Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.

Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for Staphylococcus aureus, the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC (P = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) (P < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.

Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission.

BACKGROUND: In order to study the micro-epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) effectively, the molecular typing method used must be able to distinguish between different MRSA strains. Pulsed-field gel electrophoresis (PFGE) can detect small genetic differences but is limited in its potential to distinguish isolates within a major lineage. Whole-genome sequencing (WGS) provides sufficient resolution to support or exclude links between otherwise indistinguishable isolates, but lacks the practical utility of conventional typing methods. AIM: To explore the utility of WGS in a hierarchical approach with PFGE to help establish possible sources of MRSA cross-transmission in the intensive care setting. METHODS: Possible transmission routes from donor to recipient via the hands of staff, the air or environmental surfaces were identified. Focused molecular typing used PFGE to explore these transmission hypotheses. WGS was applied when an acquisition event involved a common PFGE pulsotype. FINDINGS: Thirty-eight of the 78 acquisition events could not be explored as clinical isolates were not available. PFGE excluded all potential donors from 26 of the remaining 40 acquisition events, but did identify a probable source in 14 new colonizations. Within the hypotheses tested, PFGE supported links between patients occupying the same bay, the same bed space, adjacent isolation rooms and different wards. When a patient source was not identified, PFGE implicated the ward environment and the hands of staff. However, WGS disproved three of these transmission pathways. CONCLUSION: WGS can complement conventional typing methods by confirming or refuting possible MRSA transmission hypotheses. Epidemiological data are crucial in this process.

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.

Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.

In vitro activity of teicoplanin combined with colistin versus multidrug-resistant strains of Acinetobacter baumannii.

OBJECTIVES: Antimicrobial treatment of multidrug-resistant Acinetobacter baumannii (MDRAB) remains an important therapeutic challenge. With isolates resistant to all conventional agents now reported, clinicians are increasingly forced to turn to unorthodox combination treatments in the hope that these may be efficacious. Although a potent interaction between vancomycin and colistin has been demonstrated, there are concerns regarding the inherent toxicity of combining these agents in clinical practice. As teicoplanin has less nephrotoxic potential than vancomycin, we assessed whether a colistin/teicoplanin combination would have similar antimicrobial activities in vitro. METHODS: The antimicrobial activity of colistin alone and in combination with teicoplanin was assessed versus a collection of MDRAB belonging to a number of epidemic lineages present in the UK. Synergy studies were undertaken using microtitre plate chequerboard assays, an Etest agar dilution method and standard time-kill methodology. RESULTS: The combination of teicoplanin and colistin was bactericidal versus all of the strains tested. In chequerboard assays, fractional inhibitory concentration indices of <0.5 were obtained, consistent with significant in vitro synergy. Using the Etest method the MIC of teicoplanin fell from >256 mg/L to ≤2 mg/L in the presence of subinhibitory concentrations of colistin. CONCLUSIONS: Significant synergy was observed when colistin was combined with teicoplanin versus MDRAB in vitro. This may represent a useful therapeutic combination for the treatment of A. baumannii infections, especially when renal toxicity is a significant concern.

Modifications to CHROMagar Acinetobacter for improved selective growth of multi-drug resistant Acinetobacter baumannii.

Performance of CHROMagar Acinetobacter was assessed for the selective isolation and identification of Acinetobacter baumannii. The medium was effective in suppressing the growth of other Gram-positive and Gram-negative species while the addition of KPC supplement ensured growth of only carbapenem resistant A baumannii.

Polymicrobial necrotizing fasciitis involving enterobacteria producing CTX-M-15 extended-spectrum ß-lactamases.

Necrotizing fasciitis due to multiple Gram-negative organisms in a Nigerian patient is described. Morganella morganii and Citrobacter freundii carrying the CTX-M-15 extended-spectrum ß-lactamase gene were isolated, highlighting the emergence of this ß-lactamase in Western Africa and its successful spread amongst a wider range of members of the Enterobacteriaceae.

Potent synergy and sustained bactericidal activity of a vancomycin-colistin combination versus multidrug-resistant strains of Acinetobacter baumannii.

Multidrug-resistant Acinetobacter baumannii (MDRAB) presents an increasing challenge to health care. Although colistin has been used as a treatment of last resort, there is concern regarding its potential for toxicity and the emergence of resistance. The mechanism of action of colistin, however, raises the possibility of synergy with compounds that are normally inactive against Gram-negative organisms by virtue of the impermeability of the bacterial outer membrane. This study evaluated the effect of colistin combined with vancomycin on 5 previously characterized epidemic strains and 34 MDRAB clinical isolates by using time-kill assay, microdilution, and Etest methods. For all the isolates, significant synergy was demonstrated by at least one method, with reductions in the MIC of vancomycin from >256 µg/ml to ≤48 µg/ml for all strains after exposure to 0.5 µg/ml colistin. This raises the possibility of the clinical use of this combination for infections due to MDRAB, with the potential for doses lower than those currently used.

Novel variants of the Smqnr family of quinolone resistance genes in clinical isolates of Stenotrophomonas maltophilia.

BACKGROUND: Recent analysis of Stenotrophomonas maltophilia has identified a novel family of resistance genes (Smqnr) encoding pentapeptide repeat proteins, which confer low-level resistance to quinolones. This study describes further novel variants present in clinical isolates of S. maltophilia and investigates their effect on resistance to a number of quinolones in an Escherichia coli host. METHODS: PCR for Smqnr alleles was carried out on a selection of S. maltophilia from clinical specimens, and amplicons were cloned and transformed in E. coli TOP10 cells. Transformed colonies carrying the plasmid were tested for susceptibility to a range of quinolones by MIC determination. DNA sequences were determined and translated peptide sequences compared with known SmQnr sequences. RESULTS: Thirteen isolates were found to contain Smqnr alleles, of which six corresponded to previously identified Smqnr sequences, while seven were novel variants. Increases in quinolone MICs compared with wild-type E. coli TOP10 were seen for all strains transformed with Smqnr alleles. CONCLUSIONS: There is considerable diversity within Smqnr alleles. S. maltophilia may be a significant reservoir for the dissemination of quinolone resistance elements to Enterobacteriaceae.

Failure of the MicroScan WalkAway system to detect heteroresistance to carbapenems in a patient with Enterobacter aerogenes bacteremia.

We report the failure of the automated MicroScan WalkAway system to detect carbapenem heteroresistance in Enterobacter aerogenes. Carbapenem resistance has become an increasing concern in recent years, and robust surveillance is required to prevent dissemination of resistant strains. Reliance on automated systems may delay the detection of emerging resistance.

Evaluation of CHROMagar Acinetobacter for detection of enteric carriage of multidrug-resistant Acinetobacter baumannii in samples from critically ill patients.

CHROMagar Acinetobacter was used to screen stool and perineal swabs for enteric carriage of multidrug-resistant Acinetobacter baumannii in samples from critically ill patients. Results were compared with a molecular assay resulting in sensitivity and specificity of culture compared to PCR of 91.7% and 89.6%, respectively.

A review of clinical and microbiological outcomes following treatment of infections involving multidrug-resistant Acinetobacter baumannii with tigecycline.

OBJECTIVES: Multidrug-resistant Acinetobacter baumannii (MRAB) is an increasing problem in UK hospitals, with many strains now resistant to all available antibiotics except polymyxins. Tigecycline has been used for the treatment of MRAB as it demonstrates activity in vitro, but there are limited data on its clinical efficacy in Gram-negative infections, especially those involving the lower respiratory tract or bacteraemia. PATIENTS AND METHODS: A retrospective study of the clinical and microbiological outcomes of all patients treated with tigecycline for MRAB over an 18 month period was undertaken. RESULTS: Thirty-four patients received tigecycline for MRAB or polymicrobial infection involving MRAB. Twenty-three (68%) had a positive clinical outcome: microbiological clearance was demonstrated in 10 of these. The overall mortality was 41% (n = 14), with nine deaths directly attributable to sepsis. Three patients had episodes of Gram-negative bacteraemia while receiving treatment with tigecycline, with documented resistance occurring in one patient. Overall, the correlation between microbiological and clinical outcomes was poor. CONCLUSIONS: While tigecycline retains excellent in vitro activity against MRAB, its clinical efficacy remains uncertain. A prospective study, including the use of tigecycline in combination with other antimicrobial agents, should be undertaken to define its role in the treatment of MRAB.

The PYRIN domain: a member of the death domain-fold superfamily.

PYRIN domains were identified recently as putative protein-protein interaction domains at the N-termini of several proteins thought to function in apoptotic and inflammatory signaling pathways. The approximately 95 residue PYRIN domains have no statistically significant sequence homology to proteins with known three-dimensional structure. Using secondary structure prediction and potential-based fold recognition methods, however, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein-protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. An homology model of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1, a member of the Apaf-1/Ced-4 family of proteins, was constructed using the three-dimensional structures of the FADD and p75 neurotrophin receptor DDs, and of the Apaf-1 and caspase-9 CARDs, as templates. Validation of the model using a variety of computational techniques indicates that the fold prediction is consistent with the sequence. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction.

High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Application to the study of trypsin-inhibitor complexes and trypsinogen activation by NMR spectroscopy.

We describe here the high-level expression of bovine trypsinogen in E. coli, its refolding and activation to beta-trypsin, and the selective incorporation of (15)N-labeled alanine through supplementation of the growth medium. Using this procedure, we expressed (15)N-labeled S195A trypsinogens, both on a wild-type and on a D189S background, in amounts suitable for NMR spectroscopy. 2D [(1)H-(15)N]-HSQC NMR was used to follow conformational changes upon activation of trypsinogen and formation of noncovalent complexes between S195A or S195A/D189S trypsin and protein proteinase inhibitors of different structural families and different sizes, as well as to examine the effects of introduction of the D189S mutation. Spectra of good quality were obtained for both trypsins alone and in complexes of increasing size with the proteinase inhibitors BPTI (total molecular mass 31 kDa), SBTI (total molecular mass 44 kDa), and the serpin alpha(1)-proteinase inhibitor Pittsburgh (alpha(1)PI Pittsburgh) (total molecular mass 69 kDa). Assignments of alanines 55 and 56, close to the active site histidine, and of alanine 195, present in the S195A variant used for most of the studies, were made by mutagenesis. These three alanines, together with two others, probably close to the S1 specificity pocket, were very sensitive to complex formation. In contrast, the remaining 10 alanines were invariant in chemical shift in all 3 of the noncovalent complexes formed, reflecting the conservation of structure in complexes with BPTI and SBTI known from X-ray crystal structures, but also indicating that there is no change in backbone conformation for the noncovalent complex with alpha(1)PI, for which there is no crystal structure. This was true both for S195A and for S195A/D189S trypsins. This high-level expression and labeling approach will be of great use for solution NMR studies on trypsin-serpin complexes, as well as for structural and mechanistic studies on trypsin variants.

Formation of a noncovalent serpin-proteinase complex involves no conformational change in the serpin. Use of 1H-15N HSQC NMR as a sensitive nonperturbing monitor of conformation.

A structural understanding of the nature and scope of serpin inhibition mechanisms has been limited by the inability so far to crystallize any serpin-proteinase complex. We describe here the application of [(1)H-(15)N]-HSQC NMR on uniformly and residue-selectively (15)N-labeled serpin alpha(1)-proteinase inhibitor (Pittsburgh variant with stabilizing mutations) to provide a nonperturbing and exquisitely sensitive means of probing the conformation of the serpin alone and in a noncovalent complex with inactive, serine 195-modified, bovine trypsin. The latter should be a good model both for the few examples of reversible serpin-proteinase complexes and for the initial Michaelis-like complex formed en route to irreversible covalent inhibition. Cleavage of the reactive center loop, with subsequent insertion into beta-sheet A, caused dramatic perturbation of most of the NMR cross-peaks. This was true for both the uniformly labeled and alanine-specifically labeled samples. The spectra of uniformly or leucine- or alanine-specifically labeled alpha(1)-proteinase inhibitor in noncovalent complex with unlabeled inactive trypsin gave almost no detectable chemical shift changes of cross-peaks, but some general increase in line width. Residue-specific assignments of the four alanines in the reactive center loop, at P12, P11, P9, and P4, allowed specific examination of the behavior of the reactive center loop. All four alanines showed higher mobility than the body of the serpin, consistent with a flexible reactive center loop, which remained flexible even in the noncovalent complex with proteinase. The three alanines near the hinge point for insertion showed almost no chemical shift perturbation upon noncovalent complex formation, while the alanine at P4 was perturbed, presumably by interaction with the active site of bound trypsin. Reporters from both the body of the serpin and the reactive center loop therefore indicate that noncovalent complex formation involves no conformational change in the body of the serpin and only minor perturbation of the reactive center loop in the region which contacts proteinase. Thus, despite the large size of serpin and serpin-proteinase complex, 45 and 69 kDa respectively, NMR provides a very sensitive means of probing serpin conformation and mobility, which should be applicable both to noncovalent and to covalent complexes with a range of different proteinases, and probably to other serpins.

Soft tissue surgery in the oral and maxillofacial region.

The practice of dentistry is most often perceived as the treatment of the hard tissues of the oral region, specifically the teeth and jaws. However, there are many disorders and conditions involving surgical treatment of the soft tissues that extend to the adjacent and associated structures of the oral and maxillofacial surgery region.

The kappa opioid nalbuphine produces gender- and dose-dependent analgesia and antianalgesia in patients with postoperative pain.

Nalbuphine, pentazocine, and butorphanol, mixed agonist/antagonist opioids that induce analgesia by acting predominantly at kappa opioid receptors, have recently been shown in single-dose studies to have greater analgesic efficacy in women than in men. In the current experiments, the first placebo controlled dose response study of opioid analgesic efficacy that examines for gender differences, nalbuphine (5, 10, or 20 mg) and placebo were evaluated in 62 men and 69 women for the treatment of moderate to severe postoperative pain following extraction of impacted wisdom teeth. In a randomized, open injection, double blind experimental design, pain intensity was recorded on a 10 cm visual analog scale (VAS) immediately prior to drug administration (baseline) and at 20 min intervals thereafter. Although responses to placebo were similar in men and women, for all doses of nalbuphine women exhibited significantly greater analgesic response than men, compatible with our previous results. Unexpectedly, men receiving the 5 mg dose of nalbuphine experienced significantly greater pain than those receiving placebo; only the 20 mg dose of nalbuphine in men produced significant analgesia compared to placebo. While a similar antianalgesic effect was not observed in women, only the 10 mg dose of nalbuphine produced significant analgesia compared to placebo. These results suggest that the optimal analgesic dose of nalbuphine for women is lower than the highest dose that can be safely administered. In contrast, the antianalgesic effect of nalbuphine suggests avoidance of its routine use for postoperative analgesia in men until further studies clarify this issue. Because gender differences in other mixed kappa agonists/antagonists (i.e. pentazocine and butorphanol) have previously been shown, these results may generally apply to this class of opioid analgesics.

Benzodiazepine mediated antagonism of opioid analgesia.

Activation of supraspinal gamma-aminobutyric acid-A (GABAA) receptors is known to result in antagonism of opioid analgesia. Since benzodiazepines enhance the action of GABA at GABAA receptors, we hypothesized that administration of these agents for preoperative sedation might antagonize the analgesic effects of opioids administered postoperatively. If so, then administration of the benzodiazepine antagonist flumazenil should enhance postoperative morphine analgesia. In a double-blind, placebo-controlled study of patients who received a preoperatively administered benzodiazepine (diazepam) for sedation and a postoperatively administered opioid (morphine) for analgesia, we investigated opioid-benzodiazepine interactions affecting postoperative dental pain. We found that flumazenil significantly enhanced morphine analgesia consistent with the hypothesis that the preoperatively administered benzodiazepine exerts an ongoing antianalgesic effect. In addition, we followed these patients over the first and second postoperative days to determine if there were differences between the drug groups in post-discharge pain, analgesic consumption, or side-effects. Participants receiving flumazenil reported significantly less post-discharge nausea and used significantly less ibuprofen. Since post-discharge pain levels were not significantly different, these results suggest that the patients receiving flumazenil required less analgesic medication to achieve a comparable level of pain control. In summary, our results indicate that the benzodiazepine antagonist flumazenil enhances morphine analgesia and decreases post-discharge side-effects as well as post-discharge need for analgesic medication.

Kappa-opioids produce significantly greater analgesia in women than in men.

Sex differences in human responses to nociceptive stimuli and painful pathological conditions have generally indicated that women report higher pain levels or exhibit less tolerance than men for given stimulus intensities (reviewed in ref. 1 and 2). However, studies have not evaluated sex differences in analgesic responses. We recently reported that the opioid agonist-antagonist pentazocine, which acts predominantly at kappa-receptors, produced significantly better postoperative analgesia in females than in males in patients who underwent surgery for the removal of their third molars (wisdom teeth). In the current study, we evaluated the hypothesis that this sex difference is a characteristic of kappa-opioid agonism. In order to determine whether there are sex differences associated with kappa-opioid agonism, the analgesic efficacy of two other predominantly kappa-opioid analgesics, nalbuphine and butorphanol; was compared in males and females who underwent surgery for the removal of third molar teeth. We found that both nalbuphine and butorphanol produced significantly greater analgesia in females as compared with males. Considering our earlier findings, we conclude that kappa-opioid analgesia is greater in females than in males, probably reflecting a difference in kappa-opioid-activated endogenous pain modulating circuits.