Mutations within therplDGene of Linezolid-Nonsusceptible Streptococcus pneumoniae Strains Isolated in the United States

ABSTRACTThree invasiveStreptococcus pneumoniaestrains nonsusceptible to linezolid were isolated in the United States between 2001 and 2012 from the CDC's Active Bacterial Core surveillance. Linezolid binds ribosomal proteins where structural changes within its target site may confer resistance. Our study identified mutations and deletions near the linezolid binding pocket of two of these strains within therplDgene, which encodes ribosomal protein L4. Mutations in the 23S rRNA alleles or therplVgene were not detected.

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Linezolid Surveillance Results for the United States (LEADER Surveillance Program 2014)

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02803-15 ◽

2016 ◽

Vol 60 (4) ◽

pp. 2273-2280 ◽

Cited By ~ 51

Author(s):

Robert K. Flamm ◽

Rodrigo E. Mendes ◽

Patricia A. Hogan ◽

Jennifer M. Streit ◽

James E. Ross ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Streptococcus Pneumoniae ◽

Ribosomal Proteins ◽

The United States ◽

23S Rrna ◽

Surveillance Program ◽

Coagulase Negative Staphylococci ◽

Content Type ◽

Mrsa Strains ◽

Viridans Group Streptococci

ABSTRACTThelinezolidexperience andaccuratedetermination ofresistance (LEADER) surveillance program has monitored linezolid activity, spectrum, and resistance since 2004. In 2014, a total of 6,865 Gram-positive pathogens from 60 medical centers from 36 states were submitted. The organism groups evaluated wereStaphylococcus aureus(3,106), coagulase-negative staphylococci (CoNS; 797), enterococci (855),Streptococcus pneumoniae(874), viridans group streptococci (359), and beta-hemolytic streptococci (874). Susceptibility testing was performed by reference broth microdilution at the monitoring laboratory. Linezolid-resistant isolates were confirmed by repeat testing. PCR and sequencing were performed to detect mutations in 23S rRNA, L3, L4, and L22 proteins and acquired genes (cfrandoptrA). The MIC50/90forStaphylococcus aureuswas 1/1 μg/ml, with 47.2% of isolates being methicillin-resistantStaphylococcus aureus. Linezolid was active against allStreptococcus pneumoniaestrains and beta-hemolytic streptococci with a MIC50/90of 1/1 μg/ml and against viridans group streptococci with a MIC50/90of 0.5/1 μg/ml. Among the linezolid-nonsusceptible MRSA strains, one strain harboredcfronly (MIC, 4 μg/ml), one harbored G2576T (MIC, 8 μg/ml), and one containedcfrand G2576T with L3 changes (MIC, ≥8 μg/ml). Among CoNS, 0.75% (six isolates) of all strains demonstrated linezolid MIC results of ≥4 μg/ml. Five of these were identified asStaphylococcus epidermidis, four of which containedcfrin addition to the presence of mutations in the ribosomal proteins L3 and L4, alone or in combination with 23S rRNA (G2576T) mutations. Six enterococci (0.7%) were linezolid nonsusceptible (≥4 μg/ml; five with G2576T mutations, including one with an additionalcfrgene, and one strain withoptrAonly). Linezolid demonstrated excellent activity and a sustained susceptibility rate of 99.78% overall.

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Detection of a Newcfr-Like Gene,cfr(B), in Enterococcus faecium Isolates Recovered from Human Specimens in the United States as Part of the SENTRY Antimicrobial Surveillance Program

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01473-15 ◽

2015 ◽

Vol 59 (10) ◽

pp. 6256-6261 ◽

Cited By ~ 81

Author(s):

Lalitagauri M. Deshpande ◽

Deborah S. Ashcraft ◽

Heather P. Kahn ◽

George Pankey ◽

Ronald N. Jones ◽

...

Keyword(s):

United States ◽

Enterococcus Faecium ◽

Ribosomal Proteins ◽

Medical Center ◽

The United States ◽

Gene Location ◽

Rrna Genes ◽

23S Rrna ◽

Surveillance Program ◽

Content Type

ABSTRACTTwo linezolid-resistantEnterococcus faeciumisolates (MICs, 8 μg/ml) from unique patients of a medical center in New Orleans were included in this study. Isolates were initially investigated for the presence of mutations in the V domain of 23S rRNA genes and L3, L4, and L22 ribosomal proteins, as well ascfr. Isolates were subjected to pulsed-field gel electrophoresis (just one band difference), and one representative strain was submitted to whole-genome sequencing. Gene location was also determined by hybridization, andcfrgenes were cloned and expressed in aStaphylococcus aureusbackground. The two isolates had one out of six 23S rRNA alleles mutated (G2576T), had wild-type L3, L4, and L22 sequences, and were positive for acfr-like gene. The sequence of the protein encoded by thecfr-like gene was most similar (99.7%) to that found inPeptoclostridium difficile, which shared only 74.9% amino acid identity with the proteins encoded by genes previously identified in staphylococci and non-faeciumenterococci and was, therefore, denominated Cfr(B). When expressed inS. aureus, the protein conferred a resistance profile similar to that of Cfr. Two copies ofcfr(B) were chromosomally located and embedded in a Tn6218similar to thecfr-carrying transposon described inP. difficile.This study reports the first detection ofcfrgenes inE. faeciumclinical isolates in the United States and characterization of a newcfrvariant,cfr(B).cfr(B) has been observed in mobile genetic elements inE. faeciumandP. difficile, suggesting potential for dissemination. However, further analysis is necessary to access the resistance levels conferred bycfr(B) when expressed in enterococci.

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Macrolide-Resistant Mycoplasma pneumoniae in the United States as Determined from a National Surveillance Program

Journal of Clinical Microbiology ◽

10.1128/jcm.00968-19 ◽

2019 ◽

Vol 57 (11) ◽

Cited By ~ 9

Author(s):

K. B. Waites ◽

A. Ratliff ◽

D. M. Crabb ◽

L. Xiao ◽

X. Qin ◽

...

Keyword(s):

United States ◽

Clinical Significance ◽

Mycoplasma Pneumoniae ◽

The United States ◽

Antimicrobial Treatment ◽

23S Rrna ◽

Surveillance Program ◽

National Surveillance ◽

Radiographic Findings ◽

Content Type

ABSTRACT There are sparse data to indicate the extent that macrolide-resistant Mycoplasma pneumoniae (MRMp) occurs in the United States or its clinical significance. Between 2015 and 2018, hospitals in 8 states collected and stored respiratory specimens that tested positive for M. pneumoniae and sent them to the University of Alabama at Birmingham, where real-time PCR was performed for detection of 23S rRNA mutations known to confer macrolide resistance. MRMp was detected in 27 of 360 specimens (7.5%). MRMp prevalence was significantly higher in the South and East (18.3%) than in the West (2.1%). A2063G was the predominant 23S rRNA mutation detected. MICs for macrolide-susceptible M. pneumoniae (MSMp) were ≤0.008 μg/ml, whereas MICs for MRMp were 16 to 32 μg/ml. Patients with MRMp infection were more likely to have a history of immunodeficiency or malignancy. Otherwise, there were no other significant differences in the clinical features between patients infected with MRMp and those infected with MSMp, nor were there any differences in radiographic findings, hospitalization rates, viral coinfections, the mean duration of antimicrobial treatment, or clinical outcomes. There was no significant change in MRMp incidence over time or according to age, sex, race/ethnicity, or status as an inpatient or an outpatient. Patients with MRMp were more likely to have received a macrolide prior to presentation, and their treatment was more likely to have been changed to a fluoroquinolone after presentation. This is the first national surveillance program for M. pneumoniae in the United States. Additional surveillance is needed to assess the clinical significance of MRMp and to monitor changes in MRMp prevalence.

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Molecular Testing for Mycoplasma genitalium in the United States: Results from the AMES Prospective Multicenter Clinical Study

Journal of Clinical Microbiology ◽

10.1128/jcm.01125-19 ◽

2019 ◽

Vol 57 (11) ◽

Cited By ~ 9

Author(s):

Charlotte A. Gaydos ◽

Lisa E. Manhart ◽

Stephanie N. Taylor ◽

Rebecca A. Lillis ◽

Edward W. Hook ◽

...

Keyword(s):

United States ◽

Clinical Study ◽

Reference Method ◽

Mycoplasma Genitalium ◽

The United States ◽

23S Rrna ◽

Molecular Testing ◽

Content Type ◽

Vaginal Swabs ◽

Multicenter Clinical Study

ABSTRACT A prospective multicenter clinical study involving subjects from 21 sites across the United States was conducted to validate the performance of a new in vitro diagnostic nucleic acid amplification test (NAAT) for the detection of Mycoplasma genitalium. Seven urogenital specimen types (n = 11,556) obtained from 1,778 females, aged 15 to 74 years, and 1,583 males, aged 16 to 82 years, were tested with the Aptima Mycoplasma genitalium assay, an investigational transcription-mediated amplification (TMA) NAAT for the detection of M. genitalium 16S rRNA. Infected status for enrolled subjects was established using results obtained from testing either self-collected vaginal swab or clinician-collected male urethral swab specimens with a composite reference method consisting of three transcription-mediated amplification NAATs targeting unique regions of M. genitalium 16S or 23S rRNA. M. genitalium prevalence was 10.2% in females and 10.6% in males; prevalence was high in both symptomatic and asymptomatic subjects for both sexes. Compared to the subject infected status standard, the investigational test had sensitivity and specificity estimates, respectively, of 98.9% and 98.5% for subject-collected vaginal swabs, 92.0% and 98.0% for clinician-collected vaginal swabs, 81.5% and 98.3% for endocervical swabs, 77.8% and 99.0% for female urine, and 98.2% and 99.6% for male urethral swabs, 88.4% and 97.8% for self-collected penile meatal swabs, and 90.9% and 99.4% for male urine specimens. For all seven specimen types, within-specimen positive and negative agreements between the investigational test and the composite reference standard ranged from 94.2% to 98.3% and from 98.5 to 99.9%, respectively. These results provide clinical efficacy evidence for the first FDA-cleared NAAT for M. genitalium detection in the United States.

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Control of Ribosomal Protein L1 Synthesis in Mesophilic and Thermophilic Archaea

Genetics ◽

10.1093/genetics/152.4.1363 ◽

1999 ◽

Vol 152 (4) ◽

pp. 1363-1372

Author(s):

Alexander Kraft ◽

Christina Lutz ◽

Arno Lingenhel ◽

Peter Gröbner ◽

Wolfgang Piendl

Keyword(s):

Ribosomal Protein ◽

Binding Site ◽

Structural Gene ◽

Ribosomal Proteins ◽

Halophilic Archaea ◽

Peptide Bond ◽

Target Site ◽

Start Codon ◽

23S Rrna ◽

Ribosomal Protein Synthesis

Abstract The mechanisms for the control of ribosomal protein synthesis have been characterized in detail in Eukarya and in Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10, and MvaL12) of the mesophilic Methanococcus vannielii has been extensively investigated. As in Bacteria, regulation takes place at the level of translation. The regulator protein MvaL1 binds preferentially to its binding site on the 23S rRNA, and, when in excess, binds to the regulatory target site on its mRNA and thus inhibits translation of all three cistrons of the operon. The regulatory binding site on the mRNA, a structural mimic of the respective binding site on the 23S rRNA, is located within the structural gene about 30 nucleotides downstream of the ATG start codon. MvaL1 blocks a step before or at the formation of the first peptide bond of MvaL1. Here we demonstrate that a similar regulatory mechanism exists in the thermophilic M. thermolithotrophicus and M. jannaschii. The L1 gene is cotranscribed together with the L10 and L11 gene, in all genera of the Euryarchaeota branch of the Archaea studied so far. A potential regulatory L1 binding site located within the structural gene, as in Methanococcus, was found in Methanobacterium thermoautotrophicum and in Pyrococcus horikoshii. In contrast, in Archaeoglobus fulgidus a typical L1 binding site is located in the untranslated leader of the L1 gene as described for the halophilic Archaea. In Sulfolobus, a member of the Crenarchaeota, the L1 gene is part of a long transcript (encoding SecE, NusG, L11, L1, L10, L12). A previously suggested regulatory L1 target site located within the L11 structural gene could not be confirmed as an L1 binding site.

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Predominance of 23S rRNA Mutants among Non-Erm, Non-Mef Macrolide-Resistant Clinical Isolates of Streptococcus pneumoniae Collected in the United States in 1999-2000

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.7.3031-3033.2005 ◽

2005 ◽

Vol 49 (7) ◽

pp. 3031-3033 ◽

Cited By ~ 13

Author(s):

Todd A. Davies ◽

Karen Bush ◽

Daniel Sahm ◽

Alan Evangelista

Keyword(s):

United States ◽

Streptococcus Pneumoniae ◽

Gene Mutations ◽

The United States ◽

Clinical Isolates ◽

23S Rrna ◽

Surveillance Studies

ABSTRACT A total of 322 erythromycin-resistant pneumococci from TRUST 3 and TRUST 4 United States surveillance studies (1999-2000) were screened for 23S rRNA, L4, and L22 gene mutations. Nineteen isolates, two with mefA, had mutations at position 2058 or 2059 in 23S rRNA. Two had a 69GTG71-to-TPS substitution in L4; one of these also contained ermA.

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Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States

Applied and Environmental Microbiology ◽

10.1128/aem.00236-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3610-3618 ◽

Cited By ~ 35

Author(s):

Sokichi Shiro ◽

Syota Matsuura ◽

Rina Saiki ◽

Gilbert C. Sigua ◽

Akihiro Yamamoto ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Community Structure ◽

Geographical Distribution ◽

The United States ◽

23S Rrna ◽

Rrna Gene ◽

Scaling Analysis ◽

Internal Transcribed Spacer Region ◽

Content Type

ABSTRACTWe investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybeanRjgenotypes (non-Rj,Rj2Rj3, andRj4). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDABradyrhizobiumstrains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters wereBradyrhizobium japonicumBj123, in the northern United States, andBradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging toB. elkaniithan for the cluster belonging toB. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.

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Noninvasive Streptococcus pneumoniae Serotypes Recovered from Hospitalized Adult Patients in the United States in 2009 to 2012

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00182-15 ◽

2015 ◽

Vol 59 (9) ◽

pp. 5595-5601 ◽

Cited By ~ 17

Author(s):

Rodrigo E. Mendes ◽

Rosalind C. Hollingsworth ◽

Andrew Costello ◽

Ronald N. Jones ◽

Raul E. Isturiz ◽

...

Keyword(s):

United States ◽

Streptococcus Pneumoniae ◽

Conjugate Vaccine ◽

Pneumococcal Conjugate Vaccine ◽

Respiratory Infections ◽

Adult Population ◽

The United States ◽

Adult Patients ◽

Content Type ◽

Trends Over Time

ABSTRACTThis study was conducted to determine the serotype distribution and trends over time ofStreptococcus pneumoniaestrains associated with noninvasive infections among adult patients ≥18 years of age in the United States (2009 to 2012). A total of 2,927S. pneumoniaeisolates recovered from patients presenting with respiratory infections and obtained mainly (87.0%) from lower respiratory tract specimens (sputum) were included. The levels of the 7-valent pneumococcal conjugate vaccine (PCV7) serotypes remained stable over the 4-year study period (4.6% to 5.5%;P= 0.953). Overall, 13-valent pneumococcal conjugate vaccine (PCV13) serotypes were identified in 32.7% of samples, declining from 33.7% to 35.5% in 2009 to 2011 to 28.2% in 2012 (P= 0.007), with a significant decrease in the levels of serotypes 7F (P= 0.013) and 6A (P= 0.010). The levels of 19A remained constant (15.8% to 17.1%) during 2009 to 2011, dropping to 12.2% in 2012 (P= 0.089). The prevalence of serotypes associated with the 23-valent pneumococcal polysaccharide vaccine (PPSV23), but not PCV13, remained generally stable; however, the prevalence of serotypes 15B and 15C (15B/15C) increased from 2.7% to 6.3% (P= 0.010). The proportion of nonvaccine serotypes increased gradually during the study period (P= 0.044), particularly for serotype 35B (from 3.6% in 2009 to 8.2% in 2012;P= 0.001). Nonsusceptibility rates for penicillin (susceptible breakpoint, ≤2 μg/ml) and clindamycin against PCV7 serotypes decreased over the period. These results suggest the emergence of indirect effects following introduction of PCV13 for infants and young children; continued surveillance is needed to assess the burden of PCV13 serotypes in the adult population after the implementation of age-based recommendations in the United States.

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In VitroActivity of Delafloxacin Tested against Isolates of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00941-16 ◽

2016 ◽

Vol 60 (10) ◽

pp. 6381-6385 ◽

Cited By ~ 22

Author(s):

Robert K. Flamm ◽

Paul R. Rhomberg ◽

Michael D. Huband ◽

David J. Farrell

Keyword(s):

United States ◽

Streptococcus Pneumoniae ◽

Haemophilus Influenzae ◽

Moraxella Catarrhalis ◽

The United States ◽

Gram Negative Bacteria ◽

Gram Positive ◽

Gram Negative ◽

Content Type

ABSTRACTDelafloxacin, an investigational anionic fluoroquinolone, is active against a broad range of Gram-positive and Gram-negative bacteria. In this study, 200Streptococcus pneumoniae(plus 30 levofloxacin-resistant isolates), 200Haemophilus influenzae, and 100Moraxella catarrhalisisolates selected primarily from the United States (2014) were tested against delafloxacin and comparator agents. Delafloxacin was the most potent agent tested. MIC50and MIC90values against allS. pneumoniaeisolates were 0.008 and 0.015 μg/ml. Delafloxacin susceptibility was not affected by β-lactamase status againstH. influenzaeandM. catarrhalis.

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Decreased Ceftriaxone Susceptibility in Emerging (35B and 6C) and Persisting (19A) Streptococcus pneumoniae Serotypes in the United States, 2011-2012: Ceftaroline Remains ActiveIn Vitroamong β-Lactam Agents

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02976-14 ◽

2014 ◽

Vol 58 (8) ◽

pp. 4923-4927 ◽

Cited By ~ 17

Author(s):

Rodrigo E. Mendes ◽

Donald Biek ◽

Ian A. Critchley ◽

David J. Farrell ◽

Helio S. Sader ◽

...

Keyword(s):

United States ◽

Streptococcus Pneumoniae ◽

The United States ◽

South Atlantic ◽

Surveillance Program ◽

Content Type ◽

South Central

ABSTRACTTotals of 8.7% (103/1,190) and 21.0% (249/1,190) of theStreptococcus pneumoniaeisolates recovered from specimens collected in the United States during the 2011-2012 AWARE (AssessingWorldwideAntimicrobialResistanceEvaluation) Surveillance Program were ceftriaxone nonsusceptible according to the CLSI (≤1 μg/ml for susceptible) and EUCAST (≤0.5 μg/ml for susceptible) criteria, respectively. Decreased susceptibility to ceftriaxone (MIC, 1 μg/ml) was frequently observed among serotypes 19A (51.4%; 128/249) and 35B (29.7%; 74/249), which were most often observed in the East South Central and South Atlantic U.S. Census regions. Ceftaroline (MIC50/90, 0.12/0.25 μg/ml) remained active (≥96.8% susceptible) when tested against these less susceptible isolates.

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