Catch-22: War, Refugees, COVID-19, and the Scourge of Antimicrobial Resistance

Emergence of Extended-Spectrum Cephalosporin- and Colistin-Resistant Enterobacterales in Otherwise Healthy University Students

Resistance to last resort antibiotics has been increasing, particularly in low- and middle-income countries such as Lebanon, which has well established challenges in antimicrobial stewardship and other public health and environmental issues. However, data on the emergence of antibiotic resistance in the community in Lebanon are limited. In this study, we assessed resistance to last resort antibiotics in the fecal samples of 111 otherwise healthy university students in north Lebanon. The results showed that 47.7% of the samples harbored extended-spectrum cephalosporin-resistant isolates, while 2.7% of the samples yielded colistin-resistant isolates. Furthermore, molecular analyses showed that the β-lactamase gene group, blaCTX-M-1 group, was detected in the majority (93%) of screened extended-spectrum β-lactamase isolates. In addition, the colistin-resistant Escherichia coli isolates carried mcr-1, including the novel mcr-1.26 variant, which was previously reported in clinical samples as well as in domesticated animals and the environment in Lebanon. Taken together, these findings highlight the occurrence of resistance to important antibiotics in the community, perhaps suggesting diffuse sources, including clinical and environmental settings, and multiple factors driving the spread of multidrug-resistant bacteria and resistance determinants. There is a pressing need for comprehensive antimicrobial stewardship programs and the implementation of evidence-based practices in clinical and community settings to mitigate the increasing spread of antimicrobial resistance.

Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance

In this study, we characterized 54 clinical isolates of Shigella collected in North Lebanon between 2009 and 2017 through phenotypic and genomic analyses. The most prevalent serogroup was S. sonnei, accounting for 46.3 % (25/54) of the isolates, followed by S. flexneri (27.8 %, 15/54), S. boydii (18.5 %, 10/54) and S. dysenteriae (7.4 %, 4/54). Only three isolates were pan-susceptible, and 87 % (47/54) of the isolates had multidrug resistance phenotypes. Notably, 27.8 % (15/54) of the isolates were resistant to third-generation cephalosporins (3GCs) and 77.8 % (42/54) were resistant to nalidixic acid. 3GC resistance was mediated by the extended-spectrum beta-lactamase genes bla CTX-M-15 and bla CTX-M-3, which were present on various plasmids. Quinolone resistance was conferred by single point mutations in the gyrA DNA gyrase gene, leading to GyrA S83L, GyrA D87Y or GyrA S83A amino acid substitutions. This is the first study, to our knowledge, to provide genomic insights into the serotypes of Shigella circulating in Lebanon and the various antimicrobial resistance determinants carried by these strains.

The emergence of carbapenemase-producing Enterobacterales in hospitals: a major challenge for a debilitated healthcare system in Lebanon

Background

Carbapenem- and extended-spectrum cephalosporin-resistant Enterobacterales (CR-E and ESCR-E, respectively) are increasingly isolated worldwide. Information about these bacteria is sporadic in Lebanon and generally relies on conventional diagnostic methods, which is detrimental for a country that is struggling with an unprecedented economic crisis and a collapsing public health system. Here, CR-E isolates from different Lebanese hospitals were characterized.

Materials and methods

Non-duplicate clinical ESCR-E or CR-E isolates (N = 188) were collected from three hospitals from June 2019 to December 2020. Isolates were identified by MALDI-TOF, and their antibiotic susceptibility by Kirby-Bauer disk diffusion assay. CR-E isolates (n = 33/188) were further analyzed using Illumina-based WGS to identify resistome, MLST, and plasmid types. Additionally, the genetic relatedness of the CR-E isolates was evaluated using an Infrared Biotyper system and compared to WGS.

Results

Using the Kirby-Bauer disk diffusion assay, only 90 isolates out of the 188 isolates that were collected based on their initial routine susceptibility profile by the three participating hospitals could be confirmed as ESCR-E or CR-E isolates and were included in this study. This collection comprised E. coli (n = 70; 77.8%), K. pneumoniae (n = 13; 14.4%), Enterobacter spp. (n = 6; 6.7%), and Proteus mirabilis (n = 1; 1.1%). While 57 were only ESBL producers the remaining 33 isolates (i.e., 26 E. coli, five K. pneumoniae, one E. cloacae, and one Enterobacter hormaechei) were resistant to at least one carbapenem, of which 20 were also ESBL-producers. Among the 33 CR-E, five different carbapenemase determinants were identified: blaNDM-5 (14/33), blaOXA-244 (10/33), blaOXA-48 (5/33), blaNDM-1 (3/33), and blaOXA-181 (1/33) genes. Notably, 20 CR-E isolates were also ESBL-producers. The analysis of the genetic relatedness revealed a substantial genetic diversity among CR-E isolates, suggesting evolution and transmission from various sources.

Conclusion

This study highlighted the emergence and broad dissemination of blaNDM-5 and blaOXA-244 genes in Lebanese clinical settings. The weak AMR awareness in the Lebanese community and the ongoing economic and healthcare challenges have spurred self-medication practices. Our findings highlight an urgent need for transformative approaches to combat antimicrobial resistance in both community and hospital settings.

Antifungal Use and Resistance in a Lower-Middle-Income Country: The Case of Lebanon

Antimicrobial resistance is a serious threat, particularly in low- and middle-income countries (LMICs). Antifungal resistance is often underestimated in both healthcare and non-clinical settings. In LMICs, it is believed that the inappropriate use of antifungals, limited surveillance systems, and low diagnostic capacities are significant drivers of resistance. Like other LMICs, Lebanon lacks antifungal use and resistance surveillance programs, and the impact of antifungal resistance in the country remains unclear, especially during the unfolding economic crisis that has severely affected medical care and access to safe food and water. Interestingly, the widespread use of antifungals in medicine and agriculture has raised concerns about the development of antifungal resistance in Lebanon. In this light, we aimed to survey available antifungal drugs in the country and evaluate susceptibility patterns of prevalent fungal species to guide empiric treatments and develop antifungal stewardship programs in Lebanon. We noted that the economic crisis resulted in significant increases in antifungal drug prices. Additionally, a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar databases identified 15 studies on fungal infections and antifungal resistance conducted from 1998 to 2023 in Lebanon. While data on antifungal resistance are limited, 87% of available studies in Lebanon focused on candidiasis, while the remaining 13% were on aspergillosis. Overall, we observed a marked antimicrobial resistance among Candida and Aspergillus species. Additionally, incidences of Candida auris infections have increased in Lebanese hospitals during the COVID-19 pandemic, with a uniform resistance to fluconazole and amphotericin-B. Taken together, a One Health approach, reliable diagnostics, and prudent antifungal use are required to control the spread of resistant fungal pathogens in healthcare and agricultural settings.

Prevalence of Latent Tuberculosis Infection among Patients Undergoing Regular Hemodialysis in Disenfranchised Communities: A Multicenter Study during COVID-19 Pandemic

Background and Objectives: Due to their weakened immune response, hemodialysis (HD) patients with latent tuberculosis infection (LTBI) are at higher risk for active tuberculosis (TB) disease and are more subject to patient-to-patient transmission within dialysis units. Consequently, current guidelines advocate screening these patients for LTBI. To our knowledge, the epidemiology of LTBI in HD patients has never been examined before in Lebanon. In this context, this study aimed to determine LTBI prevalence among patients undergoing regular HD in Northern Lebanon and to identify potential factors associated with this infection. Notably, the study was conducted during the COVID-19 pandemic, which is likely to have catastrophic effects on TB and increase the risk of mortality and hospitalization in HD patients. Materials and Methods: A multicenter cross-sectional study was carried out in three hospital dialysis units in Tripoli, North Lebanon. Blood samples and sociodemographic and clinical data were collected from 93 HD patients. To screen for LTBI, all patient samples underwent the fourth-generation QuantiFERON-TB Gold Plus assay (QFT-Plus). Multivariable logistic regression analysis was used to identify the predictors of LTBI status in HD patients. Results: Overall, 51 men and 42 women were enrolled. The mean age of the study population was 58.3 ± 12.4 years. Nine HD patients had indeterminate QFT-Plus results and were therefore excluded from subsequent statistical analysis. Among the remaining 84 participants with valid results, QFT-Plus was positive in 16 patients, showing a positivity prevalence of 19% (95% interval for p: 11.3%, 29.1%). Multivariable logistic regression analysis showed that LTBI was significantly associated with age [OR = 1.06; 95% CI = 1.01 to 1.13; p = 0.03] and a low-income level [OR = 9.29; 95% CI = 1.62 to 178; p = 0.04]. Conclusion: LTBI was found to be prevalent in one in five HD patients examined in our study. Therefore, effective TB control measures need to be implemented in this vulnerable population, with special attention to elderly patients with low socioeconomic status.

Assessment of the Microbiological Acceptability of White Cheese (Akkawi) in Lebanon and the Antimicrobial Resistance Profiles of Associated Escherichia coli

Dairy foods are a staple in Lebanon, a low- and middle-income country that has been experiencing serious challenges to food safety and antimicrobial stewardship among other issues. The microbiological acceptability of dairy products has been of increasing concern. This is partially due to the failing economy and prolonged power outages that affect the quality of raw material and disrupt the dairy cold chain, respectively. Therefore, we assessed the microbiological acceptability of Akkawi, a popular white-brined cheese in Lebanon. For this purpose, we quantified the densities of Escherichia coli (a fecal indicator) and Staphylococcus aureus in cheeses collected from Lebanese retail stores. Additionally, we evaluated the antibiotic resistance profiles of the E. coli isolated from the cheese. E. coli and S. aureus were detected in 40 (80%) and 16 (32%) of the 50 cheese samples, respectively. Notably, 40 (80%) and 16 (32%) of the samples exceeded the maximum permissible limit of E. coli and S. aureus, respectively. A high percentage of the 118 E. coli isolated from the cheeses showed resistance to clinically and agriculturally important antibiotics, while 89 (75%) isolates were classified as multidrug-resistant (MDR). Given that Akkawi can be consumed without cooking, our findings highlight serious food safety and antimicrobial resistance problems that require immediate interventions.

Zoonotic Tuberculosis: A Neglected Disease in the Middle East and North Africa (MENA) Region

Mycobacterium bovis is the etiologic agent of bovine tuberculosis (BTB), a serious infectious disease in both humans and animals. BTB is a zoonotic disease primarily affecting cattle and occasionally humans infected through close contact with infected hosts or the consumption of unpasteurized dairy products. Zoonotic tuberculosis is strongly associated with poverty and poor hygiene, and low- and middle-income countries bear the brunt of the disease. BTB has been increasingly recognized as a growing public health threat in developing countries. However, the lack of effective surveillance programs in many of these countries poses a barrier to accurately determining the true burden of this disease. Additionally, the control of BTB is threatened by the emergence of drug-resistant strains that affect the effectiveness of current treatment regimens. Here, we analyzed current trends in the epidemiology of the disease as well as the antimicrobial susceptibility patterns of M. bovis in the Middle East and North Africa (MENA) region, a region that includes several developing countries. Following PRISMA guidelines, a total of 90 studies conducted in the MENA region were selected. Our findings revealed that the prevalence of BTB among humans and cattle varied significantly according to the population size and country in the MENA region. Most of the available studies were based on culture and/or PCR strategies and were published without including data on antimicrobial resistance and molecular typing. Our findings highlighted the paramount need for the use of appropriate diagnostic tools and the implementation of sustainable control measures, especially at the human/animal interface, in the MENA region.

The indelible toll of enteric pathogens: Prevalence, clinical characterization, and seasonal trends in patients with acute community-acquired diarrhea in disenfranchised communities

BACKGROUND

There is little information on the epidemiology of enteric pathogens in Lebanon, a low- and middle-income country that suffers from a myriad of public health challenges. To address this knowledge gap, we aimed to assess the prevalence of enteric pathogens, identify risk factors and seasonal variations, and describe associations between pathogens among diarrheic patients in the Lebanese community.

METHODOLOGY AND PRINCIPAL FINDINGS

A multicenter cross-sectional community-based study was conducted in the north of Lebanon. Stool samples were collected from 360 outpatients suffering from acute diarrhea. Based on fecal examination using the BioFire® FilmArray® Gastrointestinal Panel assay, the overall prevalence of enteric infections was 86.1%. Enteroaggregative Escherichia coli (EAEC) was the most frequently identified (41.7%), followed by enteropathogenic E. coli (EPEC) (40.8%) and rotavirus A (27.5%). Notably, two cases of Vibrio cholerae were identified, while Cryptosporidium spp. (6.9%) was the most common parasitic agent. Overall, 27.7% (86/310) of the cases were single infections, and the majority, 73.3% (224/310), were mixed infections. Multivariable logistic regression models showed that enterotoxigenic E. coli (ETEC) and rotavirus A infections were significantly more likely to occur in the fall and winter compared to the summer. Rotavirus A infections significantly decreased with age but increased in patients living in rural areas or suffering from vomiting. We identified strong associations in the co-occurrence of EAEC, EPEC, and ETEC infections and a higher percentage of rotavirus A and norovirus GI/GII infections among EAEC-positive cases.

CONCLUSIONS

Several of the enteric pathogens reported in this study are not routinely tested in Lebanese clinical laboratories. However, anecdotal evidence suggests that diarrheal diseases are on the rise due to widespread pollution and the deterioration of the economy. Therefore, this study is of paramount importance to identify circulating etiologic agents and prioritize dwindling resources to control them and limit outbreaks in the future.

Refugee settlements, sewage pollution, COVID-19 and the unfolding cholera outbreak in Lebanon

We have previously documented that the unsanitary conditions in the Syrian refugee settlements and pollution in Lebanon were suitable for the proliferation of infectious diseases. Here, we discuss how cholera is spreading rapidly across Lebanon, where a Syrian man from an informal settlement is thought to be the index case.

Prevalence and Molecular Mechanisms of Carbapenem Resistance among Gram-Negative Bacilli in Three Hospitals of Northern Lebanon

Carbapenem resistance (CR) is an emerging health issue. Epidemiological surveys on carbapenem-resistant Gram-negative bacilli (CR-GNB) in Lebanon remain scarce. In this study, we determined the prevalence of CR-GNB isolated between 2015 to 2019 in three hospitals in northern Lebanon: 311 CR-Enterobacterales (out of 11210; 2.8%), 155 CR-Pseudomonas (out of 1034; 15%) and 106 CR- Acinetobacter (out of 184; 57.6%) were identified. CR mechanisms were determined for 146 randomly chosen isolates: the Carba NP test revealed an enzymatic resistance to carbapenems in 109 isolates (out of 146, 74.7%). Produced carbapenemases were evaluated by the NG-Test Carba5, NG-Test OXA-23 immunochromatographic assays and PCR. Carbapenemase-producing (CP) Enterobacterales expressed bla_OXA-48-like, bla_NDM-like and bla_VIM-like genes and CP-Pseudomonas expressed bla_IMP-like and bla_VIM-like genes, whereas CP-Acinetobacter expressed bla_OXA-23-like genes. The NG-Test Carba5 results were confirmed by PCR sequencing and revealed several variants, such as NDM-19, VIM-62 and OXA-162, never described so far in Lebanon. Isolates with discordant results were sequenced by WGS and highlighted novel variants of the natural oxacillinases of Pseudomonas aeruginosa: bla_OXA-50-like genes. Their role in carbapenem resistance should be further studied. Overall, our findings highlight an alarming situation and encourage health care centers to establish performant registration systems that could help in limiting resistance spread.