Genomic Characterization of MDR Escherichia coli Harboring blaOXA-48 on the IncL/M-type Plasmid Isolated from Blood Stream Infection.

Escherichia coli is responsible for a wide variety of community and hospital acquired extraintestinal infections, and the emergence of ESBL resistant isolates is a major clinical concern. In this study, we characterized the genomic attributes of an OXA-48 and CTX-M-3 producing E. coli EC-IMP153. Whole-genome initial assembly produced 146 contigs with a combined 5,504,170 bp in size and a G+C content of 50.5%. wgSNPs-based phylogenetic comparison with 36 publically available genomes was also performed. Comprehensive genomic analysis showed that EC-IMP153 belonged to sequence type ST-405 and harbored several resistance determinants including the ß-lactam resistance genes blaOXA-48, blaCTX-M-3, blaTEM-1B, blaOXA-1, and blaCMY-70, aminoglycoside fyuA and aac(3)IId, tetracycline tet(A) and tet(R), and fluoroquinolone gyrA, parC, and mfd resistance determinants. Plasmids with the following incompatibility groups were detected in silico and confirmed using PBRT: IncI1-α, IncL, IncW, Col (BS512), and IncF. To our knowledge this is the first in-depth genomic analysis of an OXA-48 producing E. coli ST-405 isolated from a patient in Lebanon and linked to a blood stream infection. Continuous monitoring is necessary to better understand the continued diffusion of such pathogens, especially in view of the population movements triggered by unrest in the Middle East.

New epidemiology of Staphylococcus aureus infections in the Middle East.

Staphylococcus aureus is a bacterial pathogen that is distributed worldwide and represents an increasing problem, both in hospitals and in the community. Global transmission of methicillin-resistant S. aureus (MRSA) has been the subject of many studies. Determining the incidence of colonization with community-acquired MRSA in hospitalized patients and outpatients has been the aim of several studies conducted in the Middle East (western Asia). The local epidemiology within countries in this region is changing, owing to the introduction of new strains with the intercontinental exchange of several clones. Sequence type 80-MRSA-IV is one common clone detected in different countries within the region showing country-based differences, and hence more likely to form clonal lineages. MRSA is endemic in this region, and the burden and the difficulty in detecting imported strains are increasing. This is also increasing the risk of domestic and global transmission. To counter the threat associated with the high incidence of MRSA carriage and infections, systematic surveillance of both hospital and community isolates is required, along with appropriate measures designed to limit their spread. Additionally, antibiotic stewardship is needed to contain the further development of the observed resistance and to help in preserving antibiotics as precious therapeutic resources. It is critical for countries in this region to establish both national and international initiatives to develop better measurements designed to limit and control the spread of infections. Finally, more sequence-based studies are needed to better understand the pathogenicity and epidemiology of these important pathogens.

Antibiotic resistance patterns and sequencing of class I integron from uropathogenic Escherichia coli in Lebanon.

AIM: To study the prevalence and molecular basis of antimicrobial resistance in UPEC. METHODS AND RESULTS: PCR was used to detect the presence of the Class I integron variable region (VR). The VR amplicons were then characterized by partial sequencing and restriction digestion with AluI. VR negative isolates showed more antibiotic susceptibility than VR positive isolates. 30% of the isolates were positive for the VR and carried the genes dfrA7, dfrA17-aadA5, dfrA1-aadA1, dfrA12-orf5-aadA2 and bla(OXA-30)-aadA1. Five restriction patterns were detected and isolates with the same VR amplicon size had the same restriction pattern. CONCLUSIONS: Our data demonstrated that Class I integrons are widely disseminated in Lebanon and showed their importance for the occurrence and transmission of multidrug resistance. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings will facilitate greater understanding of the factors that contribute to the presence and transfer of integron-associated antibiotic resistance genes in UPEC.

Molecular characterization of Staphylococcus aureus in Lebanon.

Staphylococcus aureus is an important human pathogen and is a growing public health concern. In this study, 130 S. aureus, 93 methicillin-resistant S. aureus (MRSA) and 37 methicillin-sensitive S. aureus (MSSA), clinical isolates recovered from Lebanon were typed by protein A gene (spa) sequencing and multi-locus sequence typing (MLST). Forty-eight different spa types were identified and clustered into 30 different groups. MLST revealed 10 sequence types (STs) among the isolates. There were eight major MRSA clones defined as isolates with the same ST and the same SCCmec type. The majority of the PVL-positive isolates (53%) were ST80-MRSA-IVc. Systematic surveillance of both hospital and community isolates in Lebanon together with measures designed to limit the spread are required.

Antimicrobial resistance in relation to virulence determinants and phylogenetic background among uropathogenic Escherichia coli in Lebanon.

Escherichia coli is the most common causative agent of recurrent, uncomplicated urinary tract infections. Triplex pCR and the disc diffusion method were used to determine and correlate among the phylogenetic group, virulence determinants and antimicrobial resistance in 100 uropathogens. Group B2 represented 58% of the tested isolates with no isolates belonging to group B1. Isolates with the highest percentage of susceptibility to all antimicrobial agents used were within the B2 phylogenetic groups. 38% of the tested population were resistant to trimethoprim/sulfamethoxazole, 29% to ciprofloxacin and only 8% to nitrofurantoin. The majority of the isolates resistant to trimethoprim/sulfamethoxazole were from group B2 (52.7%), with 45% being positive to the three tested virulence determinants (efu, fbp and picU). These findings suggest that although virulence and antimicrobial resistance are mutually exclusive in Escherichia coli clinical isolates, the relationship between virulence and resistance to antimicrobial agents can vary according to the particular resistance phenotype.

Incidence of antibiotic resistance in coliforms from drinking water and their identification using the Biolog and the API identification systems.

Antibiotic-resistant bacteria were common in samples collected from an intermittent water distribution system in Lebanon. Multiply-resistant isolates were also present and most commonly to amoxycillin, cephalexin and sulfamethoxazole/trimethoprim. The aminoglycosides (amikacin, gentamicin and kanamycin) were the most effective, with almost all tested strains showing susceptibility to these antimicrobial agents. Both the Biolog GN MicroPlates and the API 20E strips can be used for the identification of coliform bacteria isolated from potable water, but the outcome of the identification should be viewed with caution. 51% of isolates were assigned similar identities by both the Biolog MicroPlates and the API 20E strips. The similarity at the species level was lower (33%) compared to that at the genus level (67%). The identification of Escherichia coli strains, which represented 30% of all tested organisms, showed 95% similarity in the assigned genus and species using both identification schemes.

Water quality problems associated with intermittent water supply.

A controlled study was conducted in Lebanon over a period of 12 months to determine bacterial regrowth in a small network supplying the Beirut suburb of Naccache that had a population of about 3,000. The residential area, which is fed by gravity, is supplied twice a week with chlorinated water from two artesian wells of a confined aquifer. A significant correlation was detected between the turbidity and the levels of heterotrophic plate count bacteria (HPC) in the samples from the distribution network as well as from the artesian wells. However, a negative significant correlation was found between the temperature and the HPC count in the samples collected from the source. A statistically significant increase in counts, possibly due to regrowth, was repeatedly established between two sampling points lying on a straight distribution line but 1 km apart. Faecal coliforms were detected in the source water but none in the network except during a pipe breakage incident with confirmed Escherichia coli reaching 40 CFU/100 mL. However, coliforms such as Citrobacter freundii, Enterobacter agglomerans, E. cloacae and E. skazakii were repeatedly isolated from the network, mainly due to inadequate chlorination. A second controlled study was conducted to determine the effect of storage on the microbial quality of household storage tanks (500 L), which were of two main types - galvanized cast iron and black polyethylene. The mean bacterial count increased significantly after 7 d storage in both tank types. A significant difference was found in the mean HPC/mL between the winter and the summer. Highest counts were found April-June although the maximum temperature was reported later in the summer. A positive correlation was established between the HPC/mL and pH, temperature and storage time.