Temporal trends and risks factors for antimicrobial resistant Enterobacteriaceae urinary isolates from outpatients in Guadeloupe.

International audienceUrinary tract infections are bacterial infections most commonly encountered in the community. The resistance rate of uropathogens to commonly prescribed antibiotics has increased worldwide but there are no published data concerning the resistance of strains isolated from community-acquired UTI in Guadeloupe. To assess the susceptibility patterns of Enterobacteriaceae strains isolated from outpatients in Guadeloupe we conducted a prospective study from December 2012 to May 2014 among outpatients consulting at private and public laboratories for urine analysis. Risk factors for E. coli resistance to amoxicillin, third-generation cephalosporin, and ciprofloxacin were also determined. To study the trends of E. coli resistance rates over the past 10 years, data on the susceptibility patterns of E. coli from 2003 to 2014 were also collected from three major laboratories for a retrospective study. During the prospective study, we isolated 1293 bacterial strains from the urine of outpatients presenting for urine analysis. The most commonly isolated bacteria were E. coli (57 %) and Klebsiella pneumoniae (15.5 %). Thirty seven per cent of the E. coli strains were resistant to amoxicillin. Resistance rates to third generation cephalosporin were low for E. coli and other Enterobacteriaceae (3.1 and 12.2 % respectively) and mostly due to the presence of an Extended Spectrum Beta-lactamase. Resistance to cotrimoxazole and ciprofloxacin was moderate (17.8 and 15.6 % respectively). However, the resistance rate of E. coli to ciprofloxacin has significantly increased during the last 10 years. Risk factors were consistent with previously reported data, especially for the increasing ciprofloxacin resistance with age. General practitioners in Guadeloupe need to be better informed to favor the prescription of fosfomycin-trometamol to reduce the risk of resistance to fluoroquinolones

Looking for Pathogens in Dust from North Africa Arriving in the French West Indies Using Metabarcoding and Cultivable Analysis

International audiencePeriodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The aim of this study was to determine the diversity and frequency of microbial agents (bacteria, eukaryotes) in NA dusts and the potential threat toward human and/or animal health by comparing microbial air composition during dust events and in control samples. In 2017 and 2018, 16 samples were collected during seven NA dust episodes and there were 9 controls. The microbial composition of the samples was characterized using a cultivable approach and by metabarcoding analyses (16S and 18S). A greater bacterial load and greater diversity were observed during the dust events, and some genera were significantly associated with the events. Some, such as Geodermatophilus, can be considered signature species of NA dust. No pathogenic species were found with the cultivable approach, whereas the metabarcoding analyses highlighted the presence of several potentially pathogenic species or known human pathogens such as Naegleria fowleri

Circulation of antibiotic resistance genes between bacteria from different origins

International audienceAn environment affected by anthropogenic activities can play an important role in the spread and concentration of antibiotic resistant bacteria. Under antibiotic selection pressure, exchanges of antibiotic resistance genes (ARG) can occur between bacteria from human, animal and environmental reservoirs. However, these processes are still poorly understood. This work aimed at focussing on the wastewater treatment process, which is a hotspot for selection and emergence of antibiotic resistant bacteria and constitutes a favourable interface for circulation of ARG between bacteria from the different reservoirs.Between 2018 and 2019, extended spectrum β-lactamase producing Enterobacteriaceae (ESBLE) (Enterobacter cloacae complex, Escherichia coli and Klebsiella pneumoniae) were isolated from 266 patients at University Hospital of Pointe-à-Pitre (Guadeloupe). Simultaneously, urban and hospital wastewaters were analysed at different steps of waste treatment and 120 stool samples were collected from animals living near the hospital sewers and the wastewater treatment plant. Enterobacteriaceae were characterised according to their antibiotic resistance profile. Strains with the same antibiotic resistance profile belonging to a particular human-environment-animals continuum were analysed using whole genome sequencing.We isolated a total of 905 ESBLE (292 from humans, 348 from wastewater and 265 from animals). The frequency of ESBLE carriers was important in wildlife and domestic animals living nearby polluted environments (70%). A first genome-based comparison was carried out on 30 ESBL producing E. coli isolated during this study and compared to ESBL producing E. coli collected in farms (n=12). Antibiotic resistance gene blaCTX-M-15 was frequent (17/42). IncFII type was the most common plasmid (15/42). E. coli ST131 was found on the clinical samples only (n=4). One cluster with wastewater and animal isolates differed by ≤ 5 single nucleotide polymorphisms.These first results suggest that animals living near sewers and wastewater treatment plants are subjected to antibiotic resistance pressure and some bacteria and antibiotic resistance genes could be closely related

Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean

International audienceHere, we describe the genome sequence of ECC486. This Enterobacter oligotrophicus strain was isolated from a wild Anolis marmoratus speciosus specimen, a lizard endemic to the territory of Guadeloupe (French West Indies). Its draft genome sequence consists of 40 contigs and contains a total of 4,504,233 bp, with a G+C content of 54.1%

Environmental reservoirs of ECC clusters VIII in Guadeloupe, French West Indies

International audienceSpecies of Enterobacter cloacae complex (ECC) are widely distributed in the environment and are part of the gut microbiota of both animals and humans. Anolis marmoratus, an endemic and anthropophilic lizard of Guadeloupe, is a natural carrier of ECC and in particular of strains resistant to third generation cephalosporins (3GCR). Bacteria belonging to this complex are also major opportunistic pathogens which draw attention by their involvement in nosocomial infections and the emergence of multidrug resistant clones. Using hsp60 genotyping, ECC is divided into 12 genetic clusters (cluster I-XII) and a loosely knit group (cluster XIII). Strains belonging to clusters III, VI and VIII are prominent in human infections.We collected ECC strains (n=155) isolated from different sources (anoles, environment and clinical samples). We characterized these strains according to their antibiotic resistance phenotypes. Nearly 28% of strains sampled from environment and anoles were resistant to 3GC. This specific resistance was related to the overexpression of the AmpC cephalosporinase. We identified the cluster for each strain by using hsp60 genotyping. Cluster VIII was predominant in A. marmoratus feces (n=37, 38.9%) and in water catchment (n=10, 45.6%). We sequenced 58 strains of C-VIII (33 from clinical isolates: 26 from France and 7 from Guadeloupe, and 25 from anoles). A Maximum likelihood analysis based on core genome alignment revealed a clear split of isolates into two main clusters depending on sources: the first one clustering most of clinical samples together (from France and Guadeloupe, n=29) but also 5 strains isolated from anoles. The second cluster was mainly constituted by strains from anoles (n=20) and by 4 clinical samples. These results suggest first that bacteria resistant to third generation cephalosporins exist in environmental reservoirs in Guadeloupe. Moreover, exchange of ECC C-VIII strains may happen between human and anoles within a One Health appr

Draft genome sequence of Enterobacter chengduensis ECC445, isolated from fresh water in the West Indies.

Objectives The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection, there is a lack of information on associated members in other compartments. Here we report the first de novo assembled and annotated whole-genome sequence of a E. chengduensis strain isolated from the environment. Data description ECC445 specimen was isolated in 2018 from a drinking water catchment point in Guadeloupe. It was clearly related to E. chengduensis species according to hsp60 typing and genomic comparison. Its whole-genome sequence is 5,211,280-bp long divided into 68 contigs, and presents a G + C content of 55.78%. This genome and associated datasets provided here will serve as a useful resource for further analyses of this rarely reported Enterobacter species

Antimicrobial use and resistance in Escherichia coli from healthy food-producing animals in Guadeloupe

International audienceBackground: Selection pressure exerted by use of antibiotics in both human and veterinary medicine is responsible for increasing antimicrobial resistance (AMR). The objectives of this study were to better understand antimicrobial use in pigs, beef cattle, and poultry on farms on Guadeloupe, French West Indies, and to acquire data on AMR in Escherichia coli in these food-producing animals. A cross-sectional survey was conducted at 45 farms on Guadeloupe, and practical use of antimicrobials was documented in declarative interviews between March and July 2018. A total of 216 fecal samples were collected between January 2018 and May 2019, comprising 124 from pigs, 75 from beef cattle, and 17 from poultry litter. E. coli isolates were obtained for further testing by isolation and identification from field samples. Antimicrobial susceptibility testing and screening for bla CTX-M , bla TEM , tetA, and tetB resistance genes by polymerase chain reaction on extracted genomic DNA were performed. Results: The study showed rational use of antimicrobials, consisting of occasional use for curative treatment by veterinary prescription. Tetracycline was the most commonly used antimicrobial, but its use was not correlated to E. coli resistance. Extended-spectrum β-lactamase (ESBL) E. coli isolates were detected in 7.3% of pigs, 14.7% of beef cattle, and 35.3% of poultry. bla CTX-M-1 was the predominant gene found in ESBL-E. coli isolates (68.8%), followed by bla CTX-M-15 (31.3%). Conclusion: Despite rational use of antimicrobials, the rate of ESBL-E. coli in food-producing animals in Guadeloupe, although moderate, is a concern. Further studies are in progress to better define the genetic background of the ESBL-E. coli isolates

Environmental reservoirs of ECC clusters VIII in Guadeloupe, French West Indies

International audienceSpecies of Enterobacter cloacae complex (ECC) are widely distributed in the environment and are part of the gut microbiota of both animals and humans. Anolis marmoratus, an endemic and anthropophilic lizard of Guadeloupe, is a natural carrier of ECC and in particular of strains resistant to third generation cephalosporins (3GCR). Bacteria belonging to this complex are also major opportunistic pathogens which draw attention by their involvement in nosocomial infections and the emergence of multidrug resistant clones. Using hsp60 genotyping, ECC is divided into 12 genetic clusters (cluster I-XII) and a loosely knit group (cluster XIII). Strains belonging to clusters III, VI and VIII are prominent in human infections.We collected ECC strains (n=155) isolated from different sources (anoles, environment and clinical samples). We characterized these strains according to their antibiotic resistance phenotypes. Nearly 28% of strains sampled from environment and anoles were resistant to 3GC. This specific resistance was related to the overexpression of the AmpC cephalosporinase. We identified the cluster for each strain by using hsp60 genotyping. Cluster VIII was predominant in A. marmoratus feces (n=37, 38.9%) and in water catchment (n=10, 45.6%). We sequenced 58 strains of C-VIII (33 from clinical isolates: 26 from France and 7 from Guadeloupe, and 25 from anoles). A Maximum likelihood analysis based on core genome alignment revealed a clear split of isolates into two main clusters depending on sources: the first one clustering most of clinical samples together (from France and Guadeloupe, n=29) but also 5 strains isolated from anoles. The second cluster was mainly constituted by strains from anoles (n=20) and by 4 clinical samples. These results suggest first that bacteria resistant to third generation cephalosporins exist in environmental reservoirs in Guadeloupe. Moreover, exchange of ECC C-VIII strains may happen between human and anoles within a One Health appr

High genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses

International audienceExtended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days. All isolated E. coli strains were evaluated for antimicrobial resistance (AMR) and by whole-genome sequencing. Multi locus sequence typing, phylogrouping, resistance genes and plasmid content were extracted from genomic data. A phylogenetic analysis based on single nucleotide polymorphism (SNP) divergence was also performed on the core genome. We isolated 35 strains belonging to the A, B1 and C phylo-groups. All but one expressed SHV-12 enzymes and one expressed CTX-M-1. Intra- and inter-horse genetic diversity of E. coli strains was identified in the genome analysis and 10 AMR profiles. Two distinct EP E. coli-resistant populations (phylo-group B1: ST4164-AMR3 and ST155-AMR2) were found in one horse, and five other resistant populations were found in the second horse (phylo-group A: ST1250-AMR1; phylo-group B1: ST1250-AMR1, ST6981-AMR1 and phylo-group C: ST10-AMR4). Some persistent EP E. coli strains were detected at least 1 month after treatment. These results indicate that EP E. coli strains isolated from horse feces show intra- and inter-host genetic diversity, even in a region with low ESBL prevalence and in horses that are rarely treated with third-generation cephalosporins. These results also suggest that horizontal gene transfer and/or selection of resistance genes probably occurs in vivo within the horse gut microbiome. Follow-up of EP E. coli resistance profiles for at least 1 month after treatment is warranted to prevent persistence of EP E. coli