First data on latent tuberculosis infection in Syrian refugees with diabetes in Lebanon.

OBJECTIVE: The association between diabetes mellitus and tuberculosis is a health-threatening double trouble. Vulnerable populations such as refugees and conflict-displaced populations may be at higher risk of both diseases. Here, we examined the prevalence of latent tuberculosis infection (LTBI) and its associated risk factors in a population of Syrian refugees with diabetes in North Lebanon. STUDY DESIGN: This is a cross-sectional study. METHODS: A total of 87 Syrian refugees with diabetes were enrolled. Demographic and clinical data were collected using a structured questionnaire, and a blood sample was obtained from each patient. LTBI was examined using the last generation QuantiFERON-TB Gold Plus assay. RESULTS: The mean age of the study population was 54.1 ± 10.5 years, and the majority were women (79.3%). LTBI was found in 1 in 5 (17/87; 19.5%) enrolled patients, with the majority being originated from Aleppo (47.05%). Infection was significantly associated only with age (P = 0.009), and its risk was 4-fold higher in patients aged ≥60 years (odds ratio: 4.1, confidence interval: 1.4-12.5, P = 0.018). CONCLUSION: This study highlights the need to implement effective tuberculosis control strategies among refugees with diabetes, with particular attention to those at older age.

Molecular epidemiology of Campylobacter isolates from broiler slaughterhouses in Tripoli, North of Lebanon.

1. The real burden of Campylobacter spp. in Lebanon is still unknown. The aims of this study were to unravel the epidemiology of Campylobacter spp. in broilers at slaughterhouses in Tripoli, North of Lebanon and to characterise their antibiotic resistance profiles.2. From May to November 2015, sampling was performed through five repeated surveys from 15 slaughterhouses that sold chicken directly to Lebanese customers. Isolates were subjected to pulsed field gel electrophoresis (PFGE) and flaA-restriction fragment length polymorphism (flaA-RFLP).3. All investigated slaughterhouses were found to be positive for Campylobacter spp. Campylobacter coli was the predominant species (38 isolates) followed by C. jejuni (eight isolates). A noticeable level of resistance was detected among isolates against ciprofloxacin (97% of C. coli and 87.5% of C. jejuni), amoxicillin (89% of C. coli and 75% of C. jejuni), gentamicin (79% of C. coli and 50% of C. jejuni), and co-amoxiclav (24% of C. coli and 25% of C. jejuni). Erythromycin and ertapenem resistance were observed only in C. coli with the following percentages 74% and 13% respectively, but not in C. jejuni. PFGE and flaA-RFLP using DdeI as restriction enzyme divided the strains into 27 and 25 types respectively.4. The high observed genetic diversity of Campylobacter spp. revealed the complexity of the spread of this genus in broilers. This study highlighted the pressing need to monitor antibiotic resistance and to ensure food safety from 'farm to fork' in Lebanon.

IS1R-mediated plasticity of IncL/M plasmids leads to the insertion of bla OXA-48 into the Escherichia coli Chromosome.

The OXA-48 carbapenemase is mainly encoded by ∼ 62-kb IncL/M plasmids. However, chromosome-mediated genes have been observed in Escherichia coli isolates. In this work, we investigated the genetic environment of OXA-48 in members of the family Enterobacteriaceae (n = 22) to understand how the OXA-48-encoding gene is transferred into the E. coli chromosome. The OXA-48-encoding gene was located within intact Tn1999.2 transposons in the ∼ 62-kb plasmids or within a truncated variant of Tn1999.2 for the OXA-48-encoding genes located in the chromosomes of E. coli bacteria. The analysis of the Tn1999.2 genetic environment revealed an inverted orientation of the transposon in five ∼ 62-kb plasmids (5/14 [35%]) and in all chromosome inserts (n = 8). The sequencing of pRA35 plasmid showed that this orientation of Tn1999.2 and the acquisition of an IS1R insertion sequence generated a 21.9-kb IS1R-based composite transposon encoding OXA-48 and designated Tn6237. The sequencing of a chromosomal insert encoding OXA-48 also revealed this new transposon in the E. coli chromosome. PCR mapping showed the presence of this element in all strains harboring an OXA-48-encoding chromosomal insert. However, different insertion sites of this transposon were observed in the E. coli chromosome. Overall, these findings indicate a plasticity of the OXA-48 genetic environment mediated by IS1R insertion sequences. The insertion sequences can induce the transfer of the OXA-encoding gene into E. coli chromosomes and thereby promote its persistence and expression at low levels.

Carbapenemase and virulence factors of Enterobacteriaceae in North Lebanon between 2008 and 2012: evolution via endemic spread of OXA-48.

OBJECTIVES: To investigate the resistance to carbapenems in Enterobacteriaceae and the underlying resistance mechanisms in North Lebanon between 2008 and 2012. METHODS: A total of 2767 Enterobacteriaceae isolates recovered from clinical samples collected in Nini Hospital (North Lebanon) were screened for a decrease in susceptibility or resistance to ertapenem (MIC >0.25 mg/L). Enterobacteriaceae were similarly screened from 183 faecal samples obtained from non-hospitalized patients. The bacterial isolates were assigned to clonal lineages by PFGE and multilocus sequence typing. Carbapenemase genes, their genetic environment and virulence genes were characterized by molecular approaches. RESULTS: The rate of Enterobacteriaceae exhibiting a decrease in susceptibility or resistance to ertapenem increased from 0.4% in 2008-10 to 1.6% in 2012 for the clinical isolates recovered from hospitalized patients. Of these isolates, scattered among seven enterobacterial species, 88% produced OXA-48 carbapenemase. However, Escherichia coli represented 73% of the OXA-48-producing Enterobacteriaceae collected in 2012 at this hospital. During the faecal carriage study performed in non-hospitalized patients, E. coli was the only species producing OXA-48. The bla(OXA-48) gene was mainly found within Tn1999.2-type transposons inserted into E. coli chromosomes or in ∼50, ∼62 or ∼85 kb plasmids. The plasmids and chromosomal inserts were related to pOXA-48a. Molecular typing of the isolates revealed clonal diversity of E. coli and Klebsiella pneumoniae producing OXA-48. OXA-48 was observed in all major E. coli phylogroups, including D and B2, and isolates harbouring virulence genes of extra-intestinal pathogenic E. coli. Although not belonging to highly virulent capsular genotypes, the OXA-48-producing K. pneumoniae harboured genes associated with virulence or host colonization. CONCLUSIONS: Horizontal transfer of related plasmids has facilitated the spread of the bla(OXA-48) gene into several Enterobacteriaceae species, including virulent E. coli. Their clonal diversity and the presence of faecal carriers in the community suggest an endemic spread of OXA-48.

[Anti-tetanus immunity among university students and health staff in North Lebanon and administration of anti-tetanus serums in two hospitals]. / Immunité antitétanique chez des étudiants universitaires et personnels de santé au Liban-Nord et administration de serum antitétanique dans deux hôpitaux.

Tetanus is a serious illness that kills about one million people a year globally. This study aimed to i) evaluate immunity against tetanus (by antibodies titres in blood) among health staff and students at the Public Health Faculty, Lebanese University, ii) explore the determinants of the anti-tetanus immunity by a questionnaire and iii) estimate anti-tetanic serum use in the emergency departments of two hospitals (1 private, 1 public) in Tripoli. Most of the participants (76.6%) had anti-tetanus antibody titres ≥ 0.1 UI/mL. There was no association between immune status and gender (P = 0.614) but more participants ≤ 25 years were immunized than those > 25 years (P < 0.001) and more students were immunized than employees (P = 0.032). There was an inverse association between anti-tetanus immunity and having visited a physician in the past year (P = 0.009). In 2011, 1037 people received anti-tetanus immunoglobulins at the hospitals, 73% at the private hospital. Vaccination campaigns targetting adults > 25 years may be warranted to assure good anti-tetanus protection and avoid administration of anti-tetanus immunoglobulins in emergency departments.

Prevalence of type b Haemophilus influenzae and antibiotic resistance in 52 clinical isolates in north Lebanon.

The aim of this study was to determine the capsular typing and type b prevalence of clinical Haemophilus influenzae strains in north Lebanon in both invasive and non-invasive disease and to determine the susceptibility pattern and the mechanism of resistance to ß-lactams [ß-lactamase-producing strains and ß-lactamase-negative ampicillin resistant (BLNAR) strains]. Fifty-two strains of clinical H. influenzae were isolated from 312 clinical specimens; the resistance pattern to ß-lactams of these strains was determined by using the disc diffusion and E-test methods followed by molecular methods such as PCR of blaTEM et blaROB genes. Nine (17.4%) of the 52 strains were resistant to ampicillin; all of them produced type TEM-1 ß-lactamase. In the susceptible strains 15.3% were not fully susceptible to ß-lactams or considered low BLNAR strains. Slide agglutination serotyping showed that 30.7% of the strains were type b.

Mycobacterium tuberculosis spoligotypes circulating in the Lebanese population: a retrospective study.

Genotyping Mycobacterium tuberculosis in Lebanon on the national level may be beneficial for assessing patients and monitoring the therapeutic response to DOTS. This study aimed to characterize the spoligotypes of clinical isolates of M. tuberculosis patients collected between April 2004 and October 2005 from all Lebanese provinces. Isolates (n = 60) were cultured and identified by their biochemical characteristics. DNA extracts of these samples were amplified by PCR and genotyped by spoligotyping. Thirteen (13) patterns of M. tuberculosis complex family strains were identified: 41.6% of the strains belonged to the T 1 family, 25.0% to LAM 9, 10.0% to Haarlem 3, 3.3% to each of CAS, LAM 8, BCG and Family 36 and 1.7% to each of Haarlem 1, LAM 10, S, M. africanum, X 1 and T 3 families. The noticeable absence of Beijing and East African Indian families was not consistent with the patterns reported in neighbouring countries. A more inclusive study of the Lebanese population is necessary to accurately identify most of the prevailing families in the country.

[Preliminary study on the prevalence of Campylobacter in childhood diarrhoea in north Lebanon]. / Etude préliminaire sur la prévalence de Campylobacter dans les diarrhées infantiles au nord du Liban.

Campylobacter species are a major cause of human diarrhoeal disease worldwide. In Lebanon, the true prevalence of Campylobacter infections and the species distribution in childhood diarrhoea are not known. This study in 2010 investigated the prevalence of Campylobacter species and its possible etiologic role in childhood diarrhoea in north Lebanon. A total of 90 stool samples from children (aged 1 month to 10 years) presenting with diarrhoea were collected from 5 hospitals. A polymerase chain reaction technique (PCR) was used for each sample forthe amplification of all Campylobacter species followed by 5 PCR reactions for the amplification of C. jejuni, C. hyointestinalis, C. coli, C. fetus and C. upsaliensis. Of the 90 samples, 10 were positive for Campylobacterspecies (11.1%):1 for C.coli, 1 for C. jejuni, 2 for both C. jejuni and C. coli, and 6 could not be identified to the species level with the available primers. Campylobacter species is frequently associated with childhood diarrhoea in north Lebanon but Campylobacter infection may be significantly underdiagnosed because the search for Campylobacter is not part of the routine stool culture.

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.

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.

First Lebanese Antibiotic Awareness Week campaign: knowledge, attitudes and practices towards antibiotics.

Antibiotic resistance (ABR) is a major global health threat that increases the risk of treatment failure and increases medical costs. One of the most common factors contributing to the spread of ABR is self-medication. The public, as well as workers in clinical and veterinary sectors, commit false practices towards appropriate antibiotic use, favouring the spread of resistance. As such, the first Lebanese Antibiotic Awareness Week campaign was initiated with a human-centred and interactive approach. The data showed a strikingly low level of antibiotic awareness. Cooperation between relevant stakeholders, policy-makers and health actors is crucial to control and overcome the problem of ABR.

Pyrosequencing for rapid detection of tuberculosis resistance to Rifampicin and Isoniazid in Syrian and Lebanese clinical isolates.

BACKGROUND: Rapid and accurate techniques are always welcomed for the detection of resistant strains of Mycobacterium tuberculosis MTB. OBJECTIVES: The objective of this study is to evaluate the pyrosequencing technology for the detection of MTB resistance to Rifampicin (RIF) and Isoniazid (INH) in Syrian and Lebanese clinical strains; 66 strains resistant to INH, among them 56 resistant also to RIF, were tested. METHODS: Four pyrosequencing assays were optimized and applied to the following loci: rpoBrpoB RIF resistance-determining region, katG, the promoter regions of inhA and ahpC-oxyR intergenic region. RESULTS: The prevalence of mutations on codon 315 of the katG gene, inhA and ahpc-oxyR were 42.4%, 21.2% and 9.0%, respectively, which make an overall sensitivity of 72.6% for INH resistance. All RIF-resistant strains contained at least one non-synonymous codon change in the sequenced rpoB region (507-533) relative to the ATCC reference strain. The RIF drug resistance region (RRDR) sequencing identified 96 modified codons representing 34 different mutations. CONCLUSIONS: The high sensitivity and the short turnaround time combined with multilocus sequencing of several isolates in parallel make pyrosequencing an attractive method for drug resistance screening for MTB.

MUS-2, a novel variant of the chromosome-encoded ß-lactamase MUS-1, from Myroides odoratimimus.

The aim of the present study was to investigate the molecular mechanism of carbapenem resistance of three imipenem-resistant isolates of Myroides odoratimimus recovered from two livestock farms of cows and pigeons by rectal swab in Lebanon in January 2014. Investigation of imipenem resistance of these isolates using the modified Hodge test, the EDTA test, the modified CarbaNP test and the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Ultraflex assay showed a carbapenemase activity due to the presence of a chromosome-encoded ß-lactamase MUS, verified by PCR. However amplification and sequencing of this chromosomal gene showed a novel variant of it designated MUS-2 by the curators of the Lahey database of ß-lactamases (http://www.lahey.org/Studies/webt.asp). Cloning of the bla MUS-2 was performed, followed by protein expression in Escherichia coli TOP 10. Pulsed-field gel electrophoresis clearly showed that the three isolates belonged to the same clone. This study reports a novel variant of the chromosome-encoded bla MUS-1 associated with carbapenem resistance in Myroides odoratimimus and shows that animals may represent a reservoir of bacteria harbouring several variants of resistance genes.

First data on Pneumocystis jirovecii colonization in patients with respiratory diseases in North Lebanon.

Pneumocystis colonization may play a role in transmission and local inflammatory response. It was explored in patients with respiratory diseases in North Lebanon. Overall prevalence reached only 5.2% (95% CI 2.13-10.47) but it was higher (17.3%) in the subpopulation of patients with chronic obstructive pulmonary disease (COPD). COPD was the only factor associated with a significantly increased risk of colonization. mtLSU genotyping revealed predominance of genotype 2, identified in five patients (71.4%), including one patient who had co-infection with genotype 3. These first data in North Lebanon confirm Pneumocystis circulation among patients with respiratory diseases and the potential for transmission to immunocompromised patients.

Taxonomic study of bacteria isolated from Lebanese spring waters: proposal for Pseudomonas cedrella sp. nov. and P. orientalis sp. nov.

Deoxyribonucleic acid relatedness studies (S1 nuclease method) have shown that 15 strains isolated from three Lebanese spring waters, belonging to the genus Pseudomonas, formed two homogeneous DNA groups, with a within-group DNA relatedness ranging from 70 to 100%. These groups are referred to as Pseudomonas cedrella sp. nov. and Pseudomonas orientalis sp.nov. These strains were previously grouped on the basis of a numerical analysis in phenons Ve, Vd, Vg, and VI. DNA relatedness with 65 strains representing 24 species of the genus Pseudomonas sensu stricto was below 50%. The highest DNA binding value (50%) was found with P. marginalis species. A comparison of the complete 16S rRNA gene sequences of the strains representing the two new deoxyribonucleic acid hybridization groups, i.e., strains CFML 96-198T and CFML 96-170T, and the sequence of other strains of the genus Pseudomonas revealed that these strains (CFML 96-198T and CFML 96-170T) fell within the 'Pseudomonas fluorescens intrageneric cluster'. The G+C contents of the DNA of P. cedrella CIP 105541T and P. orientalis CIP 105540T were 59 and 60 mol%, respectively. The two species can be differentiated from each other by the fact that P. cedrella strains hydrolyze erythritol and D-lyxose. P. cedrella grouped together a total of nine strains from phenotypic groups Ve, Vg, and VI. P. orientalis grouped together six strains from both phenotypic groups Vd and Ve.

Taxonomic study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov.

The taxonomic position of 23 strains isolated from mineral waters and previously grouped in the authentic pseudomonads on the basis of a phenotypic analysis (cluster IX, subclusters XIIIa and XIIIc of VERHILLE, S., ELOMARI, M., COROLER, L., IZARD, D., LECLERC, H. (Syst. Appl. Microbiol, 20, 137-149, 1997) has been genotypically further studied in the present work. On the basis of hybridization results, these strains were gathered into two new genomic groups for which we propose the names of Pseudomonas jessenii sp. nov. (Type strain CIP 105274) and Pseudomonas mandelii sp. nov. (Type strain CIP 105273). Deoxyribonucleic acid relatedness levels showed homologies ranging from 78 to 100% for Pseudomonas jessenii and from 77 to 100% for Pseudomonas mandelii. Furthermore, hybrization rates with 66 representative well characterized species or only partially characterized species of the genus Pseudomonas were below 53%, with delta Tm values of 7 degrees C and more. The mol% G + C content ranged from 57 to 58. The two new species presented basic morphological characteristics common to all pseudomonads. Various phenotypic features, such as denitrification, growth at 4 degrees C or 41 degrees C, trigonelline assimilation, alpha-L-glutamyl-L-histidine arylarmidase activity, growth on benzoate and meso-tartrate were found to differentiate Pseudomonas jessenii from Pseudomonas mandelii and from other Pseudomonas species. Pseudomonas jessenii encompassed a total of 9 strains from both phenotypic groups IX and XIIIa. Pseudomonas mandelii clustered a total of 13 strains from both phenotypic groups IX and XIIIc. Their clinical significance is unknown. The 16S rDNA of each type strain was sequenced and compared with the known sequences of the representative strains of the genus Pseudomonas. A phylogenetic tree was constructed to determine the intrageneric relationships within the genus Pseudomonas.

[Epidemiology of infections associated to "Burkholderia cepacia complex" in the course of cystic fibrosis]. / Epidémiologie des infections provoquées par les bactéries du "complexe Burkholderia cepacia" au course de la mucoviscidose.

Within a few years bacteriological knowledge on Burkholderia cepacia species has progressed considerably. Within bacterial classification (taxonomy), B. cepacia gathers eight species and one species on standby of nomenclature (genomovar VI); the whole of these species constitutes the "B. cepacia complex" or B. cepacia "sensu lato" and the denomination B. cepacia "sensu stricto" is attributed to the genomovar I. These new data call into question the knowledge on the clinic and the epidemiology of B. cepacia "sensu lato" infection in the course of cystic fibrosis. Among these newly described species, B. cenocepacia (formerly genomovar III) and B. multivorans (formerly genomovar II) are the most frequent species and together they represent more than 90% of infections associated to "B. cepacia complex" in the course of cystic fibrosis. B. cenocepacia is often associated to the "cepacia syndrome" which is characterized as a fatal necrotizing pneumonia with bacteremia. The progress of molecular epidemiology allowed the description of bacterial clones of which some are highly transmissible from person-to-person. Their distribution varies according to the species and the geography. The identification of these new species appears particularly difficult and, by the fact, the data on taxonomy and molecular epidemiology can be provided only by highly specialized reference centers.

[Prevalence of infection by intestinal parasites in north Lebanon: 1997-2001]. / Prevalence des parasites intestinaux au nord du Liban: 1997-2001.

We determined the prevalence of intestinal parasites in the north of Lebanon between 1997 and 2001. We analysed the parasitology records of 17126 patients and evidence of parasitic infections was found in 5 713 (33.35%) cases. There was no significant difference in prevalence for males or females for any of the parasites. The most prevalent parasites were Entamoeba coli (38.45%), Ascaris lumbricoides (37.14%), Giardia lamblia (15.39%), Ent. histolytica (4.57%) and Taenia sp. (3.3%). A comparison between our data and results of previous studies in Lebanon in 1937, 1939, 1956, 1967 and 1993 showed an increase in the prevalence of A. lumbricoides and G. lamblia in the period 1997-2001, with less marked changes in the prevalence of the other parasites.

[A 4-year study of Pseudomonas aeruginosa susceptibility to antibiotics (1998-2001) in northern Lebanon]. / Sensibilité de Pseudomonas aeruginosa aux antibiotiques: étude sur quatre ans (1998-2001) au nord du Liban.

Four hundred and sixty-four Pseudomonas aeruginosa strains were isolated in northern Lebanon at the Islami Hospital Microbiology department, in Tripoli. The purpose of this study was to evaluate the susceptibility of these strains to antibiotics, to compare this susceptibility according to the nature of the sample and the year of sampling. The results show that urinary samples were the most frequent (39.3%), followed by wound samples (21.2%), and ear samples (16.5%). The average rate of susceptible strains was 39.8% to ticarcillin, 56.9% to piperacillin, 58.2% to piperacillin + tazobactam, 74.1% to imipenem, 63.3% to ceftazidime, 60.4% to cefepime, 62.1% to aztreonam, 60.3% to netilmicin, 57.5% to gentamicin, 62.2% to tobramycin, 69% to amikacin, 100% to colistin, 45.4% to pefloxacin and ofloxacin, 57.7% to ciprofloxacin and 1.3% to rifampicin. The study showed that the strains isolated from pulmonary secretions were the most resistant to antibiotics.