Two novel lsa(E)-carrying mobile genetic elements in Streptococcus suis

Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis

OBJECTIVES

To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis.

METHODS

The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis.

RESULTS

S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA + lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA + lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1.

CONCLUSIONS

This is the first report demonstrating the functionally active UCS-optrA + lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.

Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain

Antimicrobial resistance in the laying hen production industry has become a serious public health problem. The antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified. 105 Enterococcus isolates were obtained from 115 environmental samples (air, dust, feces, flies, sewage, and soil) collected along the laying hen production chain (breeding chicken, chick, young chicken, and commercial laying hen). These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics, such as tetracycline (92.4%), streptomycin (92.4%), and erythromycin (91.4%), and all strains had multidrug resistance phenotypes. Whole genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51 pleuromutilin-resistant Enterococcus isolates, and lsa(E), which mediates resistance to pleuromutilins, always co-occurred with lnu(B). Alignments with the Mobile Genetic Elements database identified four transposons (Tn554, Tn558, Tn6261, and Tn6674) with several ARGs (erm(A), ant(9)-la, fex(A), and optrA) that mediated resistance to many clinically important antibiotics. Moreover, we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492. A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production farms. Our results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention, and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain, thereby warranting effective disinfection.

Antimicrobial resistance profiles of Streptococcus suis isolated from pigs, wild boars, and humans in France between 1994 and 2020

Streptococcus suis, an emerging zoonotic pathogen, causes invasive infections and substantial economic losses in the pig industry worldwide. Antimicrobial resistance against 22 antibiotics was studied for 200 S. suis strains collected in different geographical regions of France. Most of the strains (86%) showed resistance to at least one antibiotic with a low rate of resistance to fluoroquinolones, penicillins, pleuromutilin, and diaminopyrimidine-sulfonamides, and a higher rate to macrolides-lincosamides and tetracycline. Multi-resistance patterns were observed in 138 strains; three of them being resistant to six antibiotic families. Statistical analyses highlighted a decrease in the resistance to trimethoprim-sulfamethoxazole, in our collection, between the two periods studied-before 2010 and after 2015-as well as an impact of the geographical origin with a higher rate of resistance to macrolides-lincosamides and penicillin in Brittany than in the other French regions. Furthermore, macrolides-lincosamides and tetracycline resistance patterns were more likely to be found in pig isolates than in human and wild boar isolates. A difference in resistance was also observed between serotypes. Most of the penicillin-resistant strains belong to serotypes 1, 5, 9, 11, 12, 15, 27, and 29. Finally, penicillin and pleuromutilin resistances were mostly found in "non-clinical" isolates. The empirical treatment of human and porcine infections due to S. suis in France can therefore still be carried out with beta-lactams. However, this study emphasizes the need to monitor antimicrobial resistance in this zoonotic pathogen.

Characterization of an optrA-harbouring unconventional circularizable structure located on a novel ICESa2603 family-like integrative and conjugative element ICESsuHN38 in Streptococcus suis

OBJECTIVES

To identify the novel genetic elements involved in the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA in Streptococcus suis.

METHODS

Whole-genome DNA of the optrA-positive isolate S. suis HN38 was subjected to WGS via both Illumina HiSeq and Oxford Nanopore platforms. MICs of several antimicrobial agents (erythromycin, linezolid, chloramphenicol, florfenicol, rifampicin and tetracycline) were determined by broth microdilution. PCR assays were performed to identify the circular forms of the novel integrative and conjugative element (ICE) ICESsuHN38, but also the unconventional circularizable structure (UCS) excised from this ICE. The transferability of ICESsuHN38 was evaluated by conjugation assays.

RESULTS

S. suis isolate HN38 harboured the oxazolidinone/phenicol resistance gene optrA. The optrA gene was flanked by two copies of erm(B) genes in the same orientation, located on a novel ICESa2603 family-like ICE, designated ICESsuHN38. PCR assays revealed that a novel UCS carrying the optrA and one copy of erm(B) could be excised from ICESsuHN38. Conjugation assays confirmed that ICESsuHN38 was able to successfully transfer into the recipient strain S. suis BAA.

CONCLUSIONS

In this work, a novel optrA-carrying mobile genetic element, a UCS, was identified in S. suis. The optrA gene was flanked by copies of erm(B) and its location on the novel ICESsuHN38 will aid its horizontal dissemination.

Antibiotic Resistance Patterns and Molecular Characterization of Streptococcus suis Isolates from Swine and Humans in China

Streptococcus suis is a zoonotic pathogen that causes disease in humans after exposure to infected pigs or pig-derived food products. In this study, we examined the serotype distribution, antimicrobial resistance phenotypes and genotypes, integrative and conjugative elements (ICEs), and associated genomic environments of S. suis isolates from humans and pigs in China from 2008 to 2019. We identified isolates of 13 serotypes, predominated by serotype 2 (40/96; 41.7%), serotype 3 (10/96; 10.4%), and serotype 1 (6/96; 6.3%). Whole-genome sequencing analysis revealed that these isolates possessed 36 different sequence types (STs), and ST242 and ST117 were the most prevalent. Phylogenetic analysis revealed possible animal and human clonal transmission, while antimicrobial susceptibility testing indicated high-level resistance to macrolides, tetracyclines, and aminoglycosides. These isolates carried 24 antibiotic resistance genes (ARGs) that conferred resistance to 7 antibiotic classes. The antibiotic resistance genotypes were directly correlated with the observed phenotypes. We also identified ICEs in 10 isolates, which were present in 4 different genetic environments and possessed differing ARG combinations. We also predicted and confirmed by PCR analysis the existence of a translocatable unit (TU) in which the oxazolidinone resistance gene optrA was flanked by IS1216E elements. One-half (5/10) of the ICE-carrying strains could be mobilized by conjugation. A comparison of the parental recipient with an ICE-carrying transconjugant in a mouse in vivo thigh infection model indicated that the ICE strain could not be eliminated with tetracycline treatment. S. suis therefore poses a significant challenge to global public health and requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation. IMPORTANCE S. suis is a serious zoonotic pathogen. In this study, we investigated the epidemiological and molecular characteristics of 96 S. suis isolates from 10 different provinces of China from 2008 to 2019. A subset of these isolates (10) carried ICEs that were able to be horizontally transferred among isolates of different S. suis serotypes. A mouse thigh infection model revealed that ICE-facilitated ARG transfer promoted resistance development. S. suis requires continuous monitoring, especially for the presence of ICEs and associated ARGs that can be transferred via conjugation.

Plasmid-Assisted Horizontal Transfer of a Large lsa(E)-Carrying Genomic Island in Enterococcus faecalis

The horizontal transfer of genomic islands is essential for the adaptation and evolution of Enterococcus faecalis. In this study, three porcine E. faecalis strains, each harboring a large lsa(E)-carrying genomic island, were identified. When using the E. faecalis OG1RF as the recipient, the horizontal transfer of the lsa(E)-carrying genomic island occurred only from E. faecalis E512, which also harbored a pheromone-responsive conjugative plasmid, but not from the other two E. faecalis strains, E533 and E509, which lacked such a plasmid. Subsequently, through plasmid curing of E. faecalis E512 and plasmid introduction into E. faecalis E533, the pheromone-responsive conjugative plasmid was identified to be indispensable for the horizontal transfer of the lsa(E)-carrying genomic island and a subsequent homologous recombination between the chromosomal DNA of the donor and the recipient. In addition, the presence of a chromosomally-located conjugative transposon, Tn916, in E. faecalis E509 could not mediate the horizontal transfer of the lsa(E)-carrying genomic island, although Tn916 itself could transfer by conjugation. Thus, these data highlight the role of the pheromone-responsive conjugative plasmid in the transfer of the lsa(E)-carrying genomic island in E. faecalis, thereby establishing the dual role of pheromone-responsive conjugative plasmids in contributing to the dissemination of both plasmid-borne resistance genes and chromosomally-located genomic islands. IMPORTANCE In this study, it was shown that a pheromone-responsive conjugative plasmid played an indispensable role in the horizontal transfer of a lsa(E)-carrying genomic island. This finding indicates a dual role of the pheromone-responsive conjugative plasmid in disseminating both plasmid-borne resistance genes and chromosomally-located genomic islands. The role of the pheromone-responsive conjugative plasmid in disseminating chromosomal genomic islands is suggested to be essential in the genomic evolution of E. faecalis, which has become one of the leading nosocomial pathogens worldwide.

Emergence of extensive multidrug resistant Staphylococcus aureus carrying novel Sa-MRRlsa(E) in retail food

OBJECTIVES

The aim of this study was to investigate the prevalence and genetic environment of the multidrug resistance gene lsa(E) in food-related S. aureus in China.

METHODS

1463 S. aureus from retail food products in 39 Chinese cities were investigated to determined the prevalence of lsa(E). Furthermore, antimicrobial susceptibility testing, whole-genome sequencing (WGS) and complete genetic analysis were performed in lsa(E)-positive isolates.

RESULTS

As a result, thirty-five isolates (2.4%) were positive for the lsa(E) gene which had an extensive multidrug-resistance phenotype. ST9-t899 and ST1-t4792 were the common types in positive strains. The lsa(E) genes were located in two different types of novel multiresistance region (MRR_lsa(E)) on the chromosome. The Sa-MRR_lsa(E)-I were inserted into lctP gene. The Sa-MRR_lsa(E)-II were inserted into crtP gene and they were comprised of 7 ARGs interspersed with varieties of ISs, transposons and DNA invertase genes, showing is a novel arrangement harboring lsa(E). Part of transposon Tn1546 was inserted into downstream of lnu(B) in the novel Sa-MRR_lsa(E)-II. Both two types of Sa-MRR_lsa(E) could be excised from chromosome, indicating the Sa-MRR_lsa(E) may be transferable.

CONCLUSION

Our study is the first systematical investigation of lsa(E)-positive S. aureus in retail foods in China. It indicated that the origin of most food-related lsa(E)-positive S. aureus in China might be associated with livestock or poultry breeding farm and has been transmitted between animal and food. Moreover, the emergence of S. aureus carrying novel Sa-MRR_lsa(E), especially serve as a reservoir of antibiotic resistance traits, should warrants further attention.