Structural alterations in the translational attenuator of constitutively expressed ermC genes

Molecular basis and evolutionary cost of a novel macrolides/lincosamides resistance phenotype in Staphylococcus haemolyticus

Staphylococcus haemolyticus (S. haemolyticus) is a coagulase-negative Staphylococcus that has become one of the primary causes of nosocomial infection. After a long period of antibiotic use, S. haemolyticus has developed multiple resistance phenotypes for macrolides and lincosamides. Herein, we evaluated four S. haemolyticus clinical isolates, of which three had antibiotic resistance patterns reported previously. The fourth isolate was resistant to both erythromycin and clindamycin in the absence of erythromycin induction. This novel phenotype, known as constitutive macrolides-lincosamides-streptogramins resistance, has been reported in other bacteria but has not been previously reported in S. haemolyticus. Investigation of the isolate demonstrated a deletion in the methyltransferase gene ermC, upstream leader peptide. This deletion resulted in constitutive MLS resistance based on whole-genome sequencing and experimental verification. Continuous expression of ermC was shown to inhibit the growth of S. haemolyticus, which turned out to be the fitness cost with no MLS pressure. In summary, this study is the first to report constitutive MLS resistance in S. haemolyticus, which provides a better understanding of MLS resistance in clinical medicine. IMPORTANCE This study identified a novel phenotype of macrolides/lincosamides resistance in Staphylococcus haemolyticus which improved a better guidance for clinical treatment. It also clarified the mechanistic basis for this form of antibiotic resistance that supplemented the drug resistance mechanism of Staphylococcus. In addition, this study elaborated on a possibility that continuous expression of some resistance genes was shown to inhibit the growth of bacteria themselves, which turned out to be the fitness cost in the absence of antibiotic pressure.

Mechanisms of Bacterial Resistance to Antimicrobial Agents

During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.

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.

Genetic environment of the transferable oxazolidinone/phenicol resistance gene optrA in Enterococcus faecalis isolates of human and animal origin

OBJECTIVES

Aim of this study was to analyse 17 non-related Enterococcus faecalis isolates of human and animal origin for the genetic environment of the novel oxazolidinone/phenicol resistance gene optrA.

METHODS

WGS and de novo assembly were conducted to analyse the flanking sequences of the optrA gene in the 17 E. faecalis isolates. When optrA was located on a plasmid, conjugation assays were performed to check whether the plasmids are conjugative and to confirm the resistance phenotype associated with these plasmids.

RESULTS

All nine optrA-carrying plasmids were conjugated into E. faecalis JH2-2 and the transconjugants exhibited the optrA-associated phenotype. In these plasmids, an IS1216E element was detected either upstream and/or downstream of the optrA gene. In eight plasmids, the phenicol exporter gene fexA was found upstream of optrA and in six plasmids, a novel erm(A)-related gene for macrolide-lincosamide-streptogramin B resistance was detected downstream of optrA. When located in the chromosomal DNA, the optrA gene was found downstream of the transcriptional regulator gene araC in four isolates, or downstream of the fexA gene in another four isolates. Integration of the optrA region into a Tn558-Tn554 hybrid, located in the chromosomal radC gene, was seen in two isolates.

CONCLUSIONS

The findings of the present study extend the current knowledge about the genetic environment of optrA and suggest that IS1216E elements play an important role in the dissemination of optrA among different types of enterococcal plasmids. The mechanism underlying the integration of optrA into the chromosomal DNA requires further investigation.

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.

A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals

Methicillin-resistant Staphylococcus aureus (MRSA) is a global human health problem causing infections in both hospitals and the community. Companion animals, such as cats, dogs, and horses, are also frequently colonized by MRSA and can become infected. We sequenced the genomes of 46 multilocus sequence type (ST) 22 MRSA isolates from cats and dogs in the United Kingdom and compared these to an extensive population framework of human isolates from the same lineage. Phylogenomic analyses showed that all companion animal isolates were interspersed throughout the epidemic MRSA-15 (EMRSA-15) pandemic clade and clustered with human isolates from the United Kingdom, with human isolates basal to those from companion animals, suggesting a human source for isolates infecting companion animals. A number of isolates from the same veterinary hospital clustered together, suggesting that as in human hospitals, EMRSA-15 isolates are readily transmitted in the veterinary hospital setting. Genome-wide association analysis did not identify any host-specific single nucleotide polymorphisms (SNPs) or virulence factors. However, isolates from companion animals were significantly less likely to harbor a plasmid encoding erythromycin resistance. When this plasmid was present in animal-associated isolates, it was more likely to contain mutations mediating resistance to clindamycin. This finding is consistent with the low levels of erythromycin and high levels of clindamycin used in veterinary medicine in the United Kingdom. This study furthers the “one health” view of infectious diseases that the pathogen pool of human and animal populations are intrinsically linked and provides evidence that antibiotic usage in animal medicine is shaping the population of a major human pathogen.

Methicillin-resistant Staphylococcus aureus (MRSA) is major problem in human medicine. Companion animals, such as cats, dogs, and horses, can also become colonized and infected by MRSA. Here, we demonstrate that a shared population of an important and globally disseminated lineage of MRSA can infect both humans and companion animals without undergoing host adaptation. This suggests that companion animals might act as a reservoir for human infections. We also show that the isolates from companion animals have differences in the presence of certain antibiotic resistance genes. This study furthers the “one health” view of infectious diseases by demonstrating that the pool of MRSA isolates in the human and animal populations are shared and highlights how different antibiotic usage patterns between human and veterinary medicine can shape the population of bacterial pathogens.

Two different erm(C)-carrying plasmids in the same methicillin-resistant Staphylococcus aureus CC398 isolate from a broiler farm

During a study on plasmid-borne antimicrobial resistance among methicillin-resistant Staphylococcus aureus (MRSA) isolates from broiler farms, an MRSA isolate was identified which carried multiple plasmids. This MRSA isolate belonged to CC398 and exhibited spa type t3015 and dru type dt11a. Plasmid profiling revealed the presence of one large and two small plasmids. The resistance genes tet(L) (tetracycline resistance), dfrK (trimethoprim resistance) and aadD (kanamycin/neomycin resistance) were located on the large plasmid. Both small plasmids, designated pSWS371 and pSWS372, carried only an erm(C) gene for macrolide/lincosamide resistance. Sequence analysis revealed that the 2458-bp plasmid pSWS371 carried only a repL gene for plasmid replication in addition to the erm(C) gene. In contrast, the 3882-bp plasmid pSWS372 harbored - in addition to the erm(C) gene - three more genes: a repF gene for plasmid replication, a cop-6 gene for a small protein potentially involved in copy number control of the plasmid and a novel pre/mob gene for a protein involved in plasmid recombination and mobilization. The erm(C) genes of both small plasmids exhibited constitutive erm(C) gene expression and analysis of the respective translational attenuators identified deletions of 16 bp and 74 bp which explain the constitutive expression. The simultaneous presence of two small plasmids that carry the same resistance gene in the same MRSA isolate is a rare observation. The fact that both plasmids belong to different incompatibility groups as specified by the different rep genes, repL and repF, explains why they can stably coexist in the same bacterial cell.

Multiple mutations lead to MexXY-OprM-dependent aminoglycoside resistance in clinical strains of Pseudomonas aeruginosa

Constitutive overproduction of the pump MexXY-OprM is recognized as a major cause of resistance to aminoglycosides, fluoroquinolones, and zwitterionic cephalosporins in Pseudomonas aeruginosa. In this study, 57 clonally unrelated strains recovered from non-cystic fibrosis patients were analyzed to characterize the mutations resulting in upregulation of the mexXY operon. Forty-four (77.2%) of the strains, classified as agrZ mutants were found to harbor mutations inactivating the local repressor gene (mexZ) of the mexXY operon (n = 33; 57.9%) or introducing amino acid substitutions in its product, MexZ (n = 11; 19.3%). These sequence variations, which mapped in the dimerization domain, the DNA binding domain, or the rest of the MexZ structure, mostly affected amino acid positions conserved in TetR-like regulators. The 13 remaining MexXY-OprM strains (22.8%) contained intact mexZ genes encoding wild-type MexZ proteins. Eight (14.0%) of these isolates, classified as agrW1 mutants, overexpressed the gene PA5471, which codes for the MexZ antirepressor ArmZ [corrected], with 5 strains exhibiting growth defects at 37°C and 44°C, consistent with mutations impairing ribosome activity. Interestingly, one agrW1 mutant appeared to harbor a 7-bp deletion in the coding sequence of the leader peptide, PA5471.1, involved in ribosome-dependent, translational attenuation of PA5471 expression. Finally, DNA sequencing and complementation experiments revealed that 5 (8.8%) strains, classified as agrW2 mutants, harbored single amino acid variations in the sensor histidine kinase of ParRS, a two-component system known to positively control mexXY expression. Collectively, these results demonstrate that clinical strains of P. aeruginosa exploit different regulatory circuitries to mutationally overproduce the MexXY-OprM pump and become multidrug resistant, which accounts for the high prevalence of MexXY-OprM mutants in the clinical setting.

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.

Identification of a plasmid-borne resistance gene cluster comprising the resistance genes erm(T), dfrK, and tet(L) in a porcine methicillin-resistant Staphylococcus aureus ST398 strain

A novel plasmid-borne resistance gene cluster comprising the genes erm(T) for macrolide-lincosamide-streptogramin B resistance, dfrK for trimethoprim resistance, and tet(L) for tetracycline resistance was identified in a porcine methicillin-resistant Staphylococcus aureus sequence type 398 (ST398) strain. This erm(T)-dfrK-tet(L) region was flanked by copies of the novel IS element ISSau10. The erm(T) region resembled that of Streptococcus pyogenes plasmid pRW35. The erm(T) gene of pKKS25 was expressed constitutively due to a 57-bp deletion in the erm(T) translational attenuator.

Prevalence of methicillin-resistant and methicillin-susceptible s. aureus in the saliva of health professionals

INTRODUCTION

S. aureus is one of the main agents of nosocomial infection and is sometimes difficult to treat with currently available active antimicrobials.

PURPOSE

To analyze the prevalence of methicillin-susceptible S.aureus (MSSA) and methicillin-resistant S. aureus (MRSA) as well as the MRSA antimicrobial susceptibility profile isolated in the saliva of health professionals at a large public education hospital.

MATERIALS AND METHODS

The project was approved by the research and ethics committee of the institution under study. Three samples of saliva from 340 health professionals were collected. The saliva analysis used to identify S. aureus was based on mannitol fermentation tests, catalase production, coagulase, DNAse, and lecithinase. In order to detect MRSA, samples were submitted to the disk diffusion test and the oxacillin agar screening test. In order to identify the minimum inhibitory concentration, the Etest technique was used.

RESULTS

The prevalence of MSSA was 43.5% (148/340), and MRSA was 4.1% (14/340). MRSA detected by the diffusion disk test, was 100% resistant to penicillin and oxacillin, 92.9% resistant to erythromycin, 57.1% resistant to clindamycin, 42.9% resistant to ciprofloxacin and 57.1% resistant to cefoxetin.

CONCLUSION

This subject is important for both the education of health professionals and for preventative measures. Standard and contact-precautions should be employed in professional practice.

Clonality and occurrence of genes encoding antibiotic resistance and biofilm in methicillin-resistant Staphylococcus epidermidis strains isolated from catheters and bacteremia in neutropenic patients

Thirty methicillin-resistant Staphylococcus epidermidis strains isolated from catheters and blood cultures from neutropenic patients were studied. They were classified into 17 multidrug-resistance patterns. Polymerase cahin reaction analysis revealed that methicillin resistance was encoded by the mecA gene in all strains, and aminoglycosides resistance was due to aac(6')-Ie-aph(2'')-Ia (23 strains), ant(4')-Ia (13), and aph(3')-IIIa (1) genes. The aac(6')-Ie-aph(2'')-Ia gene was detected concomitantly with aph(3')-IIIa, and ant(4')-Ia genes in one and nine strains, respectively. Erythromycin resistance was encoded by the ermC (11 strains), ermA (6), and msrA (2) genes. The ermC gene was inducibly expressed in five strains, whereas the ermA was exclusively constitutively expressed. The icaA and icaC genes were detected in 19 strains; however, biofilm production was observed in only 16 strains. Most strains harbored multiple plasmids of variable sizes ranging from 2.2 to 70 kb, and two strains were plasmid-free. PFGE identified 15 distinct PFGE types, and five predominant genotypes were found. Our study showed the occurrence of complex genetic phenomenons. In unrelated strains, evidence of horizontal transfer of antibiotic-encoding genes and/or ica operon, and in indistinguishable strains, there is a quite good likelihood of independent steps of loss and/or gain of these genes. This genome dynamicity might have enhanced the invasiveness power of these methicillin-resistant S epidermidis strains.

Distribution and expression of macrolide resistance genes in coagulase-negative staphylococci

In total, 494 isolates of coagulase-negative staphylococci (CoNS) were identified to the species level by biochemical tests and sodA sequencing. Erythromycin resistance phenotypes were determined and specific resistance genes were identified by PCR. The prevalence of erythromycin resistance varied widely among staphylococcal species, from 0% in Staphylococcus lugdunensis to almost 90% in Staphylococcus haemolyticus. Most (63%) erythromycin-resistant isolates carried constitutively expressed erm(C) as the sole resistance determinant, with the notable exception of Staphylococcus hominis subsp. hominis, which carried inducible erm(C). The erm(A) and erm(B) determinants were comparatively rare. The msr(A) gene was carried by 20-30% of all erythromycin-resistant isolates, with little variation among species, and was combined in 16.7% of isolates with mph(C), a resistance gene of unknown clinical relevance found previously in isolates of veterinary origin. No erythromycin resistance that could not be attributed to the genes investigated was detected. It was concluded that the presence of methylases cannot be assumed in CoNS isolates that appear erythromycin-resistant and clindamycin-susceptible; thus, methods that detect the export mechanism should be used with clinically significant isolates to indicate whether use of clindamycin may be effective. In Staphylococcus epidermidis and S. haemolyticus, 46% and 66%, respectively, of erythromycin-resistant, clindamycin-susceptible isolates were susceptible to clindamycin therapy.

Modes and modulations of antibiotic resistance gene expression

Since antibiotic resistance usually affords a gain of function, there is an associated biological cost resulting in a loss of fitness of the bacterial host. Considering that antibiotic resistance is most often only transiently advantageous to bacteria, an efficient and elegant way for them to escape the lethal action of drugs is the alteration of resistance gene expression. It appears that expression of bacterial resistance to antibiotics is frequently regulated, which indicates that modulation of gene expression probably reflects a good compromise between energy saving and adjustment to a rapidly evolving environment. Modulation of gene expression can occur at the transcriptional or translational level following mutations or the movement of mobile genetic elements and may involve induction by the antibiotic. In the latter case, the antibiotic can have a triple activity: as an antibacterial agent, as an inducer of resistance to itself, and as an inducer of the dissemination of resistance determinants. We will review certain mechanisms, all reversible, that bacteria have elaborated to achieve antibiotic resistance by the fine-tuning of the expression of genetic information.

Detection and prevalence of inducible clindamycin resistance in staphylococci

Staphylococcus aureus and coagulase-negative staphylococci (CNS) are recognized as causing nosocomial and community-acquired infections in every region of the world. The resistance to antimicrobial agents among staphylococci is an increasing problem. Clindamycin (CL) is considered to be one of the alternative agents in these infections. This study demonstrates a simple, reliable method (double-disc diffusion test) for detecting inducible resistance to CL in erythromycin-resistance (ER-R) isolates of S. aureus and CNS. A total of 883 (52.3%) isolates of S. aureus and 804 (47.7%) isolates of CNS were selected from recent (2003-2005) clinical isolates recovered in the laboratory of the authors; duplicate isolates were not included. A total of 214 (12.6%) S. aureus and 308 (18.3%) CNS isolates were selected based on ER-R and CL sensitivity using standard National Committee for Clinical Laboratory Standards disc diffusion testing. A total of 1687 staphylococcal isolates were included, consisting of 27.5% meticillin-resistant S. aureus, 24.8% meticillin-sensitive S. aureus, 36.1% meticillin-resistant CNS and 11.6% meticillin-sensitive CNS isolates: 30.9% of staphylococcal isolates (214 S. aureus and 308 CNS) that were erythromycin resistant and CL sensitive were tested for inducible resistance using the D-test. A D-shaped zone around the CL was observed for 70.9% of staphylococcal isolates (81.8% of S. aureus isolates and 63.3% of CNS isolates) with an ER-R and a clindamycin-sensitive (CL-S) phenotype. The organism was positive for inducible clindamycin resistance (CL-R). There was a 21.9% level of inducible macrolide-lincosamide-streptogramin B resistance phenotype among all the staphylococcal isolates. When the S. aureus and CNS strains among all the staphylococcal isolates were compared statistically, inducible CL-R in CNS strains was determined to be 23% more positive (P=0.028, odds ratio 0.77, 95% confidence interval 0.61-0.98). When a statistical comparison was performed among ER-R but CL-S staphylococcal isolates inducible CL-R in S. aureus strains was determined to be 2.6 times more positive (P=0.000, odds ratio 2.6, 95% confidence interval 1.68-4.04). A simple, reliable method of detecting inducible resistance to CL in ER-R isolates of S. aureus and CNS is described. Clinical microbiology laboratories should use the double-disc diffusion test as standard practice with all ER-R staphylococci. CL should not be used in patients with infections caused by inducibly resistant staphylococcal isolates. Therapeutic failures may thus be avoided.

Inducible clindamycin resistance in Staphylococcus aureus isolates causing bacteremia at a university hospital in southern Taiwan

A major concern while prescribing clindamycin to treat infections caused by inducible macrolide, lincosamide, and group B streptogramin (iMLS(B))-resistant strains is clinical therapy failure. In this study, we determined the prevalence, mechanism, and clonality of the iMLS(B) phenotype in oxacillin-resistant Staphylococcus aureus (ORSA) and oxacillin-susceptible S. aureus (OSSA). Among the 729 OSSA isolates collected from July 1995 to March 2006, 72 (10%) were clindamycin sensitive (Cli(s)) and erythromycin resistant (Erm(r)), and 55 (8%) had the iMLS(B) phenotype. In the 709 ORSA isolates collected from January 1997 to March 2006, 31 (4%) were Cli(s) and Erm(r), and 29 (4%) isolates demonstrated the iMLS(B) phenotype. In OSSA, ermC was the predominant (51 of 55 isolates) genetic determinant responsible for the iMLS(B) phenotype, whereas in ORSA, ermA was predominant (27 of 29). Pulsed-field gel electrophoresis showed that 8 pulsed types (RA to RH) were present in ORSA isolates (n = 27), and pulsed type RC was predominant in 17 isolates with 5 identifiable subtypes (RC1 to RC5); this type was prevalent from November 1997 to June 2004. In the OSSA (n = 24) isolates, 14 different pulsed types (SA to SN) were identified, but none was predominant. These results indicate that the incidence of iMLS(B) resistance phenotype is higher in OSSA than ORSA in Taiwan, and the genetic determinants responsible for the iMLS(B) phenotype vary in OSSA and ORSA.

Occurrence, species distribution, antimicrobial resistance and clonality of methicillin- and erythromycin-resistant staphylococci in the nasal cavity of domestic animals

beta-Lactams and macrolides are important antibiotics for treatment of staphylococcal infections in both humans and animals. The aim of the study was to investigate the occurrence, species distribution and clonality of methicillin- and erythromycin-resistant staphylococci in the nasal cavity of dogs, horses, pigs, and cattle in Denmark. Nasal swabs were collected from a total of 400 animals, including 100 individuals of each species. Methicillin- and erythromycin-resistant staphylococci were isolated on selective media, identified by 16S rDNA sequencing, and typed by pulsed field gel electrophoresis (PFGE). Methicillin-resistant coagulase-negative staphylococci (MRCoNS) harbouring mecA were isolated from horses (50%) and dogs (13%), but not from food animals. The species identified were S. haemolyticus (n=21), S. vitulinus (n=19), S. sciuri (n=13), S. epidermidis (n=8), and S. warneri (n=2). mecA-mediated methicillin resistance in S. vitulinus was described for the first time. Methicillin-resistant S. aureus was not detected. PFGE analysis revealed the presence of specific MRCoNS clones in samples originating from the same veterinary hospital or equine farm. Erythromycin-resistant S. aureus (ERSA) was detected in 38% of pigs and all isolates harboured a constitutively expressed erm(C) gene. The vast majority (37/38) of pigs carrying ERSA originated from a farm characterized by frequent use of macrolides. Most ERSA isolates (28/38) displayed indistinguishable or closely related PFGE patterns, indicating clonal distribution within the farm. Based on the analysis of data on antimicrobial consumption, the occurrence of MRCoNS in companion animals and that of ERSA in pigs reflected national and local patterns of antimicrobial usage.

Antimicrobial resistance: mechanisms and strategies

Antimicrobial resistance is a growing threat worldwide. S. aureus strains that combine resistance and virulence genes have become a major treatment problem in Europe and the U.S. Extended-spectrum beta-lactamases are an emerging problem in many settings. Resistance mechanisms have been found for every class of antibiotic agent. Development of new classes of antibiotics or more robust versions of old classes will be essential in the years to come. Judicious use of antimicrobial agents and improved infection control methods must become health care priorities.

Influence of disk separation distance on accuracy of the disk approximation test for detection of inducible clindamycin resistance in Staphylococcus spp

We undertook this study to assess the accuracy of the clindamycin-erythromycin disk approximation test (D-test) for detection of inducible clindamycin resistance in Staphylococcus spp. One hundred sixty-three Staphylococcus aureus and 68 coagulase-negative Staphylococcus (CoNS) spp. which were erythromycin nonsusceptible but clindamycin susceptible were tested using the D-test performed at both 15-mm and 22-mm disk separations and compared with genotyping as the "gold standard." The rate of inducible clindamycin resistance was 96.3% for S. aureus and 33.8% for CoNS spp. The sensitivities of the D-tests performed at 15 mm and 22 mm were 100% and 87.7%, respectively, and specificities were 100% for both. The use of 22-mm disk separation for the D-test to detect inducible clindamycin resistance results in an unacceptably high very major error rate (12.3%). All isolates with false-negative results harbored the ermA gene, and the majority were methicillin-resistant Staphylococcus aureus. False-negative results were associated with smaller clindamycin zone sizes and double-edged zones. We recommend using a disk separation distance of </=15 mm. There is wide geographic variation in the rates of inducible clindamycin resistance, and each laboratory should determine the local rate before deciding whether to either perform the D-test routinely or else report that all erythromycin-resistant S. aureus isolates are also clindamycin resistant.

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.

Differences in the DNA sequences in the upstream attenuator region of erm(A) in clinical isolates of Streptococcus pyogenes and their correlation with macrolide/lincosamide resistance

The regulatory regions of 52 erm(A) [formerly erm(TR)] clinical Streptococcus pyogenes isolates were studied. Differences in the upstream regulatory region of erm(A) correlated with macrolide/lincosamide resistance patterns. Nine macrolide/lincosamide/streptogramin B-resistant isolates had changes in the leader sequence of erm(A) including base changes, insertions, or deletions. Isolates were also emm typed.

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.

Inducible Clindamycin Resistance in Staphylococci: Should Clinicians and Microbiologists be Concerned?

The increasing incidence of a variety of infections due to Staphylococcus aureus--and, especially, the expanding role of community-associated methicillin-resistant S. aureus (MRSA)--has led to emphasis on the need for safe and effective agents to treat both systemic and localized staphylococcal infections. Unlike most previously noted strains of health care-associated MRSA, community-acquired MRSA isolates are often susceptible to several non- beta -lactam drug classes, although they are usually not susceptible to macrolides. Several newer antimicrobial agents and a few older agents are available for treatment of systemic staphylococcal infections, but use may be limited by the relatively high cost of these agents or the need for parenteral administration. Inexpensive oral agents for treatment of localized, community-acquired MRSA infection include clindamycin, trimethoprim-sulfamethoxazole, and newer tetracyclines. Clindamycin has been used successfully to treat pneumonia and soft-tissue and musculoskeletal infections due to MRSA in adults and children. However, concern over the possibility of emergence of clindamycin resistance during therapy has discouraged some clinicians from prescribing that agent. Simple laboratory testing (e.g., the erythromycin-clindamycin "D-zone" test) can separate strains that have the genetic potential (i.e., the presence of erm genes) to become resistant during therapy from strains that are fully susceptible to clindamycin.

Practical disk diffusion method for detection of inducible clindamycin resistance in Staphylococcus aureus and coagulase-negative staphylococci

Resistance to macrolides in staphylococci may be due to active efflux (encoded by msrA) or ribosomal target modification (macrolide-lincosamide-streptogramin B [MLSB] resistance; usually encoded by ermA or ermC). MLSB resistance is either constitutive or inducible following exposure to a macrolide. Induction tests utilize closely approximated erythromycin and clindamycin disks; the flattening of the clindamycin zone adjacent to the erythromycin disk indicates inducible MLSB resistance. The present study reassessed the reliability of placing erythromycin and clindamycin disks in adjacent positions (26 to 28 mm apart) in a standard disk dispenser, compared to distances of 15 or 20 mm. A group of 130 clinical isolates of Staphylococcus aureus and 100 isolates of erythromycin-resistant coagulase-negative staphylococci (CNS) were examined by disk approximation; all CNS isolates and a subset of S. aureus isolates were examined by PCR for ermA, ermC, and msrA. Of 114 erythromycin-resistant S. aureus isolates, 39 demonstrated constitutive resistance to clindamycin, while 33 showed inducible resistance by disk approximation at all three distances. Only one isolate failed to clearly demonstrate induction at 26 mm. Of 82 erythromycin-resistant CNS isolates that contained ermA or ermC, 57 demonstrated constitutive clindamycin resistance, and 25 demonstrated inducible resistance, at 20 and 26 mm. None of the 42 S. aureus isolates or 18 CNS isolates containing only msrA and none of the erythromycin-susceptible isolates yielded positive disk approximation tests. Simple placement of erythromycin and clindamycin disks at a distance achieved with a standard disk dispenser allowed detection of 97% of S. aureus strains and 100% of CNS strains with inducible MLSB resistance in this study.

Antimicrobial growth promoters used in animal feed: effects of less well known antibiotics on gram-positive bacteria

There are not many data available on antibiotics used solely in animals and almost exclusively for growth promotion. These products include bambermycin, avilamycin, efrotomycin, and the ionophore antibiotics (monensin, salinomycin, narasin, and lasalocid). Information is also scarce for bacitracin used only marginally in human and veterinary medicine and for streptogramin antibiotics. The mechanisms of action of and resistance mechanisms against these antibiotics are described. Special emphasis is given to the prevalence of resistance among gram-positive bacteria isolated from animals and humans. Since no susceptibility breakpoints are available for most of the antibiotics discussed, an alternative approach to the interpretation of MICs is presented. Also, some pharmacokinetic data and information on the influence of these products on the intestinal flora are presented.

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.

Staphylococcus sciuri gene erm(33), encoding inducible resistance to macrolides, lincosamides, and streptogramin B antibiotics, is a product of recombination between erm(C) and erm(A)

A gene which mediates inducible resistance to macrolides, lincosamides, and streptogramin B antibiotics, designated erm(33), was detected on the Staphylococcus sciuri plasmid pSCFS1. Analysis of the erm(33) reading frame suggested that this gene was the product of a recombination between an erm(C) gene and an erm(A) gene. Such a recombination event is a novel observation for erm genes.

Molecular analysis of streptogramin resistance in enterococci

The new semi-synthetic streptogramin antibiotic combination quinupristin/dalfopristin (Synercid) is a promising alternative for a treatment of infections with multiple resistant gram-positive pathogens, e.g. glycopeptide- and multi-resistant Enterococcus faecium. Streptogramins consist of two unrelated compounds, a streptogramin A and B, which act synergistically when given in combination. Mechanisms conferring resistance against both components are essential for resistance against the combination in E. faecium. In this species resistance to streptogramin A compounds is mediated via related acetyltransferases VatD and VatE. Resistance against streptogramins B is either encoded by the widespread ermB gene cluster conferring resistance to macrolide-lincosamide-streptogramin B antibiotics or via expression of the vgbA gene, which encodes a staphylococcal-type lactonase. E. faecalis is intrinsically resistant to streptogramins. Due to a wide use of streptogramins (virginiamycins S/M) in commercial animal farming a reservoir of streptogramin-resistant E. faecium isolates had already been selected. Determinants for streptogramin resistance are localized on plasmids that can be transferred into an E. faecium recipient both in vitro in filter-matings and in vivo in the digestive tracts of rats. Hybridization and sequencing experiments revealed a linkage of resistance determinants for streptogramins A and B on definite plasmid fragments.

Molecular characterization of ketolide-resistant erm(A)-carrying Staphylococcus aureus isolates selected in vitro by telithromycin, ABT-773, quinupristin and clindamycin

The aim of this study was to investigate whether a Staphylococcus aureus strain that carried an inducibly expressed erm(A) gene might exhibit resistance to the non-inducers telithromycin, ABT-773, clindamycin, quinupristin, dalfopristin or the combination quinupristin-dalfopristin after incubation in the presence of inhibitory concentrations of any of these compounds. Whenever resistant mutants were obtained, these were investigated for the molecular basis of the altered resistance phenotype. Resistant mutants were not selected with dalfopristin or quinupristin-dalfopristin, but were obtained with the other four agents. Irrespective of which drug was used for selection, all mutants were cross-resistant to clindamycin, quinupristin, telithromycin and ABT-773, and exhibited structural alterations in the erm(A) translational attenuator. The structural alterations observed included deletions of 14, 83, 121, 131, 147 or 157 bp, three different tandem duplications of 23, 25 or 26 bp, two different types of point mutation, as well as the insertion of IS256. All these alterations either completely prevented the formation of mRNA secondary structures in the erm(A) regulatory region or favoured the formation of those mRNA secondary structures that allowed translation of the erm(A) transcripts. Deletions, which were observed in almost two-thirds of the mutants, might be explained by illegitimate recombination between different parts of the erm(A) regulatory region.

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.

Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.

Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.