Phenotypic and molecular characterization of multi-drug resistant Klebsiella spp. isolates recovered from clinical settings.

Klebsiella pneumoniae is a Gram-negative bacterium that colonizes the gastrointestinal tract and nasopharynx with many being linked to nosocomial infections. Extended-spectrum ß-lactamases (ESBL)-producing and carbapenem-resistant K. pneumoniae is recognized by the World Health Organization (WHO) as a critical public health concern. In this study, whole-genome sequencing (WGS) - based analysis was performed to understand the molecular epidemiology of multi-drug resistant Klebsiella spp. clinical isolates. Genome comparison, multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and whole-genome-SNP-based phylogenetic analysis (wg-SNP) were used for in-depth molecular characterization. in silico typing was used to determine the resistance genes, virulence factors, Inc. groups, and capsular types. All except one isolate were non-susceptible to meropenem and 89% were non-susceptible to ertapenem and imipenem. blaNDM, blaOXA-48, and blaKPC were the detected carbapenemases with blaNDM-1 found in half of the sequenced genomes. Resistance to colistin was detected in one isolate and was linked to several genetic alterations in crrB, pmrB, and pmrC genes. The most common plasmid type was IncFIB followed by IncR, and the Type 3 fimbriae, encoded by the mrkABCDF operon, was conserved among all isolates. The most common sequence- (ST) and K-type detected were ST147 and K64. The prevelance and the genomic relatedness of ST147 isolates, as shown by the data from SNP-based phylogenetic analysis, PFGE, and genomic clustering, may be an outbreak marker. However, this can only be validated through a more comprehensive study encompassing a wider sampling scheme and over an extended timeframe.

Epidemiology of pathogens causing acute diarrhea in patients presenting to the emergency departments in 4 hospitals in Lebanon.

Acute diarrhea is a prevalent disease worldwide and a cause of mortality in low and middle-income countries. In previous studies, the causative enteropathogen is found in 38% to 58% of patients, leaving a considerable diagnostic gap. In this study, we intend to determine the pathogenic agents responsible for acute diarrhea in patients presenting to the Emergency Departments of several Lebanese hospitals. A total of 100 stool samples were collected between June 2022 and June 2023 from patients presenting with acute diarrhea to the Emergency Departments. Pathogens were detected by multiplex polymerase chain reaction. The average age for the patients was 53 years old. All patients presented with diarrhea, 15 of them had fever associated. In total, 46 patients were admitted to the hospital (70%), among them 80% received Intravenous antibiotics. Campylobacter was the most common agent detected in 36%, followed by Rotavirus 19%, and Noroviruses 15%. The rest was detected at lower percentages. Bacteria accounted for 49% of cases, viruses for 39%, and parasitic infection 6%. Acute diarrhea epidemiology is understudied in Lebanon. This study is the first Lebanese data about acute diarrhea pathogens. Avoiding overuse of antibiotics in bacterial versus viral infections can be achieved while prevention campaigns can raise awareness about food and water safety at the community level.

Following the COVID-19 playbook and battling another infodemic: conspiracy beliefs around human monkeypox among the Lebanese population.

INTRODUCTION: The non-endemic multicountry outbreak of monkeypox (MPX) has emphasized the issue of conspiracy theories that go viral in times of societal crisis. Now, it is the turn of MPX to join COVID-19 in the conspiracy theory realm. Social media outlets were flooded by a scourge of misinformation as soon as MPX cases began to appear with an evident cross-pollination between diverse conspiracy theories. Given the adverse consequences of conspiracy beliefs, this study aimed to assess the extent of endorsement of MPX conspiracy beliefs among the Lebanese population and to identify its associated factors. METHODS: Using a convenience sampling technique, a web-based cross section was conducted among Lebanese adults. Data were collected using an Arabic self-reported questionnaire. Multivariable logistic regression was performed to identify the factors associated with the MPX conspiracy beliefs scale. RESULTS: Conspiracy beliefs regarding emerging viruses including MPX were detected among 59.1% of Lebanese adults. Participants endorsed particularly the conspiracy theories linking the virus to a deliberate attempt to reduce the size of the global population (59.6%), gain political control (56.6%) or pharmaceutical companies' financial gain (39.3%), in addition to the manmade origin of MPX (47.5%). Remarkably, the majority of surveyed adults exhibited a negative attitude toward the government's preparedness for a potential MPX outbreak. However, a positive attitude was revealed toward the effectiveness of precautionary measures (69.6%). Female participants and those having a good health status were less likely to exhibit a higher level of conspiracy beliefs. On the contrary, divorced or widowed adults, those having a low economic situation, poor knowledge level, and negative attitude either toward the government or precautionary measures were more prone to disclose a higher level of conspiracy beliefs. Notably, participants relying on social media to get information about MPX were also more likely to have a higher level of conspiracy beliefs compared to their counterparts. CONCLUSIONS: The widespread extent of conspiracy beliefs endorsement regarding MPX among the Lebanese population urged the policymakers to find ways to reduce people's reliance on these theories. Future studies exploring the harmful impacts of conspiracy beliefs on health behaviors are recommended.

Characterization and susceptibility of non-albicans Candida isolated from various clinical specimens in Lebanese hospitals.

Background: Invasive fungal infections have presented a challenge in treatment. In the past, it was known that the frontrunner in such infections is Candida albicans with little emphasis placed on non-albicans Candida species (NAC). Studies worldwide have shown a rise in fungal infections attributed to non-albicans Candida species. The aim of this study is to describe the epidemiology of NAC infections along with an overview of resistance in Lebanese hospitals. Methods: This is a two-year observational multi-central descriptive study. Between September 2016 and May of 2018, a total of 1000 isolates were collected from 10 different hospitals distributed all over the country. For the culture, Sabouraud Dextrose Agar was used. Antifungal Susceptibility was evaluated by determining the Minimum Inhibitory Concentration (MIC) in broth (microdilution) of the different antifungal treatments. Results: Out of the 1000 collected isolates, Candida glabrata, being the most isolated species (40.8%), followed by Candida tropicalis: 231(23.1%), Candida parapsilosis: 103(10.3%), and other NAC species at lower percentage. Most of these isolates (88.67%) were susceptible to posaconazole, 98.22% were susceptible to micafungin, and 10% were susceptible to caspofungin. Conclusion: The change of etiology of fungal infections involving a significant increase in NAC cases is alarming due to the different antifungal susceptibility patterns and the lack of local guidelines to guide the treatment. In this context, proper identification of such organisms is of utmost importance. The data presented here can help in establishing guidelines for the treatment of candida infections to decrease morbidity and mortality. Future surveillance data are needed.

When a neglected tropical zoonotic disease emerges in non-endemic countries: need to proactively fill the unveiled knowledge gaps towards human monkeypox among the Lebanese population.

INTRODUCTION: The ongoing multi-country outbreak of monkeypox (MPX) that emerges in non-endemic areas is a rare and unprecedented event that has sparked a widespread public health concern. Lebanon has reported four confirmed cases of MPX so far. Since good knowledge about the MPX virus and its associated disease is paramount for helping the Lebanese population prepare for a possible outbreak, therefore, it is important to assess their current level of knowledge regarding MPX and to identify its associated factors to highlight any knowledge gaps that need to be filled. METHODS: An online cross-sectional study was conducted over the first 2 weeks of August 2022 among adults aged 18 years and above recruited from all Lebanese provinces using a convenience sampling technique. An anonymous, Arabic, self-reported questionnaire covering all main aspects of knowledge regarding MPX was developed and adapted based on the available literature. The Chi-square test was used to determine the associations between knowledge levels and independent variables including baseline characteristics. Multivariable logistic regression was also carried out on the significant variables in the bivariate analyses to identify the factors associated with the good knowledge level. RESULTS: A total of 793 Lebanese adults participated in the study. The overall level of knowledge level regarding human MPX was poor among the Lebanese population; with only 33.04% of them having a good knowledge level ≥ 60%. Knowledge gaps and a substantial poor knowledge level were found in the majority of MPX knowledge domains especially those related to the routes of transmission (76.67%), clinical presentation and symptoms (71.63%), treatment (86.25%), and severity of the disease (91.3%). Interestingly, participants have a good knowledge level of the precautionary measures (80.45%), and the response to a suspected infection (65.20%). Female gender [(aOR = 0.870, CI 95% (0.613-0.941)], increased age 49 [aOR = 0.743, CI 95% (0.381-0.908)], and living in rural areas [aOR = 0.412, CI 95% (0.227-0.861)] were found negatively associated with a good level of knowledge. However, participants with higher educational levels [aOR = 1.243, CI 95% (1.032-3.801)], those working in the medical field [aOR = 1.932, CI 95% (1.331-3.419)], those suffering from chronic disease/immunodeficiency [aOR = 1.231, CI 95% (1.128-2.002)], and participants with moderate/high economic situations [aOR = 2.131, CI 95% (1.431-4.221)] were more likely to have a good knowledge score compared to their counterparts. CONCLUSIONS: The current study pointed out to poor knowledge level regarding MPX among the Lebanese population with substantial knowledge gaps in most aspects of MPX knowledge. The findings stress the urgent need to raise awareness and proactively fill the unveiled gaps, especially among less informed groups.

Prevalence and correlates of burnout among Lebanese health care workers during the COVID-19 pandemic: a national cross-sectional survey.

BACKGROUND: The COVID-19 pandemic has harshly burdened the healthcare systems. Health care workers (HCWs) are at substantial risk of infection and confronted several stressors as well leading them to experience burnout. This study aimed to assess the prevalence of burnout among Lebanese health HCWs and to identify its associated factors. METHODS: A cross-sectional online survey was conducted between the first of November and the end of December 2020 among Lebanese HCWs working in all active hospitals operating across the country. Data were collected using an Arabic, anonymous, self-reported questionnaire comprising four sections: (a) basic sociodemographic characteristics, (b) exposure to COVID-19 covariates, (c) occupational factors, and (d) the measurements including the Copenhagen Burnout Inventory (CBI). CBI subscale cut-off score of 50 was used to assess the prevalence of burnout among HCWs. Multinomial logistic regression analyses were performed to examine the factors associated with the different aspects of burnout. RESULTS: Out of the 1751 respondents, personal burnout (PB) was detected in its moderate and high-level aspects among 86.3% of Lebanese HCWs. Moderate and high levels of work-related burnout (WB), and client-related burnout (CB) hit 79.2% and 83.3% of HCWs, respectively. HCWs who were females, married, physicians, having a poor health status and specific living conditions (dependent child, elderly at home, family member with comorbidities, and a low income) were more likely to exhibit a high level of PB compared to no/low burnout level. Moreover, frontline HCWs, those infected by COVID-19 or those having a colleague infected by COVID-19, and those exhibiting a high perception of threat were more prone to experience a high-level PB rather than a low/no burnout. Working in a public hospital, extensive working hours, and insufficient sleeping hours were also found positively associated with high PB. However, older age and altruism were negatively associated with high PB compared to no/low PB among HCWs. As for WB, similar factors were found either positively or negatively associated with a high level of WB except health status and living conditions factors (dependent child or family member). As for CB, older age of HCWs (> 30 years) and altruism were negatively associated with high CB compared to no/low burnout level. However, working in the frontline, high threat perception, extensive working hours, insufficient sleeping hours, and low income were positively associated with high CB among HCWs compared to no/low burnout. CONCLUSION: The prevalence of burnout among Lebanese HCWs during the pandemic was significant and alarming. Enacting and implementing preventive policies and effective interventions are urgently needed to cultivate wellness among HCWs.

Epidemiology of Community-Acquired Respiratory Tract Infections in Patients Admitted at the Emergency Departments.

OBJECTIVES: Community-acquired respiratory infections (CARTIs) are responsible for serious morbidities worldwide. Identifying the aetiology can decrease the use of unnecessary antimicrobial therapy. In this study, we intend to determine the pathogenic agents responsible for respiratory infections in patients presenting to the emergency department of several Lebanese hospitals. METHODS: A total of 100 patients presenting to the emergency departments of four Lebanese hospitals and identified as having CARTIs between September 2017 and September 2018 were recruited. Specimens of upper and lower respiratory tract samples were collected. Pathogens were detected by a multiplex polymerase chain reaction respiratory panel. RESULTS: Of 100 specimens, 84 contained at least one pathogen. Many patients were detected with ≥2 pathogens. The total number of pathogens from these 84 patients was 163. Of these pathogens, 36 (22%) were human rhinovirus, 28 (17%) were Streptococcus pneumoniae, 16 (10%) were metapneumovirus, 16 (10%) were influenza A virus, and other pathogens were detected with lower percentages. As expected, the highest occurrence of pathogens was observed between December and March. Respiratory syncytial virus accounted for 2% of the cases and only correlated to paediatric patients. CONCLUSION: CARTI epidemiology is important and understudied in Lebanon. This study offers the first Lebanese data about CARTI pathogens. Viruses were the most common aetiologies of CARTIs. Thus, a different approach must be used for the empirical management of CARTI. Rapid testing might be useful in identifying patients who need antibiotic therapy.

Practice of non-pharmaceutical interventions against COVID-19 and reduction of the risk of influenza-like illness: a cross-sectional population-based study.

INTRODUCTION: While the widespread implementation of the non-pharmaceutical interventions was intended to contain the COVID-19 pandemic, such measures could be also effective in limiting the spread of other respiratory infections. This study aimed to examine the association between the implementation of personal protective measures and the occurrence of influenza-like illnesses (ILI) in the general population. METHODS: An online retrospective cross-sectional observational study was conducted in April 2021 to assess cases of ILI among Lebanese adults aged 18 years and above, from all Lebanese governorates during the 2020-2021 flu season. Data were collected using a convenience sampling method. In addition to their socio-demographic information, participants were asked about their frequency of implementing personal protective measures and if they have experienced symptoms of ILI in the previous 6 months. The overall score of the personal protective measures was computed. Multivariable logistic regression was performed to examine the association between participants' level of adoption of personal protective measures against COVID-19 and the occurrence of ILI. RESULTS: Among the 1019 Lebanese adults participating in this study, 352 (34.54%) of them reported symptoms of ILI between October 2020 and March 2021. Lebanese adults who wore their facemasks frequently or always were less likely to suffer from symptoms of ILI than others who did not wear the mask (aOR = 0.452, 95% CI = 0.349-0.693, p < 0.001). Similarly, adults who adopt the following protective measures washing hands (aOR = 0.608, 95% CI = 0.524-0.922, p < 0.001), respecting cough etiquette (aOR = 0.763, 95% CI = 0.598-0.918, p < 0.001), disinfecting surface (aOR = 0.892, 95% CI = 0.632-0.911, p = 0.012), avoiding crowded places (aOR = 0.739, 95% CI = 0.688-0.903, p = 0.049), respecting physical distancing (aOR = 0.646, 95% CI = 0.482-0.833, p = 0.031) on a regular basis (frequently/always) were less likely to report symptoms of influenza-like illnesses when compared with those who did not adhere at all to these measures. CONCLUSION: Our study highlighted the potential of personal protective measures against COVID-19 in reducing the transmission of respiratory infections such as ILI. Such findings might be invested during influenza season, particularly among groups at high risk of developing severe complications. Exploring trends detected by the national severe acute respiratory infection surveillance system is recommended to confirm the utility of these measures.

The Effect of Infection Precautions on Extended-Spectrum Beta-Lactamase Enterobacteriaceae Colonization Among Nurses in Three Beirut Hospitals.

Background and objective Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) are rapidly emerging worldwide. This study aimed to assess the effect of contact precaution (CP) on ESBL-PE-colonization rates among nurses in three hospitals in Beirut, Lebanon, where ESBL is endemic, in order to define the risk factors for colonization. Accordingly, the ongoing use of CP to prevent ESBL-PE transmission to healthy nurses was evaluated. Methods This cross-sectional study was conducted in three hospitals. Hospital 1 required CP, Hospital 2 had recently stopped CP, and Hospital 3 had stopped it three years previously. Questionnaires and stool-collection containers were distributed to all patient care nurses in those three hospitals. The Returned samples were tested using the agar dilution technique. Results A total of 269 out of 733 nurses volunteered to participate; 140 met the inclusion criteria (no recent hospitalization, antibiotic use, or known ESBL-PE colonization) and provided samples. Among them, 15% were ESBL-positive. Compared to nurses from Hospital 3, nurses from Hospital 1 were 59% less likely to be colonized, while nurses from Hospital 2 were 62% more likely to be colonized. Conclusion In hospitals where CP is in place for ESBL-positive patients, ESBL-PE prevalence in nursing staff was significantly lower. Additionally, a work experience of two to four years increased the odds of ESBL-PE colonization in comparison with longer nursing experience. CP may be a justifiable means of protection against ESBL-PE transmission to healthy nurses. The risk factors for colonization were discontinuation of CP and a shorter clinical work experience.

The dissemination of antimicrobial resistance determinants in surface water sources in Lebanon.

The prevalence of antibiotic-resistant bacteria in surface water in Lebanon is a growing concern and understanding the mechanisms of the spread of resistance determinants is essential. We aimed at studying the occurrence of resistant bacteria and determinants in surface water sources in Lebanon and understanding their mobilization and transmission. Water samples were collected from five major rivers in Lebanon. A total of 91 isolates were recovered by incubating at 37°C on Blood and MacConkey agar out of which 25 were multi-drug resistant (MDR) and accordingly were further characterized. Escherichia coli and Klebsiella pneumoniae were the most common identified MDR isolates. Conjugation assays coupled with in silico plasmid analysis were performed and validated using PCR-based replicon typing (PBRT) to identify and confirm incompatibility groups and the localization of ß-lactamase encoding genes. Escherichia coli EC23 carried a blaNDM-5 gene on a conjugative, multireplicon plasmid, while blaCTX-M-15 and blaTEM-1B were detected in the majority of the MDR isolates. Different sequence types (STs)were identified including the highly virulent E. coli ST131. Our results showed a common occurrence of bacterial contaminants in surface water and an increase in the risk for the dissemination of resistance determinants exacerbated with the ongoing intensified population mobility in Lebanon and the widespread lack of wastewater treatment.

Molecular characterization of a carbapenem-resistant Enterobacter hormaechei ssp. xiangfangensis co-harbouring blaNDM-1 and a chromosomally encoded phage-linked blaCTX-M-15 genes.

Enterobacter cloacae complex (ECC) members are rapidly emerging as successful nosocomial pathogens, especially, with the emergence of carbapenem-resistant clones. In this study, we performed a comprehensive molecular characterization of a carbapenem-resistant E. hormaechei ssp. xiangfangensis LAU_ENC1. hsp60 and average nucleotide identity (ANI) were used for its identification. The repertoire of resistance genes and phage content were analyzed. Plasmid sequences were extracted and compared to closest references. The isolate LAU_ENC1 was identified as an E. hormaechei ssp. xiangfangensis and belonged to ST-114A sub-cluster. blaNDM-1, blaCTX-M-15, blaOXA-1, and blaACT-16 genes were detected as ß-lactam resistance determinants. A chromosomal hybrid intact phage, Enterobacter phage LAU1, with blaCTX-M-15 integrated in its direct vicinity within an ISEcp1 - blaCTX-M-15 - wbuC - ∆Tn2 rare cassette was detected. blaNDM-1 was integrated within a novel IncFII conjugative plasmid, pLAU_ENC1, through an IS3000- ΔISAba125-blaNDM-1-bleMBL-//-Tn5403 cassette. To our knowledge, this is the first report of a multi-drug resistant (MDR) E. hormaechei ssp. xiangfangensis carrying a blaCTX-M-15 integrated within the proximity of a provirus chromosomal region. Treatment options for MDR ECC members are becoming scarce, thus warranting an increased monitoring of the dissemination of these pathogens in clinical settings.

Detailed characterization of an IncFII plasmid carrying blaOXA-48 from Lebanon.

BACKGROUND: The spread of carbapenem-resistant Enterobacteriaceae is an important challenge and an increasing healthcare problem. OXA-48 is a class D carbapenemase that is usually localized on a conjugative plasmid belonging to the IncL incompatibility group. METHODS: In this study, we used a combination of short- and long-read WGS approaches and molecular typing techniques to characterize the genetic environment of the smallest reported 27 029 bp IncFII plasmid carrying blaOXA-48 (pLAU-OXA48). RESULTS: The plasmid recovered from a clinical Escherichia coli isolate was positive for blaOXA-48, which was located within the Tn6237 composite transposon. Primers targeting junctions between the IncF fragment and Tn6237 for the rapid identification of pLAU-OXA48-like plasmids were designed. CONCLUSIONS: To our knowledge, this is the first report showing the complete sequence of an IncFII plasmid carrying blaOXA-48 within Tn6237 using hybrid assembly of long- and short-read sequencing.

Genomic Features of Vibrio parahaemolyticus from Lebanon and Comparison to Globally Diverse Strains by Whole-Genome Sequencing.

Gastroenteritis is a disease that can be caused by virulent strains of Vibrio parahaemolyticus in humans upon the consumption of contaminated seafood. In summer 2017, a sudden increase in the number of patients suffering from gastroenteritis due to a V. parahaemolyticus infection was observed at the Middle East Institute of Health University Hospital in Lebanon. The aim of this study was to analyze the isolates recovered from stool specimens, and to compare them using different phenotypic assays, genomic profiling techniques, and whole-genome sequencing, to achieve a better understanding of the current V. parahaemolyticus strains available in Lebanon. Virulence potential was analyzed based on the detection of the hemolysins: thermostable direct hemolysin (tdh), thermostable direct hemolysin-related hemolysin (trh), and thermolabile hemolysin (tlh). Resistance was determined by testing antibiotic susceptibility and performing PCR assays for ß-lactamases and quinolone resistance determinants. Genetic relatedness was verified by multilocus sequence typing, pulsed-field gel electrophoresis, and whole genome-based single nucleotide polymorphism analysis. All of the isolates had the tdh+, trh-, group-specific PCR+ genotype, which is a characteristic of the O3:K6 pandemic clone. The isolates were resistant to ampicillin (100%), ceftazidime (86%), ticarcillin (14%), and amikacin (14%), belonged to the sequence type ST3, and had very similar phylogenetic fingerprints. The isolates undertaken in this study exhibited almost identical resistance, virulence, and phylogenetic patterns, confirming an outbreak linked to the spread of the pandemic O3:K6 serotype in the country.

Integration of two pKPX-2-derived antibiotic resistance islands in the genome of an ESBL-producing Klebsiella pneumoniae ST3483 from Lebanon.

OBJECTIVES: Contamination of fresh water with clinically important Gram-negative bacteria in Lebanon is being investigated in-depth, especially with evidence of dissemination into clinical settings. This study aimed to report the draft genome sequence of a Klebsiella pneumoniae strain with an integrated plasmid segment harbouring two antibiotic resistance islands (ARI). It is believed that this is the first report of plasmid antibiotic resistance islands integration in the genome of K. pneumoniae. METHODS: Whole genome sequencing of the isolate was performed using Sequel platform. The genome was assembled using HGAP4. Analysis was conducted by uploading the sequence to the online databases from the Center for Genomic Epidemiology. RESULTS: The strain had a newly assigned ST 3483 with a genome size of 5385844 bp. The investigation of the antibiotic resistance islands suggested integration of two DNA segments from a previously identified IncFIA plasmid. The results revealed that the integration could have been accomplished either as a single-step integration event, with the two segments being integrated as a whole transposon mediated by the flanking IS26, or through two separate integration events involving the two segments, but independently. CONCLUSION: The sequenced genome revealed interesting aspects related to antibiotic resistance dissemination. The ARI are more stable in the genome and the chance of losing it is less probable, with the possibility of the described transposon to re-integrate in other plasmids, facilitating the dissemination of such resistance determinants.

A compilation of antimicrobial susceptibility data from a network of 13 Lebanese hospitals reflecting the national situation during 2015-2016.

Background: There is a lack of official national antimicrobial resistance (AMR) data in Lebanon. Individual hospitals generate their own antibiotic susceptibility data in the form of yearly pamphlets. Methods: In this study, antibiotic susceptibility data from 13 hospitals distributed across different governorates of Lebanon were collected to conduct a compilation-based surveillance of AMR in Lebanon for the years 2015-2016. The findings were compared with those of a previous nationwide study in this country conducted between 2011 and 2013 as well as with similar data obtained from the 2015 and 2016 European surveillance reports of AMR. To provide a clear presentation of the AMR situation, mean percent susceptibility of different antibiotic-microbe combinations was calculated. Results: During 2015-2016, the percent susceptibility of Enterobacteriaceae to third-generation cephalosporins and to carbapenems was 59 and 97%, respectively. Among Pseudomonas aeruginosa and Acinetobacter spp., carbapenem susceptibility reached 70 and 12%, respectively. Among Gram positive organisms, the percent susceptibility to methicillin in Staphylococcus aureus was 72%, that to vancomycin in Enterococcus spp. was 98% and that to penicillin in Streptococcus pneumoniae was 75%. Compared with results of 2011-2013, there was an overall trend of decreased susceptibility of bacteria to the tested antibiotics, with a variation of 5 to 10%. The antibiotic susceptibility data from Lebanon were found to be comparable with those from Eastern and South-eastern European countries. Conclusion: This study highlights the need to establish a robust national AMR surveillance system that enables data from Lebanon to be included in global AMR maps.

Genome Mining and Comparative Analysis of Streptococcus intermedius Causing Brain Abscess in a Child.

Streptococcus intermedius (SI) is associated with prolonged hospitalization and low survival rates. The genetic mechanisms involved in brain abscess development and genome evolution in comparison to other members of the Streptococcus anginosus group are understudied. We performed a whole-genome comparative analysis of an SI isolate, LAU_SINT, associated with brain abscess following sinusitis with all SI genomes in addition to S. constellatus and S. anginosus. Selective pressure on virulence factors, phages, pan-genome evolution and single-nucleotide polymorphism analysis were assessed. The structural details of the type seven secretion system (T7SS) was elucidated and compared with different organisms. ily and nanA were both abundant and conserved. Nisin resistance determinants were found in 47% of the isolates. Pan-genome and SNPs-based analysis didn't reveal significant geo-patterns. Our results showed that two SC isolates were misidentified as SI. We propose the presence of four T7SS modules (I⁻IV) located on various genomic islands. We detected a variety of factors linked to metal ions binding on the GIs carrying T7SS. This is the first detailed report characterizing the T7SS and its link to nisin resistance and metal ions binding in SI. These and yet uncharacterized T7SS transmembrane proteins merit further studies and could represent potential therapeutic targets.

Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia.

PURPOSE: Burkholderia cenocepacia is among the most common members of the Burkholderia cepacia complex (Bcc) isolated from patients with cystic fibrosis (CF). The factors triggering the high rates of morbidity and mortality in CF patients are not well elucidated. In this study, we aim to highlight the genome diversity of two clinical isolates of B. cenocepacia through comparative genome analysis. METHODOLOGY: The repertoire of virulence factors and resistance genes compared to reference strains J2315 and K56-2 was elucidated. The isolates were screened for the presence of phages and insertion sequences. Two methods were combined to obtain an accurate prediction of genomic islands (GIs): the cumulative GC profile and the IslandViewer web tool. To study evolutionary relatedness, whole genome-based single-nucleotide polymorphism (wgSNP) analysis was also performed with 43 publically available strains of the Bcc of various sequence types.Results/Key findings. Genome-based species identification of the two isolates BC-AUH and BC-BMEH confirmed the species as B. cenocepacia. Both belonged to ST-602, a double-locus variant of ST-32 (CC31), genomovar IIIA, and carried a large number of antibiotic resistance genes. Eighteen GIs were predicted in BC-AUH and BC-BMEH, occupying 9.3 and 6.1 % of the respective genomes. Comparison to J2315 revealed 89 and 85 genes unique to BC-BMEH and BC-AUH, respectively. Additionally, 1823 intergenic SNPs were detected between BC-BMEH and BC-AUH. CONCLUSION: This study mapped existing genetic variations in B. cenocepacia associated with notorious outcomes in CF patients, and the data obtained provide comprehensive, genome-inferred insights and multifactorial examination of an important human pathogen.

Extended-spectrum ß-lactamase-producing Escherichia coli in wastewaters and refugee camp in Lebanon.

AIM: To evaluate the effects of population influx of refugees on the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli in wastewater networks in Lebanon. MATERIALS & METHODS: Pulsed-field gel electrophoresis, multilocus sequence typing and antibiotic resistance genes typing were performed. RESULTS: 53.1% of isolates recovered from Al-Qaa refugee camp were positive for the tested resistant determinants compared with 49.1% from river effluents. All isolates carried aac(6)-1b and/or aac(3)-II; none carried armA, rmtB, ant(4')-Iia, aph(3')-Ia or carbapenemases. CTX-M-15, TEM-1, OXA-1, CMY-2 and SHV-12 were detected. Single and/or double substitutions were detected in GyrA and ParC. Phylogenetic group B2 and ST6470 were the most prevalent. Pulsed-field gel electrophoresis revealed 19 XbaI patterns and 17 pulsotypes. CONCLUSION: The introduction of novel resistance patterns into the wastewater network requires effective control.

Epidemiology and susceptibility profiles of diabetic foot infections in five hospitals in Lebanon.

INTRODUCTION: Approximately 80% of diabetes-related lower extremity amputations are preceded by a foot ulcer. Global studies on the epidemiology of diabetic foot ulcer (DFU) infections and guidelines detailing the most common pathogens and their respective antimicrobial susceptibilities are available. While Gram-positive cocci, mainly Staphylococcus species (spp.), were the most common organisms cultured from DFU in the United States, the Gram-negative Pseudomonas spp. were found to be the most common in some Middle Eastern countries. In Lebanon, however, such studies remain scarce. This study, conducted in Lebanon, investigated the most common organisms in DFU infections and their antimicrobial profiles. METHODOLOGY: We collected data from all documented diabetic foot infections between January 2015 and March 2016, 128 participants total, from 5 different hospitals in various regions of Lebanon. RESULTS: Among all isolates, Enterobacteriaceae (42%), Pseudomonas spp. (18.6%) and methicillin-sensitive Staphylococcus aureus (MSSA) (15.3%) were the most frequent bacteria. In addition, 72% of Pseudomonas spp. were susceptible to ciprofloxacin and 63.6% of Enterobacteriaceae were susceptible to either amoxicillin/clavulanate or ciprofloxacin, 91% were susceptible to piperacillin/tazobactam. Methicillin-resistant Staphylococcus aureus (MRSA) was only found in hospitalized patients or those who received prior antibiotics. Polymicrobial infections were documented in only 38% of patients. CONCLUSION: In Lebanon, the most appropriate empirical oral outpatient treatment would be a combination of amoxicillin/clavulanate and ciprofloxacin. As for admitted patients who have failed the oral regimen, piperacillin/tazobactam would then be the treatment of choice.

Genome sequencing and comparative analysis of an NDM-1-producing Klebsiella pneumoniae ST15 isolated from a refugee patient.

The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum ß-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted. Illumina paired-end libraries were prepared and sequenced resulting in 892,300 high-quality reads. The initial assembly produced 329 contigs with a combined 5,954,825 bp and a 56.5% G+C content. Resistome analysis revealed the presence of several ß-lactamases including NDM-1, SHV-28, CTX-M-15 and OXA-1 in addition to 18 other genes encoding for resistance, among which are aph(3')-Ia, aac(6')Ib-cr, armA, strB, strA and aadA2 genes. Additionally, five plasmids IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) and four integrated phages were detected. In silico MLST analysis revealed that the isolate was of sequence type ST15. To our knowledge this is the first in-depth genomic analysis of a NDM-1 positive K. pneumoniae ST15 in Lebanon associated with the recent population migration. The potential dissemination of such MDR strains is an important public health concern.