Tandem duplication in ermC translational attenuator of the macrolide-lincosamide-streptogramin B resistance plasmid pSES6 from Staphylococcus equorum

Small Antimicrobial Resistance Plasmids in Livestock-Associated Methicillin-Resistant Staphylococcus aureus CC398

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) isolates of the clonal complex 398 are often resistant to a number of antimicrobial agents. Studies on the genetic basis of antimicrobial resistance in these bacteria identified SCCmec cassettes, various transposons and plasmids of different sizes that harbor antimicrobial resistance genes. While large plasmids that carry multiple antimicrobial resistance genes – occasionally together with heavy metal resistance genes and/or virulence genes – are frequently seen in LA-MRSA ST398, certain resistance genes are also associated with small plasmids of up to 15 kb in size. These small resistance plasmids usually carry only one, but in rare cases also two or three antimicrobial resistance genes. In the current review, we focus on small plasmids that carry the macrolide-lincosamide-streptogramin B resistance genes erm(C) or erm(T), the lincosamide resistance gene lnu(A), the pleuromutilin-lincosamide-streptogramin A resistance genes vga(A) or vga(C), the spectinomycin resistance gene spd, the apramycin resistance gene apmA, or the trimethoprim resistance gene dfrK. The detailed analysis of the structure of these plasmids allows comparisons with similar plasmids found in other staphylococci and underlines in many cases an exchange of such plasmids between LA-MRSA ST398 and other staphylococci including also coagulase-negative staphylococci.

Antimicrobial Resistance among Staphylococci of Animal Origin

Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.

Mobile macrolide resistance genes in staphylococci

Macrolide resistance in staphylococci is based on the expression of a number of genes which specify four major resistance mechanisms: (i) target site modification by methylation of the ribosomal target site in the 23S rRNA, (ii) ribosome protection via ABC-F proteins, (iii) active efflux via Major Facilitator Superfamily (MFS) transporters, and (iv) enzymatic inactivation by phosphotransferases or esterases. So far, 14 different classes of erm genes, which code for 23S rRNA methylases, have been reported to occur in staphylococci from humans, animals and environmental sources. Inducible or constitutive expression of the erm genes depends on the presence and intactness of a regulatory region known as translational attenuator. The erm genes commonly confer resistance not only to macrolides, but also to lincosamides and streptogramin B compounds. In contrast, the msr(A) gene codes for an ABC-F protein which confers macrolide and streptogramin B resistance whereas the mef(A) gene codes for a Major Facilitator Superfamily protein that can export only macrolides. Enzymatic inactivation of macrolides may be due to the macrolide phosphotransferase gene mph(C) or the macrolide esterase genes ere(A) or ere(B). Many of these macrolide resistance genes are part of either plasmids, transposons, genomic islands or prophages and as such, can easily be transferred across strain, species and genus boundaries. The co-location of other antimicrobial or metal resistance genes on the same mobile genetic element facilitates co-selection and persistence of macrolide resistance genes under the selective pressure of metals or other antimicrobial agents.

Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname

We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.

Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes

In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.

The diversity of inducible and constitutively expressed erm(C) genes and association to different replicon types in staphylococci plasmids

The aim of this study was to analyze the diversity of the macrolide resistance gene, erm(C) in relation to structural alterations affecting the gene expression. In addition, the association of erm(C) to mobile genetic elements (MGEs) in staphylococci mainly from Danish pigs was investigated. In total, 78 erythromycin-resistant isolates were screened for erm(C) by PCR. The erm(C) genes incl. the upstream regulatory region were sequenced and the expression types were characterized phenotypically (agar diffusion test) and genotypically (sequence analysis). Phylogenetic analysis of erm(C) was compared with structural alterations affecting the gene expression. Plasmids carrying erm(C) from seven selected isolates were fully or partially sequenced. Thirty-seven isolates were shown to be erm(C) positive and erm(C) from pigs were all constitutively expressed, mainly caused by different sized deletions (118, 111, 107, 70, 66, 16 and 3 bp) in the regulatory region. Duplication (63 bp) and substitutions were also found to cause a constitutive phenotype. Only one horse isolate had an inducible expression type. Phylogenetic analysis showed that structural alterations have happened in different erm(C) allele groups and not only in one group. Furthermore erm(C) was found mainly on plasmids (~2.4–8 kb) and gene sequence types correlated with plasmid replication (rep) gene types. One erm(C) type was linked to an IS257 element able to circularize. In conclusion, structural alterations giving rise to constitutive expression of erm(C) have happened several times in the evolution of erm(C). Interestingly, the diversity of erm(C) appears to be linked to the plasmid type or MGE carrying the gene.

Investigations into the basis of chloramphenicol and tetracycline resistance in Staphylococcus intermedius isolates from cases of pyoderma in dogs

A total of 160 Staphylococcus intermedius isolates were recovered from cases of pyoderma in 2002 and were examined for susceptibility to 13 different antimicrobial agents. Ninety per cent (144) of the isolates were resistant to tetracycline, derivatives of which have been used until recently, and 18% (29) were resistant to chloramphenicol which was banned from use 13 years ago. The presence of genes encoding chloramphenicol acetyltransferase (CAT) and tetracycline resistance (tet); tet(K), (L), (M), and (O) were determined by PCR in the 29 chloramphenicol and tetracycline resistant isolates. Seventeen (59%) isolates contained the cat gene while 12 (41%) isolates did not carry the cat gene, implying there may be other genes for chloramphenicol resistance that were not detected by the primers (primer set 1) used in this study. The tet(M) gene was found in 28 (97%) of the resistant S. intermedius isolates, but none contained the tet(O) gene. All 29 isolates carried one or two tet genes; tet(K), (L), and (M), with four different distribution patterns. New PCR products, a 1.1 kb product using primer set 1 and a 0.2 kb product using primer set 2, were cloned and sequenced. A 904 bp fragment of S. aureus plamid pS194, including sequence from the streptomycin adenyltransferase gene (804 bp), was found inserted into the terminal region of the cat gene (GenBank accession no. AY604739), whilst the sequence of 0.2 kb was previously unpublished.

Molecular analysis of constitutively expressed erm(C) genes selected in vitro by incubation in the presence of the noninducers quinupristin, telithromycin, or ABT-773

A Staphylococcus aureus strain that harbored a plasmid-borne inducibly expressed erm(C) gene was cultivated in the presence of the noninducers quinupristin, telithromycin, and ABT-773. After overnight incubation, 78 mutants that displayed combined resistance to macrolides, lincosamides, streptogramin B antibiotics, and ketolides were analyzed for the genetic basis of this altered resistance phenotype. Because this resistance phenotype is indicative for constitutively expressed erm(C) genes, the erm(C) regulatory regions of all mutants were sequenced. All 78 mutants showed sequence alterations in the erm(C) translational attenuator. Seventeen different types of sequence deletions ranging from 5 bp to 121 bp and nine different types of tandem duplications of 13-100 bp, all causing constitutive erm(C) gene expression, were detected. These sequence deletions or tandem duplications either favored the formation of mRNA secondary structures in the erm(C) translational attenuator, which did not inhibit translation of the erm(C) transcripts, or completely prevented the formation of any mRNA secondary structures in the erm(C) translational attenuator. The mean frequencies of 10-6 to 10-8 by which constitutive mutants were obtained, strongly suggest that telithromycin and ABT-773 not be recommended for the treatment of staphylococci that exhibit the inducible MLSB phenotype.

Molecular detection of antimicrobial resistance

The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art.

Structural alterations in the translational attenuator of constitutively expressed ermC genes

Sequence deletions of 16, 59, and 111 bp as well as a tandem duplication of 272 bp with respect to the corresponding sequence of pT48 were identified in the regulatory regions of constitutively expressed ermC genes. Constitutive ermC gene expression as a consequence of these structural alterations is based on either the prevention of the formation of mRNA secondary structures in the translational attenuator or the preferential formation of those mRNA secondary structures which do not interfere with the translation of the ermC transcripts. A model for the development of sequence deletions in the ermC translational attenuator by homologous recombination is presented and experimentally tested by in vitro selection of constitutively expressed mutants in staphylococcal strains deficient and proficient in homologous recombination.

Molecular analysis of naturally occuring ermC-encoding plasmids in staphylococci isolated from animals with and without previous contact with macrolide/lincosamide antibiotics

A total of 16 epidemiologically unrelated macrolide-resistant staphylococcal isolates of various animal origins were investigated for the molecular basis of macrolide resistance with respect to previous contact of their host animals with macrolides and lincosamides. All isolates carried ermC-encoding plasmids of 2.3-4.0 kbp. The eight plasmids of staphylococci from animals which had not received macrolides or lincosamides showed inducible ermC gene expression and did not exhibit alterations in the ermC regulatory region. The remaining eight plasmids expressed the ermC gene constitutively. Six of these plasmids were from staphylococci from animals which had received tylosin or spiramycin as feed additives or lincomycin for therapeutic purposes. All constitutively expressed ermC genes revealed either sequence deletions or sequence duplications in their ermC regulatory region, as detected by a PCR assay and by sequence analysis. These sequence deletions and duplications found in naturally occurring plasmids corresponded closely to the mutations seen in the ermC-encoding plasmids after growth of an inducibly resistant strain in the presence of non-inducing macrolides or lincosamides under in vitro conditions.

Integration of pT181-like tetracycline resistance plasmids into large staphylococcal plasmids involves IS257

Four large staphylococcal plasmids ranging in size from 31 to 82 kbp have been shown to mediate tetracycline resistance via an integrated copy of the tet(K)-encoding plasmid pT181 which was flanked by copies of the insertion element IS257. In two cases, IS257 elements interrupted the repC reading frame of pT181 and an 8-bp sequence from within the repC gene was duplicated at the interrupted site. In the third plasmid, the IS257 elements interrupted the pT181 DNA immediately upstream of the repC coding sequence with an 8-bp duplication. In the fourth case, the IS257 elements flanked a pT181-like plasmid with one IS257 in the repC coding sequence and the other within the recombinase (pre) coding sequence, so that a section of the pT181 sequence was deleted. All four integration sites detected in this study differ from those previously described for the IS257-mediated integration of pT181-like plasmids into large plasmids or into the chromosomal DNA.