Detection and quantification of macrolide resistance mutations at positions 2058 and 2059 of the 23S rRNA gene by pyrosequencing

Identification and characterization of Shigella with decreased susceptibility to azithromycin in the United States, 2005 to 2014

OBJECTIVES

Our objectives were to identify Shigella isolates in the United States with decreased susceptibility to azithromycin (DSA) and characterize the genetic mechanisms responsible for this resistance.

METHODS

The National Antimicrobial Resistance Monitoring System (NARMS) at the US Centers for Disease Control and Prevention (CDC) collects and conducts broth microdilution antimicrobial susceptibility testing on Shigella to determine minimum inhibitory concentrations (MICs) for up to 15 drugs, including azithromycin. Isolates with decreased susceptibility to azithromycin were subjected to molecular methods (e.g., polymerase chain reaction [PCR], whole-genome sequencing, and plasmid typing/transformation) to identify the genetic mechanisms of resistance.

RESULTS

A total of 118 isolates with decreased susceptibility to azithromycin were tested-65 (55%) isolates contained only mphA, 1 (<1%) isolate contained only ermB, and 51 (43%) isolates contained both mechanisms. Seven isolates contained IncFII plasmids with mphA, ermB, or mphA and ermB, whereas one isolate contained an IncB/O plasmid with mphA. One (<1%) isolate that contained neither mphA nor ermB contained mutations in rrlH, rplD, and rplV genes and an insertion in rplV, the functions of which are not yet known.

CONCLUSION

Additional studies are needed to understand the effect on treatment outcomes, epidemiology and possible additional mechanisms responsible for the decreased susceptibility of azithromycin in Shigella.

Expanding the Scope of Protein Synthesis Using Modified Ribosomes

The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.

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.

Gene subtype analysis of Treponema pallidum for drug resistance to azithromycin

Azithromycin has been widely used for the treatment of Treponema pallidum. However, the drug resistance of T. pallidum for azithromycin is currently increasing. The aim of the present study was to analyze the association between gene subtypes of T. pallidum and drug resistance for azithromycin. The gene subtypes of T. pallidum were assayed by a polymerase chain reaction technique. Drug resistance of T. pallidum was analyzed using an antimicrobial susceptibility test. The results demonstrated that gene type tpr presented higher drug resistance compared with arp and tp0548 gene types of T. pallidum. Gene type tpr was identified as eight gene subtypes (14a/f, 14e/f, 12e/f, 12d/f, 6d/f, 11d/f, 14j/f and 8d/f) among 324 cases. It was identified that 23S rRNA A2058G mutation was observed in gene subtypes 14a/f, 14e/f and 12e/f. A2059G mutation occurred in the gene subtypes 8d/f, 12d/f, 6d/f, 11d/f and 14j/f. The proportions of azithromycin-resistant genotypes harboring either the A2058G or the A2059G mutation among the T. pallidum strains were 34.2 and 65.8%, respectively. The antimicrobial susceptibility test demonstrated that A2059G mutations exhibited a higher drug resistance for azithromycin compared with A2058G mutations. In conclusion, these results indicate that azithromycin resistance in T. pallidum is associated with gene subtype, which may contribute to the treatment of T. pallidum.

Genetic Basis and Clonal Population Structure of Antibiotic Resistance in Campylobacter jejuni Isolated From Broiler Carcasses in Belgium

Human campylobacteriosis is the leading food-borne zoonosis in industrialized countries. This study characterized the clonal population structure, antimicrobial resistance profiles and occurrence of antimicrobial resistance determinants of a set of Campylobacter jejuni strains isolated from broiler carcasses in Belgium. Minimum inhibitory concentrations (MICs) against five commonly-used antibiotics (ciprofloxacin, nalidixic acid, tetracycline, gentamicin, and erythromycin) were determined for 204 C. jejuni isolates. More than half of the isolates were resistant to ciprofloxacin or nalidixic acid. In contrast, a lower percentage of screened isolates were resistant to gentamicin or erythromycin. C. jejuni isolates resistant to ciprofloxacin and/or nalidixic acid were screened for the substitution T86I in the quinolone resistance determining region (QRDR) of the gyrA gene, while C. jejuni isolates resistant to tetracycline were screened for the presence of the tet(O) gene. These resistance determinants were observed in most but not all resistant isolates. Regarding resistance to erythromycin, different mutations occurred in diverse genetic loci, including mutations in the 23S rRNA gene, the rplD and rplV ribosomal genes, and the intergenic region between cmeR and cmeABC. Interestingly, and contrary to previous reports, the A2075G transition mutation in the 23S rRNA gene was only found in one strain displaying a high level of resistance to erythromycin. Ultimately, molecular typing by multilocus sequence typing revealed that two sequence types (ST-824 and ST-2274) were associated to quinolones resistance by the presence of mutations in the gene gyrA (p = 0.01). In addition, ST-2274 was linked to the CIP-NAL-TET-AMR multidrug resistant phenotype. In contrast, clonal complex CC-45 was linked to increased susceptibility to the tested antibiotics. The results obtained in this study provide better understanding of the phenotypic and the molecular basis of antibiotic resistance in C. jejuni, unraveling some the mechanisms which confer antimicrobial resistance and particular clones associated to the carriage and spread of resistance genes.

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.

Molecular subtyping and erythromycin resistance of Campylobacter in China

AIMS

To investigate the erythromycin resistance patterns and mechanism for Campylobacter isolates in China.

METHODS AND RESULTS

The minimum inhibitory concentrations of erythromycin on 858 Chinese Campylobacter isolates were analysed. PCR and DNA sequencing were used to identify mutations in the 23S rRNA and the presence of the ermB gene in the 158 erythromycin resistance isolates (18·4%). About 83% (131/158) had A2075G mutation in their 23S rRNA; no A2074C/G mutants were found. The ermB gene was identified in 30 Campylobacter coli isolates (19%). Four types of multidrug-resistant gene islands (MDRGIs) were found. Fifty-three types were identified by multilocus sequence typing among the resistant isolates. All isolates of STs 6322 and 1145 had the ermB gene.

CONCLUSIONS

The erythromycin resistance rate of Camp. coli (58·56%) was much higher than Campylobacter jejuni (0·67%). The insertion sites between cadF and CCO1582 and between nfsB and cinA on the chromosome might be hot spots for MDRGI transformation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Point mutation in domain V of the 23S rRNA and the ermB gene accounted for 100% of the erythromycin resistance of Campylobacter in China.

A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae

Rapid and specific detection of extended-spectrum β-lactamase-producing (ESBL) bacteria is crucial both for timely antibiotic therapy when treating infected patients as well as for appropriate infection control measures aimed at curbing the spread of ESBL-producing isolates. Whereas a variety of phenotypic methods are currently available for ESBL detection, they remain time consuming and sometimes difficult to interpret while being also affected by a lack of sensitivity and specificity. Considering the longer turnaround time (TAT) of susceptibility testing and culture results, DNA-based ESBL identification would be a valuable surrogate for phenotypic-based methods. Putative ESBL-positive Enterobacteriaceae isolates (n = 330) from clinical specimen were prospectively collected in Bulgaria, Romania and Democratic Republic of Congo and tested in this study. All isolates were assessed for ESBL-production by the E-test method and those giving undetermined ESBL status were re-tested using the combination disk test. A genotypic assay successively combining qPCR detection of blaCTX-M, blaTEM and blaSHV genes with a multiplex pyrosequencing of blaTEM and blaSHV genes was developed in order to detect the most common ESBL-associated TEM and SHV single nucleotides polymorphisms, irrespective of their plasmid and/or chromosomal location. This assay was applied on all Enterobacteriaceae isolates (n = 330). Phenotypic and genotypic results matched in 324/330 (98.2%). Accordingly, real-time PCR combined with multiplex pyrosequencing appears to be a reliable and easy-to-perform assay with high-throughput identification and fast TAT (~5 h).

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Application of Pyrosequencing® in Food Biodefense

The perpetration of a bioterrorism attack poses a significant risk for public health with potential socioeconomic consequences. It is imperative that we possess reliable assays for the rapid and accurate identification of biothreat agents to make rapid risk-informed decisions on emergency response. The development of advanced methodologies for the detection of biothreat agents has been evolving rapidly since the release of the anthrax spores in the mail in 2001, and recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence-based approaches such as Pyrosequencing(®), which has the capability to determine short DNA stretches in real time using biotinylated PCR amplicons, have potential biodefense applications. Using markers from the virulence plasmids and chromosomal regions, my laboratory has demonstrated the power of this technology in the rapid, specific, and sensitive detection of B. anthracis spores and Yersinia pestis in food. These are the first applications for the detection of the two organisms in food. Furthermore, my lab has developed a rapid assay to characterize the antimicrobial resistance (AMR) gene profiles for Y. pestis using Pyrosequencing. Pyrosequencing is completed in about 60 min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence, thus enabling rapid risk-informed decisions to be made. A typical run yields 40-84 bp reads with 94-100 % identity to the expected sequence. It also provides a rapid method for determining the AMR profile as compared to the conventional plate method which takes several days. The method described is proposed as a novel detection system for potential application in food biodefense.

Rapid identification of strains belonging to the Mycobacterium abscessus group through erm(41) gene pyrosequencing

Mycobacterium abscessus and Mycobacterium massiliense lung infections have different clarithromycin susceptibilities, making proper identification important; however, standard multi-gene sequencing in clinical laboratories is laborious and time consuming. We developed a pyrosequencing-based method for rapid identification of strains belonging to the M. abscessus group by targeting erm(41). We examined 55 isolates from new pulmonary M. abscessus infections and identified 28 M. abscessus, 25 M. massiliense, and 2 Mycobacterium bolletii isolates. Multi-gene sequencing of 16S rRNA, hsp65, rpoB, and the 16S-23S ITS region was concordant with the results of erm(41) pyrosequencing; thus, the M. abscessus group can be identified by single-nucleotide polymorphisms in erm(41). The method also enables rapid identification of polymorphic, inducible clarithromycin-resistant sequevars (T28 or C28). Pyrosequencing of erm(41) is a rapid, reliable, high-throughput alternative method for identifying and characterizing M. abscessus species. Further testing of a diverse collection of isolates is necessary to demonstrate the discriminatory power of erm(41) sequencing to differentiating species with this highly divergent group.

Which mechanisms of azithromycin resistance are selected when efflux pumps are inhibited?

The aim of this study was to develop in vitro azithromycin (AZM)-resistant mutants of Escherichia coli and Shigella spp. in the presence of Phe-Arg β-naphthylamide (PAβN) and to observe which AZM resistance mechanisms other than efflux pumps were inhibited by PAβN emerge. The frequency of mutation ranged between <6.32 × 10(-10) and 5.22 × 10(-7) for E. coli and between <5.32 × 10(-10) and 1.69 × 10(-7) for Shigella spp. The E. coli mutants showed an increase in the AZM minimum inhibitory concentration (MIC) up to 128-fold, whilst the Shigella spp. mutants presented increases in MIC levels of up to 8-fold. In one mutant, the insertion of nucleotides encoding the amino acid sequence IMPRAS was found in the rplV gene. Increases in OmpW expression were observed in all E. coli mutants compared with their respective parental isolates. The combination of antibiotics and efflux pump inhibitors appears to be a good option to reduce the frequency of mutation in clinical isolates.

Antimicrobial resistance in campylobacter: susceptibility testing methods and resistance trends

Most Campylobacter infections are self-limiting but antimicrobial treatment (e.g., macrolides, fluoroquinolones) is necessary in severe or prolonged cases. Susceptibility testing continues to play a critical role in guiding therapy and epidemiological monitoring of resistance. The methods of choice for Campylobacter recommended by the Clinical and Laboratory Standards Institute (CLSI) are agar dilution and broth microdilution, while a disk diffusion method was recently standardized by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Macrolides, quinolones, and tetracyclines are among the common antimicrobials recommended for testing. Molecular determination of Campylobacter resistance via DNA sequencing or PCR-based methods has been performed. High levels of resistance to tetracycline and ciprofloxacin are frequently reported by many national surveillance programs, but resistance to erythromycin and gentamicin in Campylobacter jejuni remains low. Nonetheless, variations in susceptibility observed over time underscore the need for continued public health monitoring of Campylobacter resistance from humans, animals, and food.

Ribosomal mutations as the main cause of macrolide resistance in Campylobacter jejuni and Campylobacter coli

The aim of this study was to examine macrolide resistance mutations in Campylobacter species. In 76 strains studied, point mutation A to G at position 2059 of the 23S rRNA gene was detected in 30 of the 33 erythromycin-resistant strains. An amino acid insertion in the ribosomal protein L22 was found in one resistant strain without a 23S rRNA mutation. The A2059G mutation is the main cause of macrolide resistance in Campylobacter species.

Phenotypic and genetic characterization of macrolide resistance in Francisella tularensis subsp. holarctica biovar I

OBJECTIVES

Francisella tularensis subsp. holarctica strains are classified as biovars I and II, which are susceptible and naturally resistant to the macrolide erythromycin, respectively. The present study was aimed at both selecting biovar I strains with increased levels of erythromycin resistance and characterizing the underlying genetic mechanisms.

METHODS

Serial cultures in the presence of increasingly high erythromycin concentrations were performed to select independent high- and intermediate-level erythromycin-resistant mutants from each of three different biovar I strains. The mutants were characterized for cross-resistance to several antibiotics, presence of mutations in the genes encoding the 23S rRNA and the L4 and L22 ribosomal proteins, and overexpression of efflux pumps.

RESULTS

Mutants displayed cross-resistance to all macrolide compounds tested but not to other classes of antibiotics. We found mutations in domain V of the 23S rRNA gene (G2057A, A2058G, A2058T and C2611T) and in the gene encoding L22, leading to either the G91D substitution or the M82K83R84 deletion. Analysis of mutants with intermediate resistance levels obtained over the course of the selection process revealed both a positive correlation between the number of mutated ribosomal operons and the resistance level, and an additional resistance mechanism in the early steps of selection.

CONCLUSIONS

We showed that high-level resistance to macrolides can be easily obtained in vitro in F. tularensis subsp. holarctica biovar I strains, thereby suggesting that in vivo selection for resistance may explain reported failures of antibiotic treatment. Ketolides were the most effective macrolides tested, which may limit the risk of selection for resistance.

From structure to function: the ecology of host-associated microbial communities

In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

In vitro activity of azithromycin against nontyphoidal Salmonella enterica

The in vitro activity of azithromycin against 1,237 nontyphoidal Salmonella enterica isolates collected from Finnish patients between 2003 and 2008 was investigated. Only 24 (1.9%) of the isolates tested and 15 (5.1%) of the 294 isolates with reduced fluoroquinolone susceptibility had azithromycin MICs of >or=32 microg/ml. These data show that azithromycin has good in vitro activity against nontyphoidal S. enterica, and thus, it may be a good candidate for clinical treatment studies of salmonellosis.

Rapid detection of aac(6')-Ib-cr quinolone resistance gene by pyrosequencing

Pyrosequencing was used to rapidly detect aac(6')-Ib and aac(6')-Ib-cr genes. This plasmid-mediated quinolone resistance determinant is increasing in extended-spectrum beta-lactamase-producing Enterobacteriaceae. This method is faster and more cost-effective than the methods previously described. Sequences obtained with this pyrosequencing method showed 100% concordance with conventional sequencing.

Pyrosequencing using the single-nucleotide polymorphism protocol for rapid determination of TEM- and SHV-type extended-spectrum beta-lactamases in clinical isolates and identification of the novel beta-lactamase genes blaSHV-48, blaSHV-105, and blaTEM-155

TEM- and SHV-type extended-spectrum beta-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla(TEM) and bla(SHV) genes. Three novel beta-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla(SHV-105) were >128, 128, and >128 microg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla(TEM-155) were >128, 64, and > 128 microg/ml, respectively. Pyrosequence analysis determined the true identity of the beta-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.

Detection of resistance to macrolides in thermotolerant campylobacter species by fluorescence in situ hybridization

The resistance of enteritis-causing Campylobacter strains to erythromycin is an emerging problem. We therefore evaluated fluorescence in situ hybridization (FISH) for the rapid detection of resistance using 74 campylobacter isolates. FISH showed specificity and sensitivity of 100% for the detection of high-level resistance.

Prospective evaluation of pyrosequencing for the rapid detection of isoniazid and rifampin resistance in clinical Mycobacterium tuberculosis isolates

A pyrosequencing-based method for the rapid detection of isoniazid (INH) and rifampin (RIF) resistance in Mycobacterium tuberculosis was evaluated in clinical practice. The method can detect the INH resistance-causing katG315 mutation, and all mutations in the RIF resistance-determining rpoB core region, in less than 6 h from cultured isolates. The method was first validated with 42 isolates, and was subsequently prospectively evaluated with 91 isolates, including clinical isolates and external quality control assessment strains, over a period of 2.5 years. The pyrosequencing results of clinical isolates were available, on average, 19 days earlier (median 19 days; range 3-43 days) than conventional susceptibility testing results. The composite data showed that the sensitivity of pyrosequencing for detecting resistance correctly was 66.7% for INH and 97.4% for RIF. The specificity of pyrosequencing was 100% for both drugs. Acceptable sensitivity for detecting resistance and the rapidness of pyrosequencing make it a valuable tool in the clinical setting.

Pyrosequencing for rapid identification of carbapenem-hydrolysing OXA-type beta-lactamases in Acinetobacter baumannii

Carbapenem-resistant Acinetobacter baumannii isolates producing carbapenem-hydrolysing oxacillinases are emerging worldwide. These enzymes are divided into four phylogenetic subgroups: OXA-23-like, OXA-51-like, OXA-24-like and OXA-58-like. A PCR-based approach linked to pyrosequencing analysis was developed to identify the genes for these beta-lactamases. Carbapenem-hydrolysing oxacillinases were rapidly and unambiguously identified in a collection of carbapenem-resistant clinical isolates of A. baumannii and Acinetobacter junii. Pyrosequencing may provide a rapid tool for identification of OXA variants, thus avoiding delays inherent in classical sequencing methods.

Typing of SHV extended-spectrum beta-lactamases by pyrosequencing in Klebsiella pneumoniae strains with chromosomal SHV beta-lactamase

In Klebsiella pneumoniae, the cooccurrence of chromosomal and plasmid-mediated beta-lactamases can hinder their accurate molecular detection. We developed a fast and reliable method that allows the typing of isolates carrying more than one SHV gene. The method is based on pyrosequencing the DNA sequence corresponding to amino acid positions 35, 238, and 240.

Rapid screening of clarithromycin resistance in Helicobacter pylori by pyrosequencing

Helicobacter pylori infections can be effectively treated with clarithromycin, a macrolide, in combination with other antibiotics, such as amoxicillin, tetracycline or metronidazole. The failure of H. pylori eradication is mainly associated with macrolide-resistant strains. Three point mutations (A2142G/C, A2143G, T2182C) in the peptidyltransferase region of domain V of the 23S rRNA have been described as being associated with clarithromycin resistance. Therefore, the determination of clarithromycin resistance by pyrosequencing was evaluated. H. pylori from 81 gastric biopsies was cultured and clarithromycin resistance was determined by Etest, as well as by pyrosequencing technology (PSQ 96 system; Biotage). The respective mutations were set in relation to the MIC measured in μg ml−1 by Etest. In this study, point mutations in positions 2142 and 2143 were associated with clarithromycin resistance. Mutations in position 2182 did not contribute to clarithromycin resistance. In addition, from 22 out of the 81 biopsies, clarithromycin resistance was determined directly without culturing H. pylori to save additional time. Identical results were obtained as compared to resistance testing with pure H. pylori strains. All results obtained by pyrosequencing were evaluated by Sanger sequencing. The data show that pyrosequencing to detect point mutation is a fast and reliable method for determining clarithromycin resistance in H. pylori, and provides the same results as the Etest.

Pyrosequencing™ of a recA gene variable region for Burkholderia cepacia complex genomovar identification

We developed an assay to identify Burkholderia cepacia complex genomovars by Pyrosequencing of a variable recA gene segment. Fifteen reference strains and 30 clinical isolates of B. cepacia complex were sequenced. Full 77-base pair target sequences were obtained from 44 of the 45 isolates, and BLAST queries of the sequences correctly identified the genomovar of these 44 isolates. Three Burkholderia multivorans isolates were identified as B. multivorans/Burkholderia ambifaria, indicating that additional identification methods may be needed for some B. multivorans strains.

Detection of azithromycin resistance in Treponema pallidum by real-time PCR

We describe a real-time PCR assay for the discrimination of azithromycin-resistant and -susceptible strains of Treponema pallidum. This assay is rapid and allows for as many as 30 clinical specimens to be analyzed simultaneously without the need for DNA sequencing.

Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications

Pyrosequencing is a relatively new method for real-time nucleotide sequencing. It has rapidly found applications in DNA sequencing, genotyping, single nucleotide polymorphism analysis, allele quantification and whole-genome sequencing within the areas of microbiology, clinical genetics and pharmacogenetics. It is fast becoming a real alternative to the traditional Sanger sequencing method although, at present, read lengths are normally limited to approximately 70 nucleotides. The pyrosequencing method involves four main stages: first, target DNA is amplified using PCR; second, double-stranded DNA is converted to single-stranded DNA templates; third, oligonucleotide primers are hybridized to a complementary sequence of interest; and, finally, the pyrosequencing reaction itself, in which a reaction mixture of enzymes and substrates catalyses the synthesis of complementary nucleotides. Data are shown as a collection of signal peaks in a pyrogram. Pyrosequencing is increasingly used for bacterial detection, identification and typing, and, recently, a commercial system became available for the identification of bacterial isolates. Pyrosequencing can also be partially or fully automated, thus enabling the high-throughput analysis of samples. Wider use of pyrosequencing may occur in the future if longer nucleotide reads are made possible, which will enable its expansion into larger nucleotide sequencing such as multilocus sequence typing and whole-genome sequencing.

Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of VITEK 2

Alpha-hemolytic streptococci are very difficult to identify by phenotypic methods. In this study, a pyrosequencing method for the identification of streptococcal species based on two variable regions of the 16S rRNA gene is described. Almost all studied streptococcal species (n = 51) represented by their type strains could be differentiated except for some closely related species of the Streptococcus bovis or S. salivarius group. The pyrosequencing results of alpha-hemolytic streptococci isolated from blood (n = 99) or from the normal pharyngeal microbiota (n = 25) were compared to the results obtained by the VITEK 2 with GP card (bioMérieux, Marcy l'Etoile, France). As expected, the results of the two methods did not completely agree, but 93 (75.0%) of the isolates assigned to the same streptococcal group by both methods and 57 (46.0%) reached consistent results at the species level. However, 10 strains remained unidentified by VITEK 2, and 4 isolates could not be assigned to any streptococcal group by pyrosequencing. Identification of members of the S. mitis and S. sanguinis groups proved difficult for both methods. Furthermore, the pyrosequencing analysis revealed great sequence variation, since only 43 (32.3%) of the 133 isolates analyzed by pyrosequencing had sequences identical to a type strain. The variation was greatest in the pharyngeal isolates, slightly lower in the blood culture isolates, and nonexistent in invasive pneumococcal isolates (n = 17) that all had the S. pneumoniae type strain sequence. The resolution of the results obtained by the two methods is impeded by the lack of a proper gold standard.

Identification of CTX-M-type extended-spectrum-beta-lactamase genes using real-time PCR and pyrosequencing

CTX-M extended-spectrum beta-lactamases (ESBLs) are increasingly prevalent worldwide among Escherichia coli bacteria, mostly in community-acquired urinary tract infections. Finding a fast and reliable technique for identification of CTX-M enzymes is becoming a challenge for the microbiology laboratory. A fast real-time PCR amplification technique, using degenerated primers specific for all the bla(CTX-M) alleles, coupled to real-time pyrosequencing was developed. The five CTX-M groups were unambiguously identified by pyrosequencing a 13-bp DNA region. Further sequencing of an additional 16-bp region allowed further division into subgroups. Phylogenetic trees constructed with the entire bla(CTX-M) genes and with both pyrosequenced regions (29 bp) gave similar results, suggesting that this technique, termed the real-time detection and sequencing method, has a powerful discriminatory ability. This high-throughput technique has been evaluated by screening 48 ESBL-producing E. coli isolates recovered from the Bicêtre hospital (France) in 2004. Forty-four of these strains were CTX-M positive by real-time PCR detection and direct pyrosequencing of the PCR products, which identified CTX-M-15 as the main CTX-M-type beta-lactamase. Pulsed-field gel electrophoresis analysis of these strains revealed that several clones, of which one CTX-M-15-positive clone was predominant (60%), were identified both in nosocomial and in community-acquired isolates. The combination of real-time PCR with pyrosequencing represents a powerful tool for epidemiological studies of CTX-M producers. This assay has the potential to be used in a diagnostic laboratory since up to 96 bacterial isolates may be screened in less than 3 h.

Pyrosequencing as a rapid tool for identification of GES-type extended-spectrum beta-lactamases

A pyrosequencing technique was used for identification of extended-spectrum beta-lactamases (ESBLs) of GES type. These beta-lactamases are isolated increasingly emerging in gram-negative bacteria worldwide. This rapid and reliable identification method is interesting, since GES variants, including not only expanded-spectrum cephalosporins but also carbapenems, cephamycins, and monobactams, are the only ESBLs that possess different hydrolysis profiles.

Rapid detection of rifampin resistance in Mycobacterium tuberculosis by Pyrosequencing technology

We developed an assay for rapid detection of rifampin resistance in Mycobacterium tuberculosis based on Pyrosequencing technology, involving a technique for real-time sequencing. A 180-bp region of the rpoB gene was amplified in clinical isolates of both rifampin-resistant and -susceptible M. tuberculosis. The PCR products were subjected to Pyrosequencing analysis using four different sequencing primers in four overlapping reactions. These four sequencing reactions covered the 81-bp region where > 96% of the mutations associated with rifampin resistance are located. The results were compared to those obtained with two other molecular methods, the line probe assay and cycle sequencing, and the phenotypic BACTEC method. The genotypic determination methods all detected the mutations that previously have been correlated with rifampin resistance. In addition, Pyrosequencing analysis and the two other molecular methods found additional mutations within the rpoB gene in phenotypically susceptible strains. We found that Pyrosequencing technology, in particular, offers high accuracy, short turnaround time, and a potentially high throughput in detection of rifampin resistance in M. tuberculosis.

Streptococcus pneumoniae isolates resistant to telithromycin

The telithromycin susceptibility of 210 erythromycin-resistant pneumococci was tested with the agar diffusion method. Twenty-six erm(B)-positive isolates showed heterogeneous resistance to telithromycin, which was manifested by the presence of colonies inside the inhibition zone. When these cells were cultured and tested, they showed stable, homogeneous, and high-level resistance to telithromycin.

Erythromycin and clindamycin resistance in group B streptococcal clinical isolates

Erythromycin (EM) and clindamycin (CM) susceptibility testing was performed on 222 clinical isolates of group B Streptococcus. A multiplex PCR assay was used to detect the ermB, ermTR, and mefA/E antibiotic resistance genes. These results were compared to the phenotypes as determined by the standard EM/CM double disk diffusion assay.

Prevalence and molecular genetics of macrolide resistance among Streptococcus pneumoniae isolates collected in Finland in 2002

The prevalence and mechanisms of macrolide resistance among 1,007 clinical pneumococcal isolates collected in Finland were investigated. Of these, 217 (21.5%) were resistant to erythromycin and 11% to clindamycin. Among the erythromycin-resistant isolates, mef(E) was present in 95 isolates (44%), mef(A) was present in 12 isolates (6%), and erm(B) was present in 90 isolates (41%). A double mechanism, mef(E) and erm(B), was detected in five isolates (2%). Ribosomal mutation was detected in 14 (6%) macrolide-resistant isolates in which no other determinant was found. Based on the telithromycin MICs, two groups of isolates were formed: 83.3% of the isolates belonged to a major group for which the telithromycin MIC range was < or =0.008 to 0.063 microg/ml, and 16.7% belonged to a minor group for which the telithromycin MIC range was 0.125 to 8 microg/ml. All except three isolates in the minor population carried a macrolide resistance gene.

Characterization of Macrolide-Resistant Campylobacter coli Isolates from Food-Producing Animals on Farms Across Japan during 2004

We investigated the susceptibilities against 7 antimicrobial agents in Campylobacter jejuni and C. coli isolates from food-producing animals in 2004. In comparison with the results of past surveillance, no significant difference was observed in resistance rates against all of the antimicrobials tested in Campylobacter isolates. However, slight increase of erythromycin (EM) resistance was found in C. coli isolates from pigs. We examined the mutation of the 23S rRNA gene and their susceptibilities against azithromycin, tylosin, and lincomycin in 44 EM-resistant isolates and 28 susceptible isolates of porcine origin. All the EM-resistant isolates contained A2075G in the 23S rRNA gene and showed cross-resistance to azithromycin, tylosin, and lyncomycin.

An investigation of the molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter

The molecular mechanisms contributing to high-level erythromycin resistance in Campylobacter jejuni and Campylobacter coli isolates were investigated. The A2075G mutation in the 23S rRNA target genes was identified in all high-level erythromycin-resistant isolates. A number of amino acid substitutions together with insertions and deletions were identified in the corresponding genes encoding L4 and L22 ribosomal proteins both of resistant and susceptible isolates. Amino acid substitutions identified in the resistant strains were located outside regions known to be altered in these proteins. The efflux pump inhibitor L-phenylalanine-L-arginine-beta-naphthylamide (PAbetaN) increased the susceptibility to erythromycin in one of four isolates displaying high-level erythromycin resistance, and reduced the minimal inhibitory concentration displayed by an erythromycin-susceptible C. coli isolate. The A2075G mutation in the 23S rRNA appeared to be the main contributor to high-level erythromycin resistance in Campylobacter. Other mutations/amino acid substitutions found in the 50S ribosomal subunit encoding proteins L4 and L22 do not appear to be linked to the high-level erythromycin-resistant phenotype. Active efflux contributes to the intrinsic resistance to erythromycin in Campylobacter and may contribute to high-level resistance in some isolates.

Molecular detection of antibiotic resistance: when and where?

Antibiotic resistance is a key issue affecting public health, and diagnostic bacteriology laboratories are essential for prompt recognition of resistant isolates. Determination of susceptibility or resistance using phenotypic tests is a 'gold standard' against which newer technologies are compared in terms of performance, cost and ease of use. Molecular methods for detecting resistance are myriad, and are used widely in academia and in reference laboratories, but gaining a significant foothold in diagnostic laboratories is proving more difficult. However, if used widely in a diagnostic setting, these techniques would impact more directly on patient care and would be valuable infection control tools, e.g. by rapidly confirming patients colonized by resistant bacteria. The cost of molecular assays may be considered prohibitive, and this is compounded by the daunting variety of proprietary platforms available; most diagnostic laboratories would prefer to invest their capital and to train their staff in a single versatile technology. In a market that has no clear leader, many laboratories are understandably reluctant to gamble on making the correct choice. If molecular detection of resistance is to achieve wide acceptance, manufacturers must broaden the repertoires of their technologies, develop more off-the-shelf applications with in-built quality control, and make them suitable for laboratory personnel with no specialist expertise in molecular biology.

Biological counterstrike: antibiotic resistance mechanisms of Gram-positive cocci

The development of antibiotic resistance by bacteria is an evolutionary inevitability, a convincing demonstration of their ability to adapt to adverse environmental conditions. Since the emergence of penicillinase-producing Staphylococcus aureus in the 1940s, staphylococci, enterococci and streptococci have proved themselves adept at developing or acquiring mechanisms that confer resistance to all clinically available antibacterial classes. The increasing problems of methicillin-resistant S. aureus and coagulase-negative staphylococci (MRSA and MRCoNS), glycopeptide-resistant enterococci and penicillin-resistant pneumococci in the 1980s, and recognition of glycopeptide-intermediate S. aureus in the 1990s and, most recently, of fully vancomycin-resistant isolates of S. aureus have emphasised our need for new anti-Gram-positive agents. Antibiotic resistance is one of the major public health concerns for the beginning of the 21st century. The pharmaceutical industry has responded with the development of oxazolidinones, lipopeptides, injectable streptogramins, ketolides, glycylcyclines, second-generation glycopeptides and novel fluoroquinolones. However, clinical use of these novel agents will cause new selective pressures and will continue to drive the development of resistance. This review describes the various antibiotic resistance mechanisms identified in isolates of staphylococci, enterococci and streptococci, including mechanisms of resistance to recently introduced anti-Gram-positive agents.