Identification of a novel conjugative plasmid carrying the multiresistance gene cfr in Proteus vulgaris isolated from swine origin in China

Total Synthesis of the Repeating Units of Proteus penneri 26 and Proteus vulgaris TG155 via a Common Disaccharide

Herein, we report the first total synthesis of the trisaccharide and tetrasaccharide repeating units of P. penneri 26 and P. vulgaris TG155, respectively, having a common disaccharide unit, 3-α-l-QuipNAc-(1 → 3)-α-d-GlcpNAc-(1 →. Striking features of the targets are the presence of rare sugar units, l-quinovosamine and l-rhamnosamine, all joined through α-glycosidic linkages. Major challenges in the formation of 1,2-cis glycosidic linkages in the case of d-glucosamine, l-quinovosamine, and d-galactosamine have been addressed.

Identification of iron-responsive genes in Proteus vulgaris

Iron is essential for almost all bacteria, and iron homeostasis is precisely controlled by the ferric uptake regulator (Fur). The Fur regulons have been well characterized in some model bacteria, yet little is known in the common opportunistic pathogen Proteus vulgaris. In this study, Fur regulon and iron-responsive genes in P. vulgaris were mainly defined by in silico and proteomic analyses. The results showed that about 250 potential Fur-regulated operons including 14 transcriptional factors were predicted, while 559 proteins exhibited differential expression in response to iron deficiency, not all being directly regulated by Fur, such as transcriptional factors lexA, recA, narL, and arcA. Collectively, these results demonstrated that Fur functioned as a global regulatory protein to repress or activate expression of a large repertoire of genes in P. vulgaris; besides, not all the iron-responsive genes were directly regulated by Fur, whereas indirectly regulated through other mechanisms such as additional transcriptional regulatory proteins.

Oxazolidinones: mechanisms of resistance and mobile genetic elements involved

The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.

Genomic Characterization of a Proteus sp. Strain of Animal Origin Co-Carrying blaNDM-1 and lnu(G)

The emergence of carbapenem-resistant Proteus represents a serious threat to global public health due to limited antibiotic treatment options. Here, we characterize a Proteus isolate NMG38-2 of swine origin that exhibits extensive drug resistance, including carbapenems. Whole-genome sequencing based on Illumina and MinION platforms showed that NMG38-2 contains 24 acquired antibiotic resistance genes and three plasmids, among which, pNDM_NMG38-2, a pPvSC3-like plasmid, is transferable and co-carries bla_NDM-1 and lnu(G). Sequence analysis of pPvSC3-like plasmids showed that they share a conserved backbone but have a diverse accessory module with complex chimera structures bearing abundant resistance genes, which are facilitated by transposons and/or homologous recombination. The acquisition of bla_NDM-1 in pNDM_NMG38-2 was due to the ISCR1-mediated integration event. Comprehensive analysis of the lnu(G)-bearing cassettes carried by bacterial plasmids or chromosomes revealed a diversification of its genetic contexts, with Tn6260 and ISPst2 elements being the leading contributors to the dissemination of lnu(G) in Enterococcus and Enterobacteriaceae, respectively. In conclusion, this study provides a better understanding of the genetic features of pPvSC3-like plasmids, which represent a novel plasmid group as a vehicle mediating the dissemination of bla_NDM-1 among bacteria species. Moreover, our results highlight the central roles of Tn6260 and ISPst2 in the spread of lnu(G).

Two novel blaNDM-1-harbouring transposons on pPrY2001-like plasmids coexisting with a novel cfr-encoding plasmid in food animal source Enterobacteriaceae

OBJECTIVES

This study reports identification of the carbapenemase-encoding gene from carbapenem-resistant Enterobacterales from food animals.

METHODS

A total of 40 bacterial isolates recovered from 475 faecal swabs obtained on one farm were tested for the presence of the bla_NDM-1 gene by PCR. Species identification of three bla_NDM-1-positive strains was conducted by MALDI-TOF/MS. Antimicrobial susceptibility testing was performed by broth microdilution. Transferability of the bla_NDM-1 and cfr genes was determined by filter mating. The genetic environment of bla_NDM-1 and cfr was analysed by whole-genome sequencing.

RESULTS

Two Proteus mirabilis (JPM24 and YPM35) and one Providencia rettgeri (YPR25) carried bla_NDM-1. The bla_NDM-1 genes were located on conjugable pPrY2001-like plasmids often reported to carry important antimicrobial resistance genes (ARGs). YPR25 and YPM35 shared two almost identical conjugable plasmids, one carrying bla_NDM-1 and the other cfr. The bla_NDM-1 gene in YPR25 (same as YPM35) and JPM24 was located in two novel transposons, designated Tn6922 and Tn6923, respectively. Tn6922 and Tn6923 carried 14 and 7 ARGs, respectively, and both contained multiple copies of IS26 in the same direction, with a high degree of similarity. Additionally, cfr was located on a plasmid with an unreported high frequency of conjugative transfer in YPR25 (same as YPM35).

CONCLUSION

We identified two novel bla_NDM-1-containing transposons (Tn6922 and Tn6923) present on pPrY2001-like plasmids. The pPrY2001-like bla_NDM-1 plasmids coexisted with a novel cfr plasmid, and both could transfer at high frequency, highlighting the importance of continuous surveillance of multiresistant Enterobacterales of animal origin that can serve as a reservoir for ARGs.

Potential dissemination mechanism of the tetC gene in Aeromonas media from the aerobic biofilm reactor under oxytetracycline stresses

The tetC gene has been found to be one of the most widely distributed tetracycline resistance (tet) genes in various environmental niches, but the detailed dissemination mechanisms are still largely unknown. In the present study, 11 tetC-containing Aeromonas media strains were isolated from an aerobic biofilm reactor under oxytetracycline stresses, and the genome of one strain was sequenced using the PacBio RSII sequencing approach to reveal the genetic environment of tetC. The tetC gene was carried by an IS26 composite transposon, named Tn6434. The tetC-carrying Tn6434 structure was detected in all of the A. media strains either in a novel plasmid pAeme2 (n=9) or other DNA molecules (n=2) by PCR screening. The NCBI database searching result shows that this structure was also present in the plasmids or chromosomes of other 13 genera, indicating the transferability of Tn6434. Inverse PCR and sequencing confirmed that Tn6434 can form a circular intermediate and is able to incorporate into a preexisting IS26 element, suggesting that Tn6434 might be responsible for the dissemination of tetC between different DNA molecules. This study will be helpful in uncovering the spread mechanism of tet genes in water environments.

Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria

Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.

Emergence of fosA3 and bla CTX-M- 14 in Multidrug-Resistant Citrobacter freundii Isolates From Flowers and the Retail Environment in China

We examined the prevalence and transmission of the fosA3 gene among Citrobacter freundii isolates from flowers and the retail environments. We identified 11 fosfomycin-resistant C. freundii strains (>256 μg/mL) from 270 samples that included petals (n = 7), leaves (n = 2), dust (n = 1) and water (n = 1). These 11 isolates were multidrug-resistant and most were simultaneously resistant to fosfomycin, cefotaxime, ciprofloxacin and amikacin. Consistently, all 11 isolates also possessed bla_CTX–M–14, bla_CMY–65/122, aac(6’)-Ib-cr, qnrS1, qnrB13/6/38 and rmtB. These fosA3-positive isolates were assigned to two distinct PFGE patterns and one (n = 9) predominated indicating clonal expansion of fosA3-positive isolates across flower markets and shops. Correspondingly, fosA3 was co-transferred with bla_CTX–M–14via two plasmid types by conjugation possessing sizes of 110 kb (n = 9) and 260 kb (n = 2). Two representatives were fully sequenced and p12-1 and pS39-1 possessed one and two unclassified replicons, respectively. These plasmids shared a distinctive and conserved backbone in common with fosA3-carrying C. freundii and other Enterobacteriaceae from human and food animals. However, the fosA3-bla_CTX–M–14-containing multidrug resistance regions on these untypable plasmids were highly heterogeneous. To the best of our knowledge, this is the first report of fosA3 and bla_CTX–M–14 that were present in bacterial contaminants from flower shops and markets. These findings underscore a public health threat posed by untypable and transferable p12-1-like and pS39-1-like plasmids bearing fosA3-bla_CTX–M–14 that could circulate among Enterobacteriaceae species and in particular C. freundi in environmental isolates.

Exploring tet(X)-bearing tigecycline-resistant bacteria of swine farming environments

Emergence of high-level tigecycline resistance tet(X) variants in animal and human Enterobacterales is posing a public health concern. Recently, novel tet(X) variants including tet(X3), tet(X4), tet(X5) and tet(X6) were detected in Enterobacterales and Acinetobacter baumannii. Here, we comprehensively investigated the prevalence of tet(X) variants among different bacterial species in swine farm environment with nanopore sequencing. The tet(X6) gene was found located on both plasmids and ICEs in Proteus, but tet(X4) was in plasmids in E. coli. To our knowledge, this is the first report of the emergence of IncA/C2-type plasmid-mediated tet(X6). The bacterial host adaptation of different tet(X) variants implies they evolved in microbiota separately, but ISCR2 should be the key element facilitating horizontal transfer of various tet(X) variants through circular intermediates. Our findings further expand the knowledge about reservoirs of mobile tigecycline resistance genes and the epidemic characteristics of tet(X) variants in animals and related environments.

Genomic and functional characterization of fecal sample strains of Proteus cibarius carrying two floR antibiotic resistance genes and a multiresistance plasmid-encoded cfr gene

The objective of this study was to investigate the molecular characteristics and horizontal transfer of florfenicol resistance gene-related sequences in Proteus strains isolated from animals. A total of six Proteus strains isolated from three farms between 2015 and 2016 were screened by polymerase chain reaction (PCR) for known florfenicol resistance genes. Proteus cibarius G11, isolated from the fecal material of a goose, was found to harbor both cfr and floR genes. Whole genome sequencing revealed that the strain harbored two copies of the floR gene: one was located on the chromosome and the other was located on a plasmid named pG11-152. Two floR-containing fragments 4028 bp in length were identical and showed transposon-like structures. The cfr gene was found on a plasmid named pG11-51 and flanked by a pair of IS26s. Thus, mobile genetic elements played an important role in floR replication and horizontal resistance gene transfer. Therefore, increasing attention should be paid to monitoring the spread of resistance genes and resistance in real time.