Avian influenza surveillance at the human-animal interface in Lebanon, 2017.

BACKGROUND: Avian influenza viruses (AIVs) cause severe diseases in poultry and humans. In Lebanon, AIV H9N2 was detected in 2006 and 2010 and H5N1 was detected in 2016. AIM: To evaluate the current circulating AIVs in Lebanon at the human-animal interface. METHODS: A total of 1000 swabs were collected from poultry from 7 Lebanese governorates between March and June 2017. Swabs were screened for influenza infection. Haemagglutinin and neuraminidase AIV subtypes were determined for positive samples. Gene segments were cloned and sequenced. Blood was collected from 69 exposed individuals. Serological studies were performed to test sera for antibodies against AIV. RESULTS: In chickens, 0.6% were positive for AIV H9N2. Sequences obtained clustered tightly with those of Israeli origin as well as Lebanese H9N2 viruses from 2010. All human samples tested negative. CONCLUSION: We recommend regular surveillance for AIVs in poultry using a One Health approach.

Prevalence of Extended-Spectrum Beta-Lactamase-Producing Gram-Negative Bacilli and Emergence of mcr-1 Colistin Resistance Gene in Lebanese Swine Farms.

Livestock are considered reservoirs of multidrug-resistant organisms that can be transferred to humans through direct/indirect routes. Once transmitted, these organisms can be responsible for infections with therapeutic challenges. The aim of this study was to determine the prevalence of extended-spectrum cephalosporin and colistin-resistant Gram-negative bacilli in Lebanese swine farms. In May 2017, 114 fecal samples were collected from swine farms in south Lebanon. Separate media supplemented with cefotaxime, ertapenem, and colistin were used for the screening of resistant organisms. Double-disk synergy test and ampC disk test were performed to detect extended-spectrum beta-lactamase (ESBL) and ampC producers, respectively. Detection of beta-lactamase and mcr genes was performed using real time PCR. Of 114 fecal samples, 76 showed growth on the medium with cefotaxime. In total, 111 strains were isolated with 94.5% being Escherichia coli. Phenotypic tests showed that 98, 6, and 7 strains were ESBL, ampC, and ESBL/ampC producers, respectively. CTX-M and CMY were the main beta-lactamase genes detected. On the medium with colistin, 19 samples showed growth. In total, 23 colistin-resistant E. coli strains harboring the mcr-1 gene were isolated. This is the first study in Lebanon determining multidrug resistance epidemiology in pigs. The prevalence of ESBLs is high and the emergence of colistin resistance is alarming.

Prevalence and Characterization of Multi-Drug-Resistant Gram-Negative Bacilli Isolated From Lebanese Poultry: A Nationwide Study.

Currently, antimicrobial resistance is one of the most prominent public health issues. In fact, there is increasing evidence that animals constitute a reservoir of antimicrobial resistance. In collaboration with the Lebanese Ministry of Agriculture, the aim of this study was to determine the prevalence of intestinal carriage of multi-drug-resistant Gram-negative Bacilli in poultry farms at the national level. Between August and December 2015, 981 fecal swabs were obtained from 49 poultry farms distributed across Lebanon. The swabs were subcultured on MacConkey agar supplemented with cefotaxime (2 µg/ml). Isolated strains were identified using MALDI-TOF mass spectrometry. Multilocus sequence typing analysis was performed for Escherichia coli. Phenotypic detection of extended spectrum ß-lactamases (ESBL) and AmpC production was performed using double disk synergy and the ampC disk test, respectively. ß-lactamase encoding genes blaCTX-M, blaTEM, blaSHV, blaFOX, blaMOX, blaEBC, blaACC, blaDHA, and blaCMY using PCR amplification. Out of 981 fecal swabs obtained, 203 (20.6%) showed bacterial growth on the selective medium. Of the 235 strains isolated, 217 were identified as E. coli (92%), eight as Klebsiella pneumoniae (3%), three as Proteus mirabilis (1%) and three as Enterobacter cloacae (1%). MLST analysis of E. coli isolates showed the presence of ST156, ST5470, ST354, ST155, and ST3224. The phenotypic tests revealed that 43.5, 28.5, and 20.5% of the strains were ampC, ESBL, and ampC/ESBL producers, respectively. The putative TEM gene was detected in 83% of the isolates, SHV in 20%, CTX-M in 53% and CMY ampC ß-lactamase gene in 65%. Our study showed that chicken farms in Lebanon are reservoirs of ESBL and AmpC producing Gram-negative bacilli. The level of antibiotic consumption in the Lebanese veterinary medicine should be evaluated. Future studies should focus on the risk factors associated with the acquisition of multi-drug-resistant organisms in farm animals in Lebanon.

Containment of Highly Pathogenic Avian Influenza A(H5N1) Virus, Lebanon, 20161.

A preparedness plan for avian influenza A(H5N1) virus infection was activated in Lebanon in 2016 after reported cases in poultry. Exposed persons were given prophylaxis and monitored daily. A total of 185 exposed persons were identified: 180 received prophylaxis, 181 were monitored, and 41 suspected cases were reported. All collected specimens were negative for virus by PCR.

Epidemiology of multi drug resistant organisms in pigs in Lebanon.

INTRODUCTION: Livestock are nowadays considered potent reservoirs of multi drug resistance. Enteric resistant organisms in animals can be transmitted to humans and be causative agents of infections with therapeutic challenges. The aim of this study is to determine the prevalence of multi drug resistant organisms in Lebanese swine farms. METHODOLOGY: In May 2017, 94 fecal samples were collected from pigs in the south of Lebanon. Three media supplemented with cefotaxime, ertapenem, colistin were used for the screening of ESBL, carbapenemase producers and colistin resistance respectively. MALDI-TOF was used for bacterial identification. Double disk synergy test, ampC disk test and carpa np test were used for the detection of ESBL, ampC and carbapenemase producers respectively. RT-PCR was performed for the screening of beta lactamase and mcr colistin resistance genes. RESULTS: 77/94 fecal samples, showed growth on the medium supplemented with cefotaxime. In total 111 strains were isolated: 94% were identified as E.coli, 6% other organisms such as E. fergusonii and K. pneumoniae. Phenotypic tests showed that 72% of isolated strains were ESBL producers while 28% were ampC beta lactamase producers. RT-PCR analysis revealed that blaCTX-M was present in 45% of isolated strains, blaTEM in 26% and blaSHV in 10%. In parallel, 22 colistin resistant E.coli strains and 1 K.pneumoniae carrying mcr-1 were isolated. CONCLUSIONS: This study showed the importance of swine farms as reservoirs of resistance in Lebanon. The emergence of colistin resistance in pigs is worrying. A re-evaluation of antibiotic consumption in pigs is therefore warranted.

Multi Drug resistant Organisms in Chicken farms and their Surrounding Environment.

INTRODUCTION: Chicken farms are nowadays regarded as reservoirs of multi-drug resistance. Studies have shown that resistant organisms can be readily transferred from animals to their surrounding ecosystem. The aim of this study is to determine if any link exists between the prevalence of multi-drug resistance in chicken farms and their surrounding environment. METHODOLOGY: In May-2017, 200 fecal swabs were collected from a chicken farm in Lebanon. Fecal samples from six workers and 41 environmental samples surrounding the farm were also taken. Three different selective media were used for the screening of multi-drug resistant and colistin resistant organisms. MALDI-TOF was used for bacterial identification. Double disk synergy test and ampC disk test were used for the screening of ESBL and ampC producers respectively. Furthermore, RT-PCR was performed for the detection of beta lactamase and mcr colistin resistance genes. RESULTS: In chicken, 315 E.coli strains were isolated: 53% were ESBL/ampC co-producers, 27% ampC and 42.5% mcr-1 positive isolates. Furthermore, 29 K.pneumoniae harboring mcr-1 were also isolated. In workers, ESBL producing E.coli were detected in 4/6 workers whereas mcr-1 carrying E.coli were detected in all workers. In the environment, ESBLs and mcr-1 positives were detected in 95% and 7% of the samples respectively. RT-PCR revealed the detection of B-lactamase genes in all samples at different rates. CONCLUSIONS: This study showed a relatively high prevalence of ESBL and mcr-1 positive isolates in chicken and their environment. MLST is in progress to determine if any link exists between multi-drug resistant organisms in these ecosystems investigated.

Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, 2016.

We report the phylogenetic analysis of the first outbreak of H5N1 highly pathogenic avian influenza virus detected in Lebanon from poultry in April 2016. Our whole-genome sequencing analysis revealed that the Lebanese H5N1 virus belongs to genetic clade 2.3.2.1c and clusters with viruses from Europe and West Africa.

Complete Genome Sequence of the First H5N1 Avian Influenza Virus Isolated from Chickens in Lebanon in 2016.

We generated the full genome of a highly pathogenic H5N1 avian influenza virus that caused an outbreak on a chicken farm in Lebnaon in April 2016. Analysis revealed that the virus belonged to clade 2.3.2.1c that recently caused outbreaks in West Africa and the United Arab Emirates.