Twelve clarithromycin-resistant Helicobacter pylori isolates (100% of resistant isolates examined) from seven different patients each contained an A-->G transition mutation within a conserved loop of 23S rRNA. A-->G transition mutations at positions cognate with Escherichia coli 23S rRNA positions 2058 and 2059 were identified. Clarithromycin-susceptible H. pylori isolates from 14 different patients displayed no polymorphisms in a conserved loop within domain V of 23S rRNA. The study is the first to report mutations in H. pylori associated with resistance to an antimicrobial agent used in established peptic ulcer treatment regimens.

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.

Fifty-four of 59 (91.5%) clarithromycin-resistant isolates of Helicobacter pylori from different patients possessed either the A2143G (formerly A2058G) or the A2144G (formerly A2059G) mutation in the gene encoding 23S rRNA. The A2143G mutation was significantly more likely to occur in isolates with MICs exceeding 64 mg/L (65% versus 30% with the A2144G mutation; P = 0.01). The majority (26 of 31; 83.9%) of isolates with the A2143G mutation had MICs exceeding 64 mg/L. Peptic ulcer disease recurred in a substantial proportion of patients infected with H. pylori strains containing either the A2143G or the A2144G mutation.

Background Staphylococcus aureus is among the most common human pathogens, with therapy complicated by the epidemic spread of methicillin-resistant Staphylococcus aureus (MRSA). Methods The SENTRY Antimicrobial Surveillance Program evaluated the in vitro activity of >20 antimicrobials against 191 460 clinical S. aureus isolates collected from 427 centers in 45 countries from 1997 to 2016. Each center contributed isolates and clinical data for consecutive episodes of bacteremia, pneumonia in hospitalized patients, urinary tract infection, and skin and skin structure infection. Results Overall, 191 460 S. aureus isolates were collected, of which 77 146 (40.3%) were MRSA, varying geographically from 26.8% MRSA in Europe to 47.0% in North America. The highest percentage of MRSA was in nosocomial isolates from patients aged >80 years. Overall, MRSA occurrences increased from 33.1% in 1997–2000 to a high of 44.2% in 2005–2008, then declined to 42.3% and 39.0% in 2009–2012 and 2013–2016, respectively. S. aureus bacteremia had a similar trend, with nosocomial and community-onset MRSA rates peaking in 2005–2008 and then declining. Vancomycin activity against S. aureus remained stable (minimum inhibitory concentration [MIC]90 of 1 mg/L and 100% susceptibility in 2016; no increase over time in isolates with a vancomycin MIC >1 mg/L). Several agents introduced during the surveillance period exhibited in vitro potency against MRSA. Conclusions In a large global surveillance program, the rise of MRSA as a proportion of all S. aureus peaked a decade ago and has declined since, consistent with some regional surveillance program reports. Vancomycin maintained high activity against S. aureus, and several newer agents exhibited excellent in vitro potencies.

This is the first report to show that A-C transversion mutations at position 2143 can confer resistance to clarithromycin in H. pylori and further support the role that mutations at position 2143 play in conferring macrolide resistance in H. pylori.

Recent work has shown that the efflux genes in Streptococcus pneumoniae that are responsible for acquired macrolide resistance can be distinguished as either mef(E) or mef(A). The genetic elements on which mef(A) and mef(E) are found also carry an open reading frame (ORF) that is 56% homologous to msr(A) in Staphylococcus. The prevalence of mef(A/E) and of the msr-like ORF [msr(D)] was evaluated in 153 mef ؉ S. pneumoniae clinical isolates collected in North America, Europe, Africa, and Asia from 1997 to 2002. Clinical isolates were screened with PCR primers specific for either mef(A) or mef(E) and for msr(D). mef(A), mef(E), and msr(D) were cloned from mef ؉ strains and transformed into a susceptible, competent strain of S. pneumoniae. The transformants were tested for antimicrobial susceptibilities and efflux pump induction. The results of this work demonstrated that mef(A) is more often isolated in parts of Europe, with some incidence in Canada, and that the msr-like gene alone can confer the efflux phenotype.Recent work has shown that the efflux genes in Streptococcus pneumoniae responsible for acquired macrolide resistance can be distinguished as either mef(E) or mef(A) (6). Originally, mef in S. pneumoniae had been labeled mef(E), while mef(A) had been reserved for Streptococcus pyogenes. The two mef genes show a 90% sequence homology between the start and stop codons, but they can be distinguished with specific primer sets. Due to sequence similarity, these genes were merged under mef(A) by Roberts et al. (16). However, for clarity in the present discussion, the genes will be referred to as mef(A) and mef(E). Whether there are sufficient differences in the epidemiology and/or function of the genes to return to separate designations has not been determined.The mef genes are carried on transposons comprised of additional open reading frames (ORFs). Both of these genetic elements also carry an ORF downstream from mef that is 56% homologous to the coding region of msr(A) in Staphylococcus. The upstream region of the msr-like gene in Streptococcus lacks the leader peptide found in the Staphylococcus msr(A) gene (17). The msr-like homologs found associated with either mef(A) or mef(E) have 98% sequence homology. Although the msr-like homolog is believed to be a part of the efflux system, it has not been previously studied independently in Streptococcus.mef(A) in S. pneumoniae has been previously described in Italy (6). Given our worldwide clinical isolate collection, we studied the prevalence rates of mef(A) versus that of mef(E) in S. pneumoniae isolates collected in Europe, Asia, and North and South America. The prevalence and geographic distributions of mef(A) versus mef(E) in 153 clinical isolates of mef ϩ S. pneumoniae from six regions of the world were evaluated in this study. The prevalence and function of the msr homolog were also evaluated. This gene has been given the designation msr(D) (M. Roberts, personal communication) and was shown to be capable of independent function when cloned and expressed i...

We have developed a rapid PCR-oligonucleotide ligation assay that can discriminate single base substitutions that are associated with clarithromycin resistance in Helicobacter pylori. Susceptible isolates were wild type at positions 2143 and 2144 (cognate to 2058 and 2059 in Escherichia coli), while 93% of the resistant isolates contained A-to-G mutations at either position and 7% of the isolates contained A-to-C mutations at position 2143. In addition, the MIC for 86% of the resistant isolates with an A2143 mutation was > or = 64 micrograms per ml, and that for 89% of the resistant isolates with an A2144 mutation was < or = 32 micrograms per ml.

The activity of ceftazidime-avibactam and many comparator agents was determined against various resistant subsets of organisms selected among 36,380 and 7,868 isolates. The isolates were consecutively collected from 94 U.S. hospitals, and all isolates were tested for susceptibility by reference broth microdilution methods in a central monitoring laboratory (JMI Laboratories). isolates resistant to carbapenems (CRE) and/or ceftazidime-avibactam (MIC ≥ 16 μg/ml) were evaluated for the presence of genes encoding extended-spectrum β-lactamases and carbapenemases. Ceftazidime-avibactam inhibited >99.9% of all at the susceptible breakpoint of ≤8 μg/ml and was active against multidrug-resistant (MDR; = 2,953; MIC, 0.25/1 μg/ml; 99.2% susceptible), extensively drug-resistant (XDR; = 448; MIC, 0.5/2 μg/ml; 97.8% susceptible), and CRE ( = 513; MIC, 0.5/2 μg/ml; 97.5% susceptible) isolates. Only 82.2% of MDR ( = 2,953) and 64.2% of ceftriaxone-nonsusceptible ( = 1,063) isolates were meropenem susceptible. Among (22.2% ceftazidime nonsusceptible), 99.8% of the isolates, including 99.3% of the ceftazidime-nonsusceptible isolates, were ceftazidime-avibactam susceptible. Only 23 of 36,380 (0.06%) isolates were ceftazidime-avibactam nonsusceptible, including 9 metallo-β-lactamase producers and 2 KPC-producing strains with porin alteration; the remaining 12 strains showed negative results for all β-lactamases tested. Ceftazidime-avibactam showed potent activity against (MIC, 2/4 μg/ml; 97.1% susceptible), including MDR (MIC, 4/16 μg/ml; 86.5% susceptible) isolates, and inhibited 71.8% of isolates nonsusceptible to meropenem, piperacillin-tazobactam, and ceftazidime ( = 628). In summary, ceftazidime-avibactam demonstrated potent activity against a large collection ( = 44,248) of contemporary Gram-negative bacilli isolated from U.S. patients, including organisms resistant to most currently available agents, such as CRE and meropenem-nonsusceptible .