Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.

This study aimed to investigate the faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in Switzerland and to genetically characterize the isolates. A total of 399 stool samples from healthy individuals employed in different food-processing plants were cultured on a selective medium containing 10 mg/L florfenicol. Resulting enterococci were screened by PCR for the presence of cfr, optrA and poxtA. A hybrid approach combining short-read and long-read WGS was used to analyse the genetic context of the cfr, optrA and poxtA genes. Enterococcus faecalis (n = 6), Enterococcus faecium (n = 6), Enterococcus gallinarum (n = 1) and Enterococcus hirae (n = 2) were detected in 15/399 (3.8%) of the faecal samples. They carried cfr + poxtA, optrA, optrA + poxtA or poxtA. Four E. faecalis harbouring optrA and one E. faecium carrying poxtA were resistant to linezolid (8 mg/L). In most optrA-positive isolates, the genetic environments of optrA were highly variable, but often resembled previously described platforms. In most poxtA-positive isolates, the poxtA gene was flanked on both sides by IS1216E elements and located on medium-sized plasmids. Faecal carriage of Enterococcus spp. harbouring cfr, optrA and poxtA in healthy humans associated with the food-production industry demonstrates the possibility of spread of oxazolidinone resistance genes into the community. Given the importance of linezolid as a last-resort antibiotic for the treatment of serious infections caused by Gram-positive pathogens, the detection of the oxazolidinone resistance determinants in enterococci from healthy humans is of concern for public health.

Nüesch-Inderbinen M ，Biggel M ，Zurfluh K ，Treier A ，Stephan R ... -  《-》

Fattening Pigs Are a Reservoir of Florfenicol-Resistant Enterococci Harboring Oxazolidinone Resistance Genes.

The use of florfenicol in farm animals may select enterococci that carry resistance genes that confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine. This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol-resistant enterococci from fattening pigs in Switzerland and to characterize a subset of the isolates using whole genome sequencing. A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr-poxtA in 1 of 31, optrA in 15 of 31, and poxtA in 15 of 31 enterococcal isolates. One randomly selected isolate per PCR-positive Enterococcus species and positive farm was selected for further analysis (n = 10). In nine of the 10 isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. Whole genome sequencing analysis showed the presence of E. faecalis (n = 1), E. faecium (n = 1), and E. hirae (n = 1), harboring optrA18, optrA7, and a new optrA allele, respectively. E. durans (n = 1), E. faecium (n = 4), and E. hirae (n = 1) carried the wild-type poxtA, and E. faecalis (n = 1) coharbored cfr(D) and poxtA2. Except for optrA7, all oxazolidinone resistance genes were found on plasmids. Multilocus sequence typing analysis identified E. faecalis ST19 and ST376, E. faecium ST80 belonging to hospital-adapted clade A1, and E. faecium ST21, ST55, ST269, and ST416 belonging to clade A2, which represents human commensals and animal strains. The occurrence of cfr(D), optrA, and poxtA in various porcine Enterococcus spp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faecium ST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain.

Nüesch-Inderbinen M ，Haussmann A ，Treier A ，Zurfluh K ，Biggel M ，Stephan R ... -  《-》

Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas.

Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs.IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.

Fioriti S ，Coccitto SN ，Cedraro N ，Simoni S ，Morroni G ，Brenciani A ，Mangiaterra G ，Vignaroli C ，Vezzulli L ，Biavasco F ，Giovanetti E ... -  《-》

Clonal spread and horizontal transfer mediate dissemination of phenicol-oxazolidinone-tetracycline resistance gene poxtA in enterococci isolates from a swine farm in China.

The emergence of the phenicol-oxazolidinone-tetracycline resistance gene poxtA becomes a significant challenge for public health, since it confers a decreased susceptibility not only to the last resort drug linezolid, but also to florfenicol and doxycycline widely used in veterinary medicine. To determine the dissemination mechanism of poxtA in enterococci isolates from different healthy pigs in the swine farm, a total of 178 florfenicol-resistant enterococci isolates were collected from 400 fresh faecal swabs in a swine farm in China. The poxtA gene was detected in 11 (6.18 %) enterococci isolates, including 8 E. faecium, 2 E. hirae and 1 E. casseliflavus isolates. Whole genome sequencing indicated that the eight poxtA-harbouring E. faecium strains belonged to four different sequence types, including ST156 and three new STs, ST1818, ST1819 and ST1820. Five out of the 11 poxtA-positive enterococci isolates also harboured optrA gene. Moreover, E. casseliflavus strain DY31 co-harboured poxtA, optrA and cfr. Seven different poxtA-harbouring plasmids were obtained through Nanopore combined with Illumina sequencing. The poxtA-harbouring plasmids exhibited high genetic variation, six out of which belonged to rep2 plasmid of Inc18 family. The poxtA gene was flanked by IS1216E in the left and/or right ends.The optrA and cfr genes were located on different plasmids, respectively, but those genes could be co-transferred with poxtA gene into the recipient E. faecalis strain by electrotransformation. Our study highlights that both clonal spread and horizontal transfer mediated by Inc18 plasmid and IS1216E promote the dissemination of poxtA in enterococci isolates from different healthy pigs in the swine farm.

Lei CW ，Chen X ，Liu SY ，Li TY ，Chen Y ，Wang HN ... -  《-》

Detection of transferable oxazolidinone resistance determinants in Enterococcus faecalis and Enterococcus faecium of swine origin in Sichuan Province, China.

The aim of this study was to detect transferable oxazolidinone resistance determinants (cfr, optrA and poxtA) in Enterococcus faecalis and Enterococcus faecium isolates of swine origin in Sichuan Province, China. A total of 158 enterococcal isolates (93 E. faecalis and 65 E. faecium) isolated from 25 large-scale swine farms (2016-2017) were screened for the presence of cfr, optrA and poxtA by PCR. The genetic environments of cfr, optrA and poxtA were characterised by whole-genome sequencing. Transfer of oxazolidinone resistance determinants was determined by conjugation or electrotransformation experiments. The transferable oxazolidinone resistance determinants cfr, optrA and poxtA were detected in zero, six and one enterococcal isolates, respectively. The poxtA gene in one E. faecalis isolate was located on a 37 990-bp plasmid that co-harboured fexB, cat, tet(L) and tet(M) and could be conjugated to E. faecalis JH2-2. One E. faecalis isolate harboured two different OptrA variants, including one variant with a single substitution (Q219H) that has not been reported previously. Two optrA-carrying plasmids, pC25-1 (45 581bp) and pC54 (64 500bp), shared a 40 494-bp identical region containing the genetic context IS1216E-fexA-optrA-erm(A)-IS1216E that could be electrotransformed into Staphylococcus aureus. Four different chromosomal optrA gene clusters were found in five strains, in which optrA was associated with Tn554 or Tn558 inserted into the radC gene. This study highlights the fact that mobile genetic elements, such as plasmids, IS1216E, Tn554 and Tn558, may facilitate the horizontal transmission of optrA and poxtA genes.

Kang ZZ ，Lei CW ，Kong LH ，Wang YL ，Ye XL ，Ma BH ，Wang XC ，Li C ，Zhang Y ，Wang HN ... -  《-》