Carbapenem- and colistin-resistant Enterobacterales in intensive care unit patients in Mediterranean countries, 2019.

Introduction: The colonization of patients by carbapenemase-producing Enterobacterales (CPE) has been associated with heightened mortality, especially in vulnerable individuals within intensive care units (ICUs). Our study aimed to comprehensively assess CPE prevalence among ICU patients across the Mediterranean region pre-COVID-19, conducting a multicenter prevalence study in the first quarter of 2019. Methods: We collected clinical data and rectal or fecal samples from 256 ICU patients for CPE testing. Additionally, we performed whole-genome sequencing on 40 representative CPE strains to document their molecular characteristics. Results: Among the 256 patients, CPE was detected in 73 samples (28.5%), with prevalence varying from 3.3 to 69.0% across participating centers. We observed 13 colistin-resistant CPE strains, affecting three ICUs. Genetic analysis revealed highly diverse E. coli and K. pneumoniae strains, predominantly from international high-risk clones. Notably, blaOXA-48 and blaNDM-1 were the most prevalent carbapenemase genes. Molecular typing uncovered potential patient clusters in six centers. Significantly, longer hospital stays were associated with increased CPE carriage (p < 0.001). Nine centers across Morocco, Tunisia, Egypt, and Lebanon voluntarily participated. Discussion: Our study provides CPE prevalence in Mediterranean ICUs and reaffirms established CPE presence in this setting but also provides updates on the molecular diversity of CPE strains. These findings highlight the imperative of reinforcing infection control measures in the participating ICUs to curtail escalated mortality rates, and of strictly applying isolation measures around patients originating from the Mediterranean region when transferred to other healthcare institutions.

Molecular Characteristics of Colistin Resistance in Acinetobacter baumannii and the Activity of Antimicrobial Combination Therapy in a Tertiary Care Medical Center in Lebanon.

(1) Background: Infections with pan-drug-resistant (PDR) bacteria, such as A. baumannii, are becoming increasingly common, especially in healthcare facilities. In this study, we selected 15 colistin-resistant clinical A. baumannii isolates from a hospital in Beirut, Lebanon, to test combination therapies and determine their sequence types (STs) and the mechanism of colistin resistance using whole-genome sequencing (WGS). (2) Methods: Antimicrobial susceptibility testing via broth microdilution against 12 antimicrobials from different classes and growth rate assays were performed. A checkerboard assay was conducted on PDR isolates using six different antimicrobials, each in combination with colistin. Genomic DNA was extracted from all isolates and subjected to WGS. (3) Results: All isolates were resistant to all tested antimicrobials with the one exception that was susceptible to gentamicin. Combining colistin with either meropenem, ceftolozane-tazobactam, or teicoplanin showed synergistic activity. Sequencing data revealed that 67% of the isolates belonged to Pasteur ST2 and 33% to ST187. Furthermore, these isolates harbored a number of resistance genes, including blaOXA-23. Mutations in the pmrC gene were behind colistin resistance. (4) Conclusions: With the rise in antimicrobial resistance and the absence of novel antimicrobial production, alternative treatments must be found. The combination therapy results from this study suggest treatment options for PDR ST2 A. baumannii-infected patients.

The Acinetobacter baumannii website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace.

Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-resistant strains. Here we introduce Ab-web (https://www.acinetobacterbaumannii.no), the first online platform for sharing expertise on A. baumannii. Ab-web is a species-centric knowledge hub, initially with 10 articles organized into two main sections, 'Overview' and 'Topics', and three themes, 'epidemiology', 'antibiotic resistance', and 'virulence'. The 'workspace' section provides a spot for colleagues to collaborate, build, and manage joint projects. Ab-web is a community-driven initiative amenable to constructive feedback and new ideas.

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.

Antibacterial effect of a diet pill supplement on the human intestinal bacteria.

INTRODUCTION: Many people worldwide attempt to lose weight or adopt strategies to control it. Some have resorted to the consumption of commercialized diet pills to achieve this goal. Multiple brands exist without clearly indicating their mechanism of action or adverse effects on human health. This study aims to determine the antibacterial effect of commercial diet pills on members of the intestinal microbiota. METHODOLOGY: Commercialized diet pills were bought from a pharmacy in the North of Lebanon. Broth microdilution test was performed to determine the Minimum Inhibitory Concentrations (MICs) of the aqueous suspension against forty-two isolates distributed into four Enterobacterales species. MIC of the digested form was determined against six different strains. GC-MS analysis was performed to elucidate the components of the diet pill compared to the manufacturer's list. RESULTS: Broth microdilution results revealed that MICs of the diet pill aqueous suspension ranged from 3.9x103-9.76x102 µg/mL for Escherichia coli, Enterobacter spp., and Proteus spp. For Klebsiella species, MIC of carbapenem-resistant isolates reached 1.95x103 µg/mL. The digested form had a significantly lower antibacterial effect compared to the aqueous suspension. GC-MS analysis results corresponded with the list of ingredients provided by the manufacturer. CONCLUSIONS: The results showed significant antibacterial activity of a commercial diet pill on different members of the human intestinal microbiota regardless of their resistance profile. Further work is needed to elucidate the antibacterial effect of the digested components to accurately understand their effect on the intestinal microflora and thus on human health.

Determination of MIC, MPC, and MSW of Ilex paraguariensis against non-typhoidal Salmonella with identification of the mechanisms of resistance and pathogenicity factors.

This study investigated the antibacterial activity of the aqueous extract of Ilex paraguariensis against 32 different strains of nontyphoidal Salmonella (NTS) through the determination of the minimum inhibitory concentration (MIC), mutant prevention concentration (MPC), and mutant selection window (MSW) and the detection of virulence genes by multiplex PCR assays. The MIC values of Ilex paraguariensis against Salmonella spp. strains varied between 0.78 mg/ml and 6.25 mg/ml with a MIC90 of 3.12 mg/ml. The highest MPC in this study was 48 mg/ml yielding a mutant selection window of 41.75 mg/ml. The MSW values of the remaining strains varied between 1.56 and 8.87 mg/ml. Genes of pathogenicity detected in Salmonella spp. isolates were most commonly the stn, sdiA, invA, sopB, invH, and sopE genes. The antibacterial activity of yerba mate extract was not affected by the antimicrobial resistance patterns or pathogenicity genes expressed. More work is needed to identify the active antibacterial compound(s) responsible for the antibacterial activity.

The impact of vaccination on the burden of invasive pneumococcal disease from a nationwide surveillance program in Lebanon: an unexpected increase in mortality driven by non-vaccine serotypes.

BACKGROUND: 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. METHODS: 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. RESULTS: The prevalence of PCV7 serotypes decreased significantly from 43.6% in the PCV7 era to 17.8% during the PCV13 era (p<0.001). PCV13-only serotypes remained stable in the PCV13 compared to the post-PCV7 eras, especially serotypes 1 and 3, whereas non-vaccine types (NVT) increased throughout the study period, especially 24 and 16F. The mortality rate increased substantially from 12.5% (PCV7 era) to 24.8% (PCV13 era). A significant decrease in AMR was observed across the three study eras. CONCLUSION: PCVs substantially impacted IPD and AMR in vaccinated and unvaccinated populations despite an increase in mortality driven by NVT. Broadening the recommendation of vaccination to include older age-groups, using higher valency vaccines, and implementing stringent antimicrobial stewardship are likely to further impact the burden of IPD.

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.

The Spread of Plasmidic AmpC in a General Lebanese Hospital Over Nine Consecutive Years and the Relationship With Restricted Isolation Protocols.

Background: The dreaded bacterial infection by extended-spectrum ß-lactamases (ESBL)-producers has always troubled the medical field whether on the public, scientific, or clinical levels. One of the lesser known ß-lactamases, which is capable of hydrolyzing broad and extended-spectrum cephalosporins-i.e., cephamycins plus oxyimino-ß-lactams-are the AmpC ß-lactamases. This group, which has also been termed occasionally-and incorrectly-as ESBL Class C, confers resistance to ß-lactamase inhibitors. The prevalence of plasmidic AmpC (pAmpC) strains is possibly still a matter of debate considering the unevenly matched data between phenotypically-detected and molecularly-detected pAmpC. Aim: In the absence of any study in Lebanon addressing the AmpC, our intention was to determine the numbers and percentages of AmpC Enterobacteriaceae isolates, notably plasmid-mediated ones, across different wards at the Centre Hospitalier du Nord (CHN), Lebanon, and highlight the importance of infection control protocols. Materials and Methods: Carriage and infection with pAmpC Enterobacteriaceae were retrospectively investigated between 2011 and 2015 and prospectively between 2016 and 2019 at the Centre Hospitalier du Nord Hospital, North Lebanon. The rise or decline in the numbers of such strains, in concordance with the allegedly intensive isolation of the patients, were analyzed. Results: Intensive care unit (ICU) data shows an initial rise in infection isolates from 2012 to 2014 and in the carriage isolates from 2012 to 2013 with later notable overall decrease in the both isolates' numbers with the application of the isolation protocols at CHN from 2014 onwards. Floors 2, 3, and 4 seemed to house the bulk of the isolates as well. Conclusion: Preventive measures, such as on-going surveillance of the hospital wards by specialized healthcare personnel and strict implementation of infection control practices, should be a top priority in any medical center in order to isolate such strains and try to put a limit for the development and the dissemination of any possible multidrug resistant strains.

Quadruple-Checkerboard: A Modification of the Three-Dimensional Checkerboard for Studying Drug Combinations.

The concept of drug-combination therapy is becoming very important mainly with the drastic increase in resistance to drugs. The Quadruple checkerboard, also called the Q-checkerboard, aims at maximizing the number of possible combinations that can be obtained between four drugs in one experiment to minimize the time and work needed to accomplish the same results with other protocols. This protocol is based on the simple micro dilution technique where the drugs are diluted and combined together in several 96-well plates. In the first set of 96-well plates, Muller-Hinton broth is added followed by the first required drug (e.g., Cefotaxime here) to serially dilute it. After the first step is done, another set of 96-well plates is used to dilute the second drug (e.g., Amikaci), which will be transferred by removing a specific volume of drug 2 and put in the corresponding wells in the first set of 96-well plates that contains drug one. The third step is done by adding the required concentrations of the third drug (e.g., Levofloxacin), to the appropriate plates in the initial set containing combination of drug 1 and 2. The fourth step is done by adding the required concentrations of the fourth drug (e.g., Trimethoprim-sulfamethoxazol) into the appropriate plates in the first set. Then, E. coli ESBL bacterial inoculum will be prepared and added. This method is important to evaluate all the possible combinations and has a wider range of possibilities to be tested furthermore for in vivo testing. Despite being a tiring technique requiring a lot of focus, the results are remarkable and time saving where a lot of combinations can be tested in a single experiment.

The potential impact of the COVID-19 pandemic on global antimicrobial and biocide resistance: an AMR Insights global perspective.

The COVID-19 pandemic presents a serious public health challenge in all countries. However, repercussions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections on future global health are still being investigated, including the pandemic's potential effect on the emergence and spread of global antimicrobial resistance (AMR). Critically ill COVID-19 patients may develop severe complications, which may predispose patients to infection with nosocomial bacterial and/or fungal pathogens, requiring the extensive use of antibiotics. However, antibiotics may also be inappropriately used in milder cases of COVID-19 infection. Further, concerns such as increased biocide use, antimicrobial stewardship/infection control, AMR awareness, the need for diagnostics (including rapid and point-of-care diagnostics) and the usefulness of vaccination could all be components shaping the influence of the COVID-19 pandemic. In this publication, the authors present a brief overview of the COVID-19 pandemic and associated issues that could influence the pandemic's effect on global AMR.

Higher Sensitivity Provided by the Combination of Two Lateral Flow Immunoassay Tests for the Detection of COVID-19 Immunoglobulins.

SARS-Cov-2 was identified in Wuhan, China in December 2019. The World Health Organization (WHO) declared it a pandemic in March of 2020. COVID-19 has now been reported on every continent. In the United States, the total number of confirmed reported cases of COVID-19 has exceeded 1.8 million with the total death exceeding 100,000 people. The most common investigational diagnostics of this disease are RT-PCR and serology testing. The objective of this work was to validate two commercial kits for the detection of IgM and IgG using lateral flow immunoassay tests and to study the effect of the combination of both serology kits for better detection of immunoglobulins. A total of 195 patients presenting with respiratory symptoms suggestive of infection with SARS-Cov-2 were subject to serology and molecular testing. Two lateral flow immunochromatographic assay kits were used: the Healgen Scientific for SARS-CoV-2 IgM/IgG and the Raybiotech for SARS-CoV-2 IgM/IgG. Sensitivity and specificity of each kit alone and in combination were determined and compared. The limit of detection, inter and intra test variations, as well interfering substances and cross reactivity were also studied for both kits. The results show sensitivities for IgM detection varying between 58.9 and 66.2% for the kits alone and 87.7% of the combination of both kits. IgG detection was not significantly affected by this combination. Both kits manifested high specificities (99.2-100%). Both kits showed high clinical performance in terms of cross reactivity and interfering substances. Our results suggest using combinatory testing for the serology of COVID-19 after a full evaluation study, assessing all the parameters affecting their clinical performance before deciding on this combination.

Advocacy for Increased International Efforts for Antimicrobial Stewardship Actions in Low-and Middle-Income Countries on Behalf of Alliance for the Prudent Use of Antimicrobials (APUA), Under the Auspices of the International Society of Antimicrobial Chemotherapy (ISAC).

Antimicrobial stewardship (AMS) is a set of coordinated strategies to improve the use of antimicrobials, to enhance patient outcomes, reduce antimicrobial resistance, and decrease unnecessary costs. The pioneer years of AMS were restricted to high-income countries (HIC), where overconsumption of antibiotics was associated with emergence of multidrug-resistant (MDR) bacteria. AMS in low- and middle-income countries (LMIC) is also necessary. However, programs effective in HIC may not perform as well in LMIC, because (i) While decreased consumption of antibiotics may be an appropriate target in overconsuming HIC, this may be dangerous in LMIC, where many patients die from the lack of access to antibiotics; (ii) although AMS programs in HIC can be designed and monitored through laboratory surveillance of resistance, surveillance programs are not available in many LMIC; (iii) the heterogeneity of health care systems implies that AMS programs must be carefully contextualized. Despite the need to individually tailor AMS programs in LMIC, international collaborations remain highly valuable, through the dissemination of high-quality documents and educational material, that may be shared, adapted where needed, and adopted worldwide. This process, facilitated by modern communication tools, combines many benefits, including: (i) saving time, a precious dimension for health care workers, by avoiding the duplication of similar works in different settings; (ii) taking advantage of colleagues skills, and initiatives, through open access to the work performed in other parts of the world; (iii) sharing experiences, so that we all learn from each others' successes and failures.

Dissemination of Multidrug-Resistant and mcr-1 Gram-Negative Bacilli in Broilers, Farm Workers, and the Surrounding Environment in Lebanon.

Poultry are currently regarded as reservoirs from which multidrug resistance can be readily transferred to the surrounding ecosystem. The aim of this study was to explore the prevalence of extended spectrum beta-lactamases (ESBLs) and ampC and mcr-1 Gram-negative bacilli in chicken, farmers, and environment in Lebanon. In May 2017, we revisited the farm where the first mcr-1 was detected in 2015 in Lebanon. Overall 200 chicken fecal swabs, 6 farmers' fecal samples, and 41 environmental samples were collected. Real time (RT)-PCR was performed for beta-lactamases and mcr genes' screening using newly designed primers/probes. Multilocus sequence typing (MLST) was also performed. ESBL/ampCs were found in 118 samples from chicken, 4 from workers, and all environmental ones. mcr-1 was detected in all chicken and farmers' samples from which 314 and 7 strains were isolated, respectively. Three mcr-1 Escherichia coli strains were isolated from litter and feed. Compared to 2015, the prevalence of ESBL/ampC producers, TEM and CTX-M genes increased significantly in 2017. Main spectra profiles dendrogram of isolated E. coli strains in 2015/2017 and MLST revealed the presence of different clones and sequence types. The evolution of resistance appears to be multi-clonal and related to the diffusion of plasmids carrying ESBL and mcr-1 genes. More work is needed to quantify the magnitude of this emerging problem in Lebanon.