimicrobial agents since the 1970s. Increased resistance appears linked to armed conflicts, notably since widespread media stories amplified clinical reports in the wake of the American invasion of Iraq in 2003. Antimicrobial resistance is usually assumed to arise through selection pressure exerted by antimicrobial treatment, particularly where treatment is inadequate, as in the case of low dosing, substandard antimicrobial agents, or shortened treatment course. Recently attention has focused on an emerging pathogen, multi-drug resistant A. baumannii (MDRAb). MDRAb gained media attention after being identified in American soldiers returning from Iraq and treated in US military facilities, where it was termed “Iraqibacter.” However, MDRAb is strongly associated in the literature with war injuries that are heavily contaminated by both environmental debris and shrapnel from weapons. Both may harbor substantial amounts of toxic heavy metals. Interestingly, heavy metals are known to also select for antimicrobial resistance. In this review we highlight the potential causes of antimicrobial resistance by heavy metals, with a focus on its emergence in A. baumanni in war zones.

A latex agglutination-based test for the rapid detection of Listeria monocytogenes in foods was developed. An antilisteriolysin O (LLO) monoclonal antibody (HID5E12D7; IgG2b) covalently bound to polystyrene amidine-modified latex beads was used in a slide agglutination assay. The latex reagent detected 0.1 ng/ml of LLO in phosphate-buffered saline plus bovine serum albumin. It reacted with culture supernatants of L. monocytogenes but not with other Listeria species or Streptococcus groups A through G. The listeriolysin O latex agglutination assay (LLOLAT) was applied to 24-h and 48-h USDA primary enrichment cultures of 208 food samples obtained from refrigerators of listeriosis patients enrolled in a study to determine the role of foods in sporadic listeriosis. Of 19 samples positive by cultural techniques, 17 were positive by the LLOLAT. Cultures with low (