Macrolide-lincosamide-streptogramin B resistance in Staphylococcus lentus results from the integration of part of a transposon into a small plasmid

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.

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.

Antibiotic-resistant Enterococcus faecalis in abattoir pigs and plasmid colocalization and cotransfer of tet(M) and erm(B) genes

This study was conducted to determine plasmid colocalization and transferability of both erm(B) and tet(M) genes in Enterococcus faecalis isolates from abattoir pigs in Canada. A total of 124 E. faecalis isolates from cecal contents of abattoir pigs were examined for antibiotic susceptibility. High percentages of resistance to macrolides and tetracyclines were found. Two predominant multiresistance patterns of E. faecalis were examined by PCR and sequencing for the presence of genes encoding antibiotic resistance. Various combinations of antibiotic resistance genes were detected; erm(B) and tet(M) were the most common genes. Plasmid profiling and hybridization revealed that both genes were colocated on a ~9-kb transferable plasmid in six strains with the two predominant multiresistant patterns. Plasmid colocalization and cotransfer of tet(M) and erm(B) genes in porcine E. faecalis isolates indicates that antibiotic coselection and transferability could occur via this single genetic element. To our knowledge, this is the first report on plasmid colocalization and transferability of erm(B) and tet(M) genes in E. faecalis on a mobile genetic element of ~9 kb. Physical linkage between important antibiotic resistance determinants in enterococci is of interest for predicting potential transfer to other bacterial genera.

New MLSB resistance gene erm(43) in Staphylococcus lentus

The search for a specific rRNA methylase motif led to the identification of the new macrolide, lincosamide, and streptogramin B resistance gene erm(43) in Staphylococcus lentus. An inducible resistance phenotype was demonstrated by cloning and expressing erm(43) and its regulatory region in Staphylococcus aureus. The erm(43) gene was detected in two different DNA fragments, of 6,230 bp and 1,559 bp, that were each integrated at the same location in the chromosome in several S. lentus isolates of human, dog, and chicken origin.

Transcriptional and translational control of the mlr operon, which confers resistance to seven classes of protein synthesis inhibitors

The methyltransferase genes erm(B) and cfr are adjacent to each other in the chromosome of methicillin-resistant Staphylococcus aureus strain CM05. Analyses of the transcriptional organization of the erm(B) and cfr genes in the chromosome of strain CM05 showed that the two genes are organized into an operon, designated mlr (for modification of the large ribosomal subunit), which is controlled by the erm(B) promoter. Analysis of the translation control and the inducibility of the erm(B) and cfr genes in the mlr operon showed that despite the presence of putative regulatory short open reading frames, both genes are expressed constitutively. The combined action of the two methyltransferases encoded in the mlr operon results in modification of two specific residues in 23S rRNA, A2058 and A2503, and renders cells resistant to all clinically useful antibiotics that target the large ribosomal subunit. Furthermore, simultaneous modification of both rRNA sites synergistically enhances resistance to 16-member-ring macrolides.

Antimicrobial resistance of coagulase-negative staphylococci from bovine subclinical mastitis with particular reference to macrolide–lincosamide resistance phenotypes and genotypes

OBJECTIVES

The aim of this study was to analyse coagulase-negative staphylococci (CoNS) for their resistance to antimicrobial agents approved for the control of pathogens involved in bovine mastitis, with particular reference to macrolide and/or lincosamide (ML) resistance and the resistance genes involved.

METHODS

A total of 298 CoNS collected between 2003 and 2005 in Germany from cases of subclinical mastitis in dairy cows were identified to the species level and investigated for their MICs by broth microdilution. ML-resistant isolates were subjected to plasmid profiling and electrotransformation experiments. The ML resistance genes were detected using PCR and hybridization. Selected PCR products were cloned and sequenced.

RESULTS

The CoNS isolates used in this study showed a low level of resistance to all antimicrobial agents tested (0-7.4%) except ampicillin (18.1%). In the erythromycin-resistant and/or pirlimycin-resistant isolates, the ML resistance genes erm(B), erm(C), msr(A), mph(C) and lnu(A) were present, either alone or in different combinations. Isolates carrying erm methylase genes or the exporter gene msr(A) showed higher MICs than those harbouring only the genes mph(C) or lnu(A) coding for inactivating enzymes. Most of the ML resistance genes were found on plasmids.

CONCLUSIONS

This is the first report of pirlimycin MICs for CoNS collected from cases of bovine subclinical mastitis in Germany. After 3-5 years of veterinary therapeutic use, pirlimycin resistance was rarely detected among CoNS. The finding that five different resistance genes--present in various combinations--were responsible for ML resistance underlines the heterogeneous character of this resistance trait.

Staphylococcal tetracycline–MLSB resistance plasmid pSTE2 is the product of an RSA-mediated in vivo recombination

OBJECTIVES

The complete nucleotide sequence of the 6913 bp plasmid pSTE2 from Staphylococcus lentus, which mediates inducible resistance to tetracyclines, macrolides and lincosamides, was determined. The plasmid was analysed for potential reading frames and structural features to gain insight into its development from potential ancestor plasmids.

METHODS

Plasmid pSTE2 was transformed into Staphylococcus aureus RN4220. Suitable restriction fragments were cloned into E. coli plasmid vectors and sequenced. In vitro susceptibility testing was performed to confirm the resistance phenotype mediated by this plasmid.

RESULTS

Plasmid pSTE2 consisted of two parts, each of which corresponded closely to previously identified staphylococcal plasmids. The initial 4439 bp represented a pT181-analogous tet(K)-carrying tetracycline resistance plasmid, whereas the remaining 2474 bp represented a pPV141-related erm(C)-carrying macrolide-lincosamide-streptogramin B resistance plasmid. Both putative parental plasmids harboured the staphylococcal recombination site A (RSA) and the pT181-like plasmid also carried the recombinase gene pre whose product acts at RSA. Analysis of the junctions of the pT181-like and the pPV141-like homologous parts in pSTE2 suggested that plasmid pSTE2 developed from pT181- and pPV141-like ancestor plasmids by cointegrate formation at RSA.

CONCLUSION

Plasmid pSTE2 is the first completely sequenced plasmid from S. lentus and represents the product of an in vivo derived RSA-mediated recombination between two compatible plasmids.

Heat shock treatment increases the frequency of loss of an erythromycin resistance-encoding transposable element from the chromosome of Lactobacillus crispatus CHCC3692

A 3,165-bp chromosomally integrated transposon, designatedTn3692, of the gram-positive strain Lactobacillus crispatus CHCC3692 contains an erm(B) gene conferring resistance to erythromycin at concentrations of up to 250 micrograms/ml. Loss of this resistance can occur spontaneously, but the rate is substantially increased by heat shock treatment. Heat shock treatment at 60 degrees C resulted in an almost 40-fold increase in the frequency of erythromycin-sensitive cells (erythromycin MIC, 0.047 micrograms/ml). The phenotypic change was followed by a dramatic increase in transcription of the transposase gene and the concomitant loss of an approximately 2-kb DNA fragment carrying the erm(B) gene from the 3,165-bp erm transposon. In cells that were not subjected to heat shock, transcription of the transposase gene was not detectable. The upstream sequence of the transposase gene did not show any homology to known heat shock promoters in the gene data bank. Significant homology (>99%) was observed between the erythromycin resistance-encoding gene from L. crispatus CHCC3692 and the erm(B) genes from other gram-positive bacteria, such as Streptococcus agalactiae, Streptococcus pyogenes, Enterococcus faecium, and Lactobacillus reuteri, which strongly indicates a common origin of the erm(B) gene for these species. The transposed DNA element was not translocated to other parts of the genome of CHCC3692, as determining by Southern blotting, PCR analysis, and DNA sequencing. No other major aberrations were observed, as judged by colony morphology, growth performance of the strain, and pulsed-field gel electrophoresis. These observations suggest that heat shock treatment could be used as a tool for the removal of unwanted antibiotic resistance genes harbored in transposons flanked by insertion sequence elements or transposases in lactic acid bacteria used for animal and human food production.

A new Bacteroides conjugative transposon that carries an ermB gene

The erythromycin resistance gene ermB has been found in a variety of gram-positive bacteria. This gene has also been found in Bacteroides species but only in six recently isolated strains; thus, the gene seems to have entered this genus only recently. One of the six Bacteroides ermB-containing isolates, WH207, could transfer ermB to Bacteroides thetaiotaomicron strain BT4001 by conjugation. WH207 was identified as a Bacteroides uniformis strain based on the sequence of its 16S rRNA gene. Results of pulsed-field gel electrophoresis experiments demonstrated that the transferring element was normally integrated into the Bacteroides chromosome. The element was estimated from pulsed-field gel data to be about 100 kb in size. Since the element appeared to be a conjugative transposon (CTn), it was designated CTnBST. CTnBST was able to mobilize coresident plasmids and the circular form of the mobilizable transposon NBU1 to Bacteroides and Escherichia coli recipients. A 13-kb segment that contained ermB was cloned and sequenced. Most of the open reading frames in this region had little similarity at the amino acid sequence level to any proteins in the sequence databases, but a 1,723-bp DNA segment that included a 950-bp segment downstream of ermB had a DNA sequence that was virtually identical to that of a segment of DNA found previously in a Clostridium perfringens strain. This finding, together with the finding that ermB is located on a CTn, supports the hypothesis that CTnBST could have entered Bacteroides from some other genus, possibly from gram-positive bacteria. Moreover, this finding supports the hypothesis that many transmissible antibiotic resistance genes in Bacteroides are carried on CTns.

Identification of a truncated Tn1721-like transposon located on a small plasmid of Escherichia coli isolated from Varanus indicus

The 9.1 kb plasmid pDEWT1 was isolated from an Escherichia coli strain obtained from the faeces of a free-living lizard (Varanus indicus) in Indonesia. This plasmid mediated tetracycline resistance via a tet gene of hybridization class A. Molecular analysis of a 7755 bp segment of plasmid pDEWT1 including the tetR-tet(A) region and its flanking areas suggested that pDEWT1 harboured a truncated copy of the tet(A)-carrying transposon Tn1721 in which the part responsible for chemotaxis and transposition functions was lost. Analysis of the sequences at the integration site revealed the presence of the 5-bp direct repeat TACTT. The sequences upstream and downstream of the integration site showed striking homology to sequences of a non-coding region detectable on a small cryptic plasmid from Yersinia enterocolitica.

Trends in antimicrobial susceptibility in relation to antimicrobial usage and presence of resistance genes in Staphylococcus hyicus isolated from exudative epidermitis in pigs

From 1996 to 2001 a total of 467 Staphylococcus hyicus isolates from exudative epidermitis (EE) in pigs in Denmark were examined for susceptibility to 13 different antimicrobial agents. The presence of selected genes encoding macrolide (erm(A), erm(B) and erm(C)), penicillin (blaZ), streptogramin (vat, vga, vga(B), vat(B), vat(D) and vat(E)), streptomycin (aadE) and tetracycline resistance (tet(K), tet(L), tet(M) and tet(O)) were determined in selected isolates. The occurrence of erythromycin resistance increased from 33% in 1996 to a maximum of 62% in 1997 and decreased to 26% in 2001. Resistance to sulphametazole increased from 17% in 1996 to 30% in 1998 but has since decreased to 4% in 2001. Resistance to trimethoprim increased to 51% in 1997 and decreased to 21% in 2001. Resistance to tetracycline (21-31%) remained relatively constant during 1996-2000, but increased to 47% in 2001. Resistance to penicillin (54-75%) streptomycin (33-53%) and tetracycline (21-47%) remained relatively constant over the time investigated. All 48 penicillin resistant isolates examined contained the blaZ gene and 40 (85%) of the streptomycin resistant isolates the aadE gene. It was not possible to detect any streptogramin resistance gene in four streptogramin resistant isolates. Of the 55 erythromycin resistant isolates examined, five contained erm(A), 13 erm(B), 35 erm(C) and two both erm(A) and erm(C). The presence of erm(B) was confirmed by hybridization to plasmid profiles in all 13 PCR-positive isolates. Of 52 tetracycline resistant isolates examined, two contained tet(L), 38 tet(K) and 12 both tet(K) and tet(L).

Unusual inducible cross resistance to macrolides, lincosamides, and streptogramins B by methylase production in clinical isolates of Staphylococcus aureus

Clinical strains of Staphylococcus aureus UCN7 and UCN8 were inducibly resistant to erythromycin, clindamycin, lincomycin, and quinupristin. This unusual inducible MLS(B) resistance was due to the presence of an erm(A) or an erm(B) gene, which both encode a ribosomal methylase, in S. aureus UCN8 and UCN7, respectively. The inducible cross resistance expressed by S. aureus UCN8 was associated with an 83-bp deletion in the attenuator of the erm(A) gene that removed the second of the two leader peptides and several inverted repeats. The presence of an inducible erm(B) gene in S. aureus UCN7 conferred a cross-resistance MLS(B) phenotype, similar to that usually observed in streptococci. Therefore, in S. aureus, besides the classical inducible MLS(B) phenotype characterized by inducible resistance to 14- to 15-membered ring macrolides, an additional type of inducible cross resistance to macrolides, lincosamides, and streptogramins B due to variants of erm(A) or erm(B) genes exist.

Comparative molecular analysis of erythromycin-resistance determinants in staphylococcal isolates of poultry and human origin

The ermA, ermB, ermC and msrA/msrB genes were detected in multidrug-resistant Staphylococcus spp. strains by PCR. Among 25 human clinical staphylococcal isolates the ermA, ermB, ermC and the msrA/msrB genes were detected in 88, 72, 4 and 100% of the strains, respectively. Among 24 poultry isolates the ermA, ermB, ermC and the msrA/msrB genes were detected in 100, 16.6, 50 and 12.5% of the strains, respectively. The ermA gene was found exclusively on the chromosome, whereas the ermC gene was found on 2.4-4.2 kb plasmids. Restriction fragment length polymorphism (RFLP) analysis of the ermA gene with Eco RI revealed five patterns (25.0, 21.0, 10.5, 6.2 and 4. 8 kb) for the clinical strains and two (8.0 and 6.2 kb) for the poultry strains. The 6.2 kb RFLP pattern, in both the poultry and human clinical isolates, indicates a common lineage for the ermA gene.

Plasmid-encoded tetracycline resistance in Salmonella enterica subsp. enterica serovars choleraesuis and typhimurium: identification of complete and truncated Tn1721 elements

During routine screening of Salmonella enterica subsp., S. enterica isolates of animal origin for plasmid-encoded tetracycline resistance, two tetracycline resistance plasmids, the 50 kbp plasmid pGFT3 of Salmonella choleraesuis and the 9.5 kbp plasmid pGFT4 of Salmonella typhimurium var. Copenhagen DT002, were detected. The respective tetracycline resistance genes (tet) were identified by hybridization and PCR analysis to belong to hybridization class A. Conjugation experiments identified plasmid pGFT3 as a conjugative plasmid. Molecular analysis of the tet(A) gene area and the flanking regions identified a complete Tn1721-like transposon on plasmid pGFT3 and a truncated Tn1721-like element on plasmid pGFT4. The complete Tn1721-like element was integrated into a transposase reading frame of a truncated Tn3 transposon also located on plasmid pGFT3. The truncated Tn1721-like element of plasmid pGFT4 lacked the entire transposase part. This Tn1721-relic was integrated in an unknown reading frame which on amino acid level showed homology to the Rop protein of Escherichia coli. A model for the deletion of the transposase part was developed on the basis of the sequences present at the termini of the truncated Tn1721-like element.

Presence of erm gene classes in gram-positive bacteria of animal and human origin in Denmark

A classification of the different erm gene classes based on published sequences was performed, and specific primers to detect some of these classes designed. The presence of ermA (Tn554), ermB (class IV) and ermC (class VI) was determined by PCR in a total of 113 enterococcal, 77 streptococcal and 68 staphylococcal erythromycin resistant isolates of animal and human origin. At least one of these genes was detected in 88% of the isolates. Four isolates contained more than one erm gene. ermB dominated among the enterococci (88%) and streptococci (90%) and ermC among staphylococci (75%) with ermA (Tn554) present in some isolates (16%). Variations in the presence of the different genes when comparing staphylococcal isolates of human and animal origin were observed.

Induction of ermAMR from a clinical strain of Enterococcus faecalis by 16-membered-ring macrolide antibiotics

We cloned the MLSB resistance determinant by PCR from a clinical isolate of Enterococcus faecalis 373, which is induced more strongly by a 16-membered-ring macrolide, tylosin, than by erythromycin. To elucidate the molecular basis of resistance of E. faecalis 373, we analyzed the cloned gene, designated ermAMR, by site-directed mutagenesis and reporter gene assay. Our results showed that an arginine-to-cysteine change in the seventh codon of the putative leader peptide endowed tylosin with resistance inducibility and that TAAA duplication enabled the control region to express the downstream methylase gene at a drastically increased level.

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.