COVID-19 in children: Could pertussis vaccine play the protective role?

While COVID-19 continues to spread across the globe, diligent efforts are made to understand its attributes and dynamics to help develop treatment and prevention measures. The paradox pertaining to children being the least affected by severe illness poses exciting opportunities to investigate potential protective factors. In this paper, we propose that childhood vaccination against pertussis (whooping cough) might play a non-specific protective role against COVID-19 through heterologous adaptive responses in this young population. Pertussis is a vaccine-preventable infectious disease of the respiratory tract and it shares many similarities with COVID-19 including transmission and clinical features. Although pertussis is caused by a bacterium (Bordetella pertussis) while COVID-19 is a viral infection (SARS-CoV-2), previous data showed that cross-reactivity and heterologous adaptive responses can be seen with unrelated agents of highly divergent groups, such as between bacteria and viruses. While we build the arguments of this hypothesis on theoretical and previous empirical evidence, we also outline suggested lines of research from different fields to test its credibility. Besides, we highlight some concerns that may arise when attempting to consider such an approach as a potential public health preventive intervention against COVID-19.

Molecular epidemiology of nonpharyngeal group A streptococci isolates in northern Lebanon

Aim: To characterize the epidemiology of group A Streptococcus (GAS) involved in nonpharyngeal infections sparingly addressed in Lebanon. Materials & methods: A collection of 63 nonpharyngeal GAS isolates recovered between 2010 and 2019 from northern Lebanon were analyzed through emm typing, virulence gene profiling, FCT typing and antibiotic susceptibility analysis. Results & conclusion: A total of 29 emm subtypes was detected, with emm1 being the most dominant. A great intraclonal divergence driven by the loss and gain of superantigens or by the structural variability within the FCT regions was unraveled. The resistance rates for erythromycin and tetracycline were 8 and 20.6%, respectively. The 30-valent vaccine coverage was 76%. This study evidences the complexity of the neglected GAS pathogen in Lebanon.

Investigation of an XDR-Acinetobacter baumannii ST2 outbreak in an intensive care unit of a Lebanese tertiary care hospital

Aim: We sought to investigate the genetic epidemiological relatedness of carbapenem-resistant Acinetobacter baumannii (CRAB) strains of a suspected outbreak in a Lebanese tertiary care hospital to implement necessary infection prevention and control measures. Methods: Twenty-eight nonduplicate CRAB isolates detected among hospitalized patients between January 2016 and July 2017 were studied by real-time polymerase chain reaction (PCR), pulsed-field gel electrophoresis and multilocus sequence typing analyses. Results: Twenty-seven isolates harbored blaOXA-23, of which one also carried blaNDM-1. The isolates distributed temporally in two presumably episodes were stratified by pulsed-field gel electrophoresis into many clusters. Although several clones have become endemic in the hospital, we have rapidly implemented appropriate infection prevention and control measures, achieving full eradication from August 2017 to November 2019. Conclusion: We have successfully investigated and controlled a polyclonal outbreak of OXA-23 producing ST2 CRAB.

Levels of heavy metals, total petroleum hydrocarbons, and microbial load in commercially valuable fish from the marine area of Tripoli, Lebanon

The present study aimed at evaluating the levels of microbiological contamination, total petroleum hydrocarbons (TPHs), and heavy metals (As, Cd, Hg, and Pb) in the edible tissues of commonly consumed fish (8 species) collected from the marine area of Tripoli, Northern Lebanon. Total coliform levels in all sampled fish, and Escherichia coli levels in Liza ramada only, exceeded the permissible limits set by FAO/WHO 2002. Staphylococcus aureus counts were within the recommended thresholds, while sulfate-reducing bacteria levels were the highest in fish of the genus Liza. Salmonella species and Listeria monocytogenes were not detected in all fish analyzed. Analysis of heavy metals levels showed that arsenic exhibited the highest levels among the assessed metals in all genera. Levels of As in Epinephelus, Diplodus, Oblada, and Liza were above the acceptable limits, while Cd levels were below the permissible limits set by the European Commission. Significant negative correlation was found between levels of As and Hg in muscle tissues and fish size (length). Levels of TPHs were the highest in fish of the genus Epinephelus. Significant difference in TPHs contamination was found within three fish genera, with Epinephelus being the most contaminated.

Update on invasive fungal infections in the Middle Eastern and North African region

In the recent years, the epidemiology of invasive fungal infections (IFIs) has changed worldwide. This is remarkably noticed with the significant increase in high-risk populations. Although surveillance of such infections is essential, data in the Middle Eastern and North African (MENA) region remain scarce. In this paper, we reviewed the existing data on the epidemiology of different IFIs in the MENA region. Epidemiological surveillance is crucial to guide optimal healthcare practices. This study can help to guide appropriate interventions and to implement antimicrobial stewardship and infection prevention and control programs in countries.

Seroprevalence of hepatitis E virus in pregnant women in northern Lebanon

Background

Hepatitis E virus is the main cause of acute hepatitis globally. Infection is especially serious in pregnant women in whom the death rate can reach 25%. The prevalence of hepatitis E virus in pregnant women in Lebanon is not known.

Aims

This study aimed to investigate the seroprevalence of hepatitis E virus infection in a sample of pregnant women in northern Lebanon.

Methods

A total of 450 pregnant women from Tripoli, North Lebanon were enrolled in the study. Sera were tested for the presence of anti-hepatitis E virus IgG antibodies using an ELISA technique. Information was collected on the sociodemographic characteristics of the women and their risk factors for hepatitis E virus infection (drinking-water source, blood transfusion and contact with animals).

Results

Only one woman was positive for hepatitis E virus giving a prevalence of 0.22%. She had good living conditions, socioeconomic status and educational level and reported no exposure to any risk factors associated with hepatitis E virus infection. Most of the women (87.3%) had a medium or high income level, 47.1% had a university education and 64.9% drank bottled water. Only a small proportion were exposed to risk factors for hepatitis E virus infection: 14.7% had direct contact with animals and 3.8% had had a blood transfusion.

Conclusion

The prevalence of hepatitis E virus infection in the sample was low (0.22%). However, further epidemiological studies among other population groups are required to determine the national prevalence of hepatitis E virus in Lebanon.

Prevalence of anti-hepatitis E virus IgG antibodies in sera from hemodialysis patients in Tripoli, Lebanon

Hepatitis E virus (HEV) is an important global public health concern. Several studies reported a higher HEV prevalence in patients undergoing regular hemodialysis (HD). In Lebanon, the epidemiology of HEV among HD patients has never been investigated previously. In this study, we examine the seroprevalence of HEV infection among 171 HD patients recruited from three hospital dialysis units in Tripoli, North Lebanon. Prevalence of anti-HEV IgG antibodies was evaluated in participant's sera using a commercial enzyme-linked immunosorbent assay (ELISA). The association of socio-demographic and clinical parameters with HEV infection in patients was also evaluated. Overall, 96 women and 75 men were enrolled in this study. Anti-HEV IgG antibodies were found positive in 37/171 HD patients showing a positivity rate of 21.63%. Among all examined variables, only the age of patients was significantly associated with seropositivity (P = 0.001). This first epidemiological study reveals a high seroprevalence of HEV infection among Lebanese HD patients. However, further evaluations that enroll larger samples and include control groups are required to identify exact causative factors of the important seropositivity rate in this population.

Challenges in identification of enteroinvasive Escherichia coli and Shigella spp. in Lebanon

This study aimed to evaluate the routine identification tools available in Lebanon for differentiation of Escherichia coli and Shigella spp. The identification of 43 isolates defined as Shigella spp. by Api 20E was accessed using MALDI-TOF, serological testing, duplex PCR targeting ipaH (present in Shigella spp. and enteroinvasive E. coli "EIEC") and lacY (found in E. coli including EIEC but not Shigella spp.) as well as gyrB gene sequencing. Antibiotic susceptibility was investigated as well as Shiga-toxin production. All isolates were identified as E. coli by MALDI-TOF while the PCR showed a disparate group of 26 EIEC, 11 Shigella spp., 5 E. coli and 1 inactive E. coli. However, the sequencing of gyrB gene, which was recently described as a suitable marker for distinguishing E. coli and Shigella spp., identified all isolates as E. coli. Antibiotic resistance was noticeable against ß-lactams, rifampicin, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin. The most common variants of beta-lactamase genes were blaTEM-1, blaCTX-M-15, and blaCTX-M-3. A great discordance between the used methods in identification was revealed herein. An accurate identification technique able to distinguish E. coli from Shigella spp. in routine laboratories is a pressing need in order to select the appropriate treatment and assess the epidemiology of these bacteria.

Distribution of emm types and macrolide resistance determinants among group A streptococci in the Middle East and North Africa region

OBJECTIVES

The aim of this review was to provide an updated scenario on the epidemiology of group A streptococci (GAS) in the Middle East and North Africa (MENA) region with a special spotlight on the most prevalent emmtypes and macrolide resistance profiles.

METHODS

This review briefly summarises the disease burden for GAS in the MENA region.

RESULTS

Whilst the burden of invasive GAS infections is difficult to assess in the MENA region, the GAS prevalence ranged from 2.5% up to 42.4% in pharyngitis patients and from 2.4% up to 35.4% in healthy carriers.emm1, emm12, emm89, emm4, emm28 and emm3were responsible for the major GAS burden in the MENA region. The coverage rate of the new M protein-based vaccine candidate (30-valent) varied from 42% to 100% according to the country. The rate of erythromycin resistance differed substantially between countries from low to moderate or high.

CONCLUSION

These data add more shreds of evidence on the neglected GAS burden in the MENA region. Systematic surveillance of invasive GAS infections along with molecular characterisation of GAS isolates are strongly recommended to track the trends of circulating clones and to evaluate the potential coverage of vaccine candidates.

Cytokinin Sensing in Bacteria

Although it has long been known that bacteria detect and react to plant chemicals to establish an interaction, the cellular signaling mechanisms involved in these perception processes have hitherto remained obscure. Some exciting recent advances in the field have described, for the first time, how some phytopathogenic bacteria sense the host plant hormones, cytokinins. These discoveries not only advance the understanding of cell signaling circuitries engaged in cytokinin sensing in non-plant organisms, but also increase our knowledge of the broad role of these ancient molecules in regulating intra- and interspecific communications.

Qishta-A Lebanese Heat Concentrated Dairy Product Characteristics and Production Procedures

This study aims at exploring the chemical composition of a traditional Lebanese dairy product known as Qishta, describing the process of how to prepare it and understanding the mechanisms leading to its formation. The process of making Qishta can be divided into two phases: a hot phase during which milk is heated in a stainless-steel large shallow vessel, and a cold phase consisting of draining, cooling and packaging. According to milk temperature, two reaction zones were identified: zone A with an average temperature of 100 °C, and zone B with an average temperature of 60 °C. The results showed that Qishta had a moisture, fat, protein, lactose and ash content of 68%, 11.7%, 12.1%, 5.4% and 1.6%, respectively. Our findings showed that Qishta is a lipoprotein product having an equal amount of fat and proteins (≈12%); this composition is almost similar to that of Ricotta cheese made from whole milk. In addition, our results assert that the interactions between caseins and whey proteins lead to gel formation. Milk initial fat percentage had a significant effect on Qishta production. The highest yields were obtained when the initial fat percentage was 3.6% (182.5 g of Qishta).

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

BACKGROUND

Carbapenem-resistant Enterobacteriaceae are considered by WHO as "critical" priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largely unknown as well as factors contributing to the acquisition of carbapenemase genes.

METHODS

We first analyzed the whole-genome sequence and the evolution of the E. coli sequence type (ST) 410 and its disseminated clade expressing the carbapenemase OXA-181. We reconstructed the phylogeny of 19 E. coli ST enriched in CP-Ec and corresponding to a total of 2026 non-redundant isolates. Using the EpiCs software, we determined the significance of the association between specific mutations and the acquisition of a carbapenemase gene and the most probable order of events. The impact of the identified mutations was assessed experimentally by genetic manipulations and phenotypic testing.

RESULTS

In 13 of the studied STs, acquisition of carbapenemase genes occurred in multidrug-resistant lineages characterized by a combination of mutations in ftsI encoding the penicillin-binding protein 3 and in the porin genes ompC and ompF. Mutated ftsI genes and a specific ompC allele related to that from ST38 inducing reduced susceptibility to diverse β-lactams spread across the species by recombination. We showed that these mutations precede in most cases the acquisition of a carbapenemase gene. The ompC allele from ST38 might have contributed to the selection of CP-Ec disseminated lineages within this ST. On the other hand, in the pandemic ST131 lineage, CP-Ec were not associated with mutations in ompC or ftsI and show no signs of dissemination.

CONCLUSIONS

Lineages of CP-Ec have started to disseminate globally. However, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by β-lactams from diverse families. This process did not yet occur in the high-risk lineage ST131.

Prevalence and genetic diversity of Campylobacter spp. in the production chain of broiler chickens in Lebanon and its association with the intestinal protozoan Blastocystis sp

Campylobacter jejuni is recognized as the most common foodborne pathogen associated with human gastroenteritis worldwide. Broilers are frequently infected by the bacteria and are considered the main source of exposure to humans. However, despite its public health impact, no recent data are currently available in Lebanon about Campylobacter spp. in poultry and human population. Therefore, this study aimed to determine the prevalence and genetic diversity of Campylobacter spp. in 227 ceca and on 227 carcasses of broiler chickens collected in Lebanese slaughterhouses. Overall, the prevalence of Campylobacter was shown to reach 67.0% in ceca and 17.2% on carcasses of Lebanese poultry. The only 2 Campylobacter species identified were C. jejuni and C. coli, with a slightly higher prevalence of C. coli in ceca and of C. jejuni on carcasses. A high level of genetic diversity was reported among the 51 C. jejuni isolates selected, since 25 distinct profiles were identified according to the comparative genomic fingerprinting typing method based on a subset of 40 genes using the 90% similarity threshold. Predominant clusters observed in Lebanese poultry isolates were also frequently found among French human clinical cases, highlighting that broiler chickens represent a potential reservoir for human campylobacteriosis. In addition, a significantly higher prevalence of Campylobacter spp. was found in slaughterhouse workers than in a cohort of hospitalized patients with no contact with poultry, confirming that contaminated broiler chickens in slaughterhouse appeared to be a non-negligible source of Campylobacter spp. transmission. Interestingly, a significant association between Campylobacter spp. and Blastocystis sp. has been observed. This correlation suggested that the presence of Campylobacter spp. would be favored when Blastocystis sp. is present and, similarly, the absence of one would favor the absence of the other. This is the first large-scale investigation focusing on the impact of Campylobacter spp. in broiler chickens in Lebanon and confirmed the need to implement prevention and control measures in the poultry production to reduce the burden of campylobacteriosis in the human population.

Advances in understanding and managing Scedosporium respiratory infections in patients with cystic fibrosis

Introduction: Considered for a long time to be exclusively responsible for chronic localized infections, fungi of the genus Scedosporium have recently received a renewed interest because of their recognition as common colonizing agents of the respiratory tract of patients with cystic fibrosis, and of the description of severe disseminated infections in patients undergoing lung transplantation. Recently, several studies have been carried out on these opportunistic pathogens, which led to some advances in the understanding of their pathogenic mechanisms and in the biological diagnosis of the airway colonization/respiratory infections caused by these fungi.Areas covered: From a bibliographic search on the Pubmed database, we summarize the current knowledge about the taxonomy of Scedosporium species, the epidemiology of these fungi and their pathogenic mechanisms, and present the improvements in the detection of the airway colonization and diagnosis of Scedosporium respiratory infections, the difficulties in their therapeutic management, and the antifungal drugs in development.Expert opinion: As described in this review, many advances have been made regarding the taxonomy and ecology of Scedosporium species or the molecular determinants of their pathogenicity, but also in the management of Scedosporium infections, particularly by improving the biological diagnostic and publishing evidence for the efficacy of combined therapy.

Recent trends in the epidemiology, diagnosis, treatment, and mechanisms of resistance in clinical Aspergillus species: A general review with a special focus on the Middle Eastern and North African region

Globally, more than billion people suffer from fungal infections each year. The early diagnosis of aspergillosis is mandatory for successful treatment outcome. As careful testing takes time, epidemiological surveillance is crucial to guide individual patient therapy and to promote a high standard of health care. In this paper, we first present current trends in the epidemiology and antifungal susceptibility patterns of Aspergillus spp. in Middle Eastern and North African (MENA) countries in order to support infectious disease specialists and health workforces in this geographic area to treat adequately patients with aspergillosis. Then we discuss the existing literature data regarding the available diagnostic tools and antifungal resistance mechanisms of Aspergillus spp. Although a limited number of studies were reviewed here, the currently available data show that Aspergillus infections are not negligible in the MENA region, and that the emergence of antifungal resistance is a growing health issue, especially among immunocompromised patients.

Characterization of lactobacilli strains isolated from baby's feces for their potential immunobiotic application

BACKGROUND AND OBJECTIVES

Several LAB species were evaluated and characterized for potential probiotic use. Besides the antimicrobial activity, probiotics showed recently a capacity to prevent and to alleviate inflammatory and chronic diseases. Immunomodulation effect is one of the modes of actions of such probiotics, called immunobiotics, which can be used in several chronic diseases such as Inflammatory Bowel Diseases (IBD). The aim of this study was to isolate, identify and characterize lactobacilli strains from healthy baby's feces in order to select some strains with potential immunobiotic application especially strains which can stimulate anti-inflammatory responses.

MATERIALS AND METHODS

Forty-two LAB strains were isolated and identified by the MALDI-TOF / MS technique. In addition, strains were subjected to several assessments such as antimicrobial activity, the capacity to form biofilm in polystyrene microplate and immunomodulation activity in a PBMC model.

RESULTS

Results showed that the majority of strains (90.4%) were identified as Lactobacillus. However, among these, only 39.4% of lactobacilli strains were not identified at the species level. All isolated lactobacilli strains showed an anti-inflammatory effect. Moreover, 7 strains were considered as good probiotic candidates based on their characteristics such as their antibacterial activities, formation of the strongest biofilm and their ability to stimulate an anti-inflammatory response in PBMCs model.

CONCLUSION

Two strains (Lactobacillus spp S14 and Lactobacillus spp S49) which showed the best immunobiotic characteristics, could be selected and evaluated more deeply in vivo model as well as in human clinical study to ensure their effectiveness in inflammatory diseases such as IBD.

First report on seroprevalence and risk factors of Toxoplasma gondii infection in sheep and goats in North Lebanon

INTRODUCTION

Toxoplasmosis is of dual importance in both public and veterinary health due to the respective risk of transplacental transmission in primo-infected pregnant women and economic losses caused by abortions in mammals. One of the main routes of Toxoplasma gondii transmission to humans is the consumption of raw or undercooked meats containing parasitic cysts. Here, we performed the first epidemiological study to determine the seroprevalence and the risk factors of toxoplasmosis in livestock in Lebanon.

METHODOLOGY

Using a modified agglutination test with a cut-off of 1:40, we tested the positivity rate of Immunoglobulin G antibodies in the sera of 100 sheep and 80 goats collected from 18 different livestock farms located in North Lebanon between March and June 2018.

RESULTS

Anti-Toxoplasma gondii IgG antibodies were detected in 42% of sheep and 34% of goats. Adults (> 1 year) were significantly more infected by T. gondii than the lambs (< 1 year) in both species (p < 0.05).

CONCLUSIONS

These findings indicated that food animals are highly exposed to T. gondii in Lebanon and could be potentially a major risk factor of T. gondii infection to humans. Consequently, national prophylactic strategies should be implemented to control and to prevent T. gondii transmission between animals and humans.

Plasmid-mediated quinolone resistance: Mechanisms, detection, and epidemiology in the Arab countries

Quinolones are an important antimicrobial class used widely in the treatment of enterobacterial infections. Although there are multiple mechanisms of quinolone resistance, attention should be paid to plasmid-mediated genes due to their ability to facilitate the spread of quinolone resistance, the selection of mutants with a higher-level of quinolone resistance, and the promotion of treatment failure. Since their discovery in 1998, plasmid-mediated quinolone resistance (PMQR) mechanisms have been reported more frequently worldwide especially with the extensive use of quinolones in humans and animals. Nevertheless, data from the Arab countries are rare and often scattered. Understanding the prevalence and distribution of PMQR is essential to stop the irrational use of quinolone in these countries. This manuscript describes the quinolone resistance mechanisms and particularly PMQR among Enterobacteriaceae as well as their methods of detection. Then the available data on the epidemiology of PMQR in clinical and environmental isolates from the Arab countries are extensively reviewed along with the other associated resistance genes. These data shows a wide dissemination of PMQR genes among Enterobacteriaceae isolates from humans, animals, and environments in these countries with increasing rates over the years and a common association with other antibiotic resistance genes as bla_CTX-M-15. The incontrovertible emergence of PMQR in the Arab countries highlights the pressing need for effective stewardship efforts to prevent the selection of a higher rate of quinolone resistance and to preserve these crucial antibiotics.

The epidemiology of Candida species in the Middle East and North Africa

In recent decades, the epidemiology of invasive candidiasis (IC) has progressively changed worldwide. This notably includes emergence of several Candida species. Although some surveillance programs provided global trends in IC epidemiology, data from countries from the Middle East and North Africa (MENA) remain scarce. In this manuscript, we reviewed the existing available data on the epidemiology of Candida species associated with IC, particularly candidemia, in MENA region regarding species distribution. As witnessed worldwide, an evident shift of Candidaalbicans towards non-albicansCandida (NAC) has been observed in the MENA region. The worrying emergence of multi-drug resistant Candida species in MENA calls for a better understanding of their epidemiology. This represents an essential prerequisite for the implementation of effective infection control strategies and surveillance systems to prevent IC among high-risk patients.

Prevalence of Staphylococcus aureus methicillin-sensitive and methicillin-resistant nasal carriage in food handlers in Lebanon: a potential source of transmission of virulent strains in the community

Purpose

To determine the prevalence and virulence determinant genes of nasal colonization by Staphylococcus aureus among food handlers in Tripoli, Lebanon.

Methodology

Within a cross-sectional study design, nasal swab specimens were collected. Epidemiological and microbiological investigations were performed through conventional culture and MALDI-TOF-MS. Antibiotic susceptibility patterns and genetic virulence determinants including enterotoxin genes were also investigated for all isolates.

Results

The data herein show that S. aureus nasal carriage is highly prevalent (23.8 %), and that the rate of methicillin-resistant S. aureus (MRSA) carriage was twice as high as in our last report in 2008. Several enterotoxin genes were detected in five isolates including one MRSA and four methicillin-sensitive S. aureus.

Conclusion

To our knowledge, this is the first investigation in the last decade to examine the carriage prevalence of S. aureus among food handlers in Lebanon. This work reports a concerning level of MRSA, and enterotoxin-producing S. aureus nasal carriage, which could potentially act as a contamination reservoir and lead to food poisoning.

Drug-Resistant Tuberculosis, Lebanon, 2016 - 2017

In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.

Update on the epidemiological typing methods for Acinetobacter baumannii

The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.