Results from the Survey of Antibiotic Resistance (SOAR) 2015-17 in the Middle East (Kuwait, Lebanon and Saudi Arabia): data based on CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints.

OBJECTIVES: To determine antibiotic susceptibility of Streptococcus pneumoniae and Haemophilus influenzae isolates from community-acquired respiratory tract infections (CA-RTIs) collected in 2015-17 from Kuwait, Lebanon and Saudi Arabia. METHODS: MICs were determined by CLSI broth microdilution and susceptibility was assessed using CLSI, EUCAST (dose-specific) and pharmacokinetic/pharmacodynamic (PK/PD) breakpoints. RESULTS: A total of 139 S. pneumoniae isolates were collected from four centres in Kuwait, Lebanon and Saudi Arabia in 2015-17 and 55 H. influenzae isolates were collected and analysed from Saudi Arabia over the same time period. Pneumococci from all three countries were commonly non-susceptible to penicillin based on CLSI oral or low-dose IV penicillin using EUCAST breakpoints (39% in Kuwait to 57.1% in Lebanon) but by CLSI IV and EUCAST high-dose breakpoints most isolates were susceptible (∼90% in Kuwait and Saudi Arabia, and 100% in Lebanon). Isolates from Lebanon were highly susceptible to most other antibiotics (>90%) except cefaclor, oral cefuroxime and cefpodoxime (EUCAST breakpoints only). Overall, susceptibility was significantly lower in Kuwait and Saudi Arabia than Lebanon. Although all H. influenzae isolates (Saudi Arabia only) were ß-lactamase negative, 3.6% and 12.7% were ampicillin resistant by CLSI and EUCAST breakpoints, respectively. Otherwise susceptibility was high in H. influenzae. The application of different EUCAST breakpoints for low and higher doses for some of the antibiotics (amoxicillin, amoxicillin/clavulanic acid, ampicillin, penicillin, ceftriaxone, clarithromycin, erythromycin, levofloxacin and trimethoprim/sulfamethoxazole) allowed, for the first time in a SOAR study, the effect of raising the dosage on susceptibility to be quantified. CONCLUSIONS: Relatively low antibiotic susceptibility was observed in S. pneumoniae from Kuwait and Saudi Arabia in contrast to Lebanon, where rates of susceptibility were generally higher. Isolates of H. influenzae from Saudi Arabia were susceptible to most antibiotics. These factors are important in decision making for empirical therapy of CA-RTIs.

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.

BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced. RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Description of 'Blautia phocaeensis' sp. nov. and 'Lachnoclostridium edouardi' sp. nov., isolated from healthy fresh stools of Saudi Arabia Bedouins by culturomics.

We report here the main characteristics of 'Blautia phocaeensis' strain Marseille-P3441 sp. nov. and 'Lachnoclostridium edouardi' strain Marseille-P3397 sp. nov., that were isolated from a faecal specimen of a 42-year-old female Saudi Bedouin. We used a bacterial culturomics approach combined with taxono-genomics.

Description of 'Arabia massiliensis' gen. nov., sp. nov., 'Gordonibacter massiliensis' sp. nov., and 'Bacilliculturomica massiliensis' gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman.

We report here the main characteristics of 'Arabia massiliensis' strain Marseille-P3078T gen. nov., sp. nov., 'Gordonibacter massiliensis' Marseille-P2775T sp. nov. and 'Bacilliculturomica massiliensis' strain Marseille-P3303 gen. nov., sp. nov. The culturomics approach combined with taxonogenomics was used to characterize these strains, which were all isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman.

Description of 'Beduinibacterium massiliense' gen. nov., sp. nov., 'Massilimaliae massiliensis' gen. nov., sp. nov., 'Provencibacterium massiliense' gen. nov., sp. nov. and 'Oscilibacter massiliensis' sp. nov., isolated from a faecal specimen of a 19-year-old healthy Saudi Arabian Bedouin by culturomics.

We report here the main characteristics of 'Beduinibacterium massiliense' strain Marseille-P3337T gen. nov., sp. nov., 'Massilimaliae massiliensis' Marseille-P2963T gen. nov., sp. nov., 'Provencibacterium massiliense' Marseille-P2780T gen. nov., sp. nov. and 'Oscilibacter massiliensis' Marseille-P2778T sp. nov., all isolated from the stool of a Bedouin from Saudi Arabia. We used a bacterial culturomics approach combined with taxonogenomics.

'Arthrobacter saudimassiliensis' sp. nov. a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia.

We report here the main characteristics of 'Arthrobacter saudimassiliensis' strain 11W110_airT (CSUR P1223), a new species of the Arthrobacter genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

'Lysinibacillus saudimassiliensis' sp. nov., a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia.

We report here the main characteristics of 'Lysinibacillus saudimassiliensis' strain 13S34_airτ (CSUR = P1222), a new species of the Lysinibacillus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

'Jeotgalicoccus saudimassiliensis' sp. nov., a new bacterial species isolated from air samples in the urban environment of Makkah, Saudi Arabia.

We report here the main characteristics of 'Jeotgalicoccus saudimassiliensis' strain 13MG44_airT (CSUR P1221), a new species of the Jeotgalicoccus genus that was isolated from air samples in the city environment of Makkah, Saudi Arabia, during the pilgrim period of Hajj 2012.

"Raoultibacter massiliensis" gen. nov., sp. nov., a new bacterium isolated from the human gut of a Saudi Bedouin.

We propose the description of a new bacterial genus and new bacterial species, "Raoultibacter massiliensis," isolated from a faecal specimen of a 19-year-old healthy Saudi Bedouin.

'Beduinella massiliensis', gen. nov., sp. nov. a new genus representing a new family in the phylum Firmicutes, and proposal of Beduinellaceae fam. nov.

We report here the main characteristics of a new bacterium named 'Beduinella massiliensis' strain Marseille-P2846(T) (CSURP2846P) that was isolated from a faecal specimen of a 50-year-old Saudi Bedouin female and propose the creation of a new family 'Beduinellaceae'.

Comparison of the gut microbiota of people in France and Saudi Arabia.

BACKGROUND/OBJECTIVES: The gut microbiota contributes to energy acquisition from food, and changes in the gut microbiome are associated with obesity. The eating habits of Saudis are much different than those of Europeans, and our objective was to compare the fecal microbiota of obese and normal weight Saudis and French. SUBJECTS/METHODS: Illumina MiSeq deep sequencing was used to test the gut microbiota of 9 normal weight and 9 obese individuals from Saudi Arabia and 16 normal weight and 12 obese individuals from France. RESULTS: Obese French possessed significantly more relative Proteobacteria (P=0.002) and Bacteroidetes (P=0.05) and had lower richness and biodiversity at all the operational taxonomic unit (OTU) cutoffs (P<0.05) than normal weight French. Obese Saudis possessed significantly more Firmicutes (P=0.001) without a difference in richness (P=0.2) and biodiversity (P=0.3) compared with normal weight Saudis. We found a common bacterial species core of 23 species existing in ⩾50% of obese and normal weight Saudis and 29 species in ⩾50% of obese and normal weight French. Actinomyces odontolyticus, Escherichia coli and Ruminococcus obeum were present in at least 50% of all individuals tested. French individuals had significantly higher richness and biodiversity compared with Saudis at all the OTU cutoffs (P<0.05). CONCLUSION: Microbiota differences between obese and normal weight French were not similar to those between obese and normal weight Saudis. The studies of different populations can result in contrasting data regarding the associations of the gut microbiota and obesity.

Epidemiological characterization of P. aeruginosa isolates of intensive care units in Egypt and Saudi Arabia.

This study aimed to characterize Pseudomonas aeruginosa isolates in 2 intensive care units in Egypt and Saudi Arabia. P. aeruginosa isolates from patients' and staff hands and environmental samples were typed using antibiotyping and ERIC-PCR. In Egypt, isolates from suction apparatus tubing and drainage containers (A7) and AV tubing (A8) were linked to those from patients who had these antibiotypes. In Saudi Arabia, isolates from suction apparatus tubing (A6) and AV tubing (A7) were linked to patients with the same antibiotypes. In Egypt, patients' isolates had ERIC VII, VIll and IX patterns linked to suction apparatus tubing, AV machine tubes and drainage containers. In Saudi Arabia, patients' isolates had ERIC VIII and XI patterns linked to suction apparatus tubing and AV machines. In Egypt and Saudi Arabia, ERIC typing gave higher discriminatory indices (0.801 and 0.785 respectively) than the antibiotyping (0.7123 and 0.728 respectively). ERIC was superior to antibiotyping and should be used in tracing sources of infection.

Epidemiological characterization of P. aeruginosa isolates of intensive care units in Egypt and Saudi Arabia

This study aimed to characterize Pseudomonas aeruginosa isolates in 2 intensive care units in Egypt and Saudi Arabia. P. aeruginosa isolates from patients' and staff hands and environmental samples were typed using antibiotyping and ERIC-PCR. In Egypt, isolates from suction apparatus tubing and drainage containers [A7] and AV tubing [A8] were linked to those from patients who had these antibiotypes. In Saudi Arabia, isolates from suction apparatus tubing [A6] and AV tubing [A7] were linked to patients with the same antibiotypes. In Egypt, patients' isolates had ERIC VII, VIII and IX patterns linked to suction apparatus tubing, AV machine tubes and drainage containers. In Saudi Arabia, patients' isolates had ERIC VIII and XI patterns linked to suction apparatus tubing and AV machines. In Egypt and Saudi Arabia, ERIC typing gave higher discriminatory indices [0.801 and 0.785 respectively] than the antibiotyping [0.7123 and 0.728 respectively]. ERIC was superior to antibiotyping and should be used in tracing sources of infection

Serratia marcescens-contaminated baby shampoo causing an outbreak among newborns at King Abdulaziz University Hospital, Jeddah, Saudi Arabia.

During November 2008 to January 2009, 11 babies in the neonatal intensive care (NICU) and three babies in the nursery were infected with Serratia marcescens at King Abdulaziz University Hospital in Saudi Arabia. Overall, fifteen infections were identified among 11 newborns in the NICU: septicaemia (five cases), purulent conjunctivitis (three), urinary tract infection (two), meningitis (two) and cellulitis (one). Three newborns in the nursery had three infections: purulent conjunctivitis (two cases) and omphalitis (one). Thirteen of 14 babies recovered fully but one died from S. marcescens meningitis and septicaemia. All infections were traced to intrinsically contaminated baby shampoo introduced to the units five days before the first reported case. The outbreak terminated following withdrawal of the shampoo product.