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In May 2022, the first case of monkeypox virus (MPXV) infection in the United States in the current global outbreak was identified. As part of the public health and health care facility response, a contact tracing and exposure investigation was done.To describe the contact tracing, exposure identification, risk stratification, administration of postexposure prophylaxis (PEP), and exposure period monitoring for contacts of the index patient, including evaluation of persons who developed symptoms possibly consistent with MPXV infection.Contact tracing and exposure investigation.Multiple health care facilities and community settings in Massachusetts.Persons identified as contacts of the index patient.Contact notification, risk stratification, and symptom monitoring; PEP administration in a subset of contacts.Epidemiologic and clinical data collected through standard surveillance procedures at each facility and then aggregated and analyzed.There were 37 community and 129 health care contacts identified, with 4 at high risk, 49 at intermediate risk, and 113 at low or uncertain risk. Fifteen health care contacts developed symptoms during the monitoring period. Three met criteria for MPXV testing, with negative results. Two community contacts developed symptoms. Neither met criteria for MPXV testing, and neither showed disease progression consistent with monkeypox. Among 4 persons with high-risk exposures offered PEP, 3 elected to receive PEP. Among 10 HCP with intermediate-risk exposures for which PEP was offered as part of informed clinical decision making, 2 elected to receive PEP. No transmissions were identified at the conclusion of the 21-day monitoring period, despite the delay in recognition of monkeypox in the index patient.Descriptions of exposures are subject to recall bias, which affects risk stratification.In a contact tracing investigation involving 166 community and health care contacts of a patient with monkeypox, no secondary cases were identified.None.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection related to initial infection. We aimed to evaluate the characteristics of SARS-CoV-2 reinfection and persistent RNA detection using independent genomic, clinical, and laboratory assessments.MethodsAll individuals at a large academic medical center who underwent a SARS-CoV-2 nucleic acid amplification test (NAAT) ≥45 days after an initial positive test, with both tests between 14 March and 30 December 2020, were analyzed for potential reinfection. Inclusion criteria required having ≥2 positive NAATs collected ≥45 days apart with a cycle threshold (Ct) value ResultsAmong 1569 individuals with repeat SARS-CoV-2 testing ≥45 days after an initial positive NAAT, 65 (4%) met cohort inclusion criteria. Viral genomic analysis characterized mutations present and was successful for 14/65 (22%) subjects. Six subjects had genomically supported reinfection, and 8 subjects had genomically supported persistent RNA detection. Compared to viral genomic analysis, clinical and laboratory assessments correctly distinguished reinfection from persistent RNA detection in 12/14 (86%) subjects but missed 2/6 (33%) genomically supported reinfections.ConclusionsDespite good overall concordance with viral genomic analysis, clinical and Ct value-based assessments failed to identify 33% of genomically supported reinfections. Scaling-up genomic analysis for clinical use would improve detection of SARS-CoV-2 reinfections.

Many data-driven patient risk stratification models have not been evaluated prospectively. We performed and compared the prospective and retrospective evaluations of 2 Clostridioides difficile infection (CDI) risk-prediction models at 2 large academic health centers, and we discuss the models’ robustness to data-set shifts.

A large, ongoing multicountry outbreak of human monkeypox has the potential to cause considerable morbidity and mortality. Therapeutics for the treatment of smallpox, a related Orthopoxvirus, may be used and affect the natural history of monkeypox. We present 3 patients from our hospitals treated with tecovirimat, a pan-Orthopoxvirus inhibitor currently available under an expanded access investigational new drug protocol for monkeypox.

Background Isolation of hospitalized persons under investigation (PUIs) for coronavirus disease 2019 (COVID-19) reduces nosocomial transmission risk. Efficient evaluation of PUIs is needed to preserve scarce healthcare resources. We describe the development, implementation, and outcomes of an inpatient diagnostic algorithm and clinical decision support system (CDSS) to evaluate PUIs. Methods We conducted a pre-post study of CORAL (COvid Risk cALculator), a CDSS that guides frontline clinicians through a risk-stratified COVID-19 diagnostic workup, removes transmission-based precautions when workup is complete and negative, and triages complex cases to infectious diseases (ID) physician review. Before CORAL, ID physicians reviewed all PUI records to guide workup and precautions. After CORAL, frontline clinicians evaluated PUIs directly using CORAL. We compared pre- and post-CORAL frequency of repeated severe acute respiratory syndrome coronavirus 2 nucleic acid amplification tests (NAATs), time from NAAT result to PUI status discontinuation, total duration of PUI status, and ID physician work hours, using linear and logistic regression, adjusted for COVID-19 incidence. Results Fewer PUIs underwent repeated testing after an initial negative NAAT after CORAL than before CORAL (54% vs 67%, respectively; adjusted odd ratio, 0.53 [95% confidence interval, .44–.63]; P Conclusions CORAL is an efficient and effective CDSS to guide frontline clinicians through the diagnostic evaluation of PUIs and safe discontinuation of precautions.

Background Cutaneous mold infections commonly result from an array of traumatic injuries that involve direct inoculation of contaminated soil into wounds. Here, we explored the use of antimicrobial blue light (aBL; 405 nm wavelength) and the combination of aBL with quinine hydrochloride (aBL + Q-HCL) for the treatment of cutaneous mold infections. Methods Efficacy of aBL and aBL + Q-HCL in killing clinically important pathogenic molds (Aspergillus fumigatus, Aspergillus flavus, and Fusarium oxyprorum) was investigated. Ultraperformance liquid chromatography identified and quantified endogenous porphyrins in the mold conidia. Finally, a mouse model of dermabrasion wound infected with a bioluminescent variant of A. fumigatus was developed to investigate the efficacy of aBL in treating cutaneous mold infections. Results We demonstrated that mold conidia are tolerant to aBL, but Q-HCL enhances efficacy. Transmission electron microscopy revealed intracellular damage by aBL. aBL + Q-HCL resulted in intracellular and cell wall damage. Porphyrins were observed in all mold strains, with A. fumigatus having the highest concentration. aBL and aBL + Q-HCL effectively reduced the burden of A. fumigatus within an established dermabrasion infection and limited recurrence posttreatment. Conclusions aBL and aBL + Q-HCL may offer a novel approach for the treatment of mold infections.

SARS-CoV-2 reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection related to initial infection. We aimed to evaluate the characteristics of SARS-CoV-2 reinfection and persistent RNA detection using independent genomic, clinical, and laboratory assessments.All individuals at a large academic medical center who underwent a SARS-CoV-2 nucleic acid amplification test (NAAT) ≥ 45 days after an initial positive test, with both tests between March 14th and December 30th, 2020, were analyzed for potential reinfection. Inclusion criteria required having ≥2 positive NAATs collected ≥45 days apart with a cycle threshold (Ct) value35 at repeat testing. For each included subject, likelihood of reinfection was assessed by viral genomic analysis of all available specimens with a Ct value35, structured Ct trajectory criteria, and case-by-case review by infectious diseases physicians.Among 1,569 individuals with repeat SARS-CoV-2 testing ≥45 days after an initial positive NAAT, 65 (4%) met cohort inclusion criteria. Viral genomic analysis characterized mutations present, and was successful for 14/65 (22%) subjects. Six subjects had genomically-supported reinfection and eight subjects had genomically-supported persistent RNA detection. Compared to viral genomic analysis, clinical and laboratory assessments correctly distinguished reinfection from persistent RNA detection in 12/14 (86%) subjects but missed 2/6 (33%) genomically-supported reinfections.Despite good overall concordance with viral genomic analysis, clinical and Ct value-based assessments failed to identify 33% of genomically-supported reinfections. Scaling-up genomic analysis for clinical use would improve detection of SARS-CoV-2 reinfections.

We describe an approach to the evaluation and isolation of hospitalized persons under investigation (PUIs) for coronavirus disease 2019 (COVID-19) at a large US academic medical center. Only a small proportion (2.9%) of PUIs with 1 or more repeated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) nucleic acid amplification tests (NAATs) after a negative NAAT were diagnosed with COVID-19.

Objective:To describe an investigation into 5 clinical cases of carbapenem-resistantAcinetobacter baumannii(CRAB).Design:Epidemiological investigation supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates.Setting:A tertiary-care academic health center in Boston, Massachusetts.Patients or participants:Individuals identified with CRAB clinical infections.Methods:A detailed review of patient demographic and clinical data was conducted. Clinical isolates underwent phenotypic antimicrobial susceptibility testing and WGS. Infection control practices were evaluated, and CRAB isolates obtained through environmental sampling were assessed by WGS. Genomic relatedness was measured by single-nucleotide polymorphism (SNP) analysis.Results:Four clinical cases spanning 4 months were linked to a single index case; isolates differed by 1–7 SNPs and belonged to a single cluster. The index patient and 3 case patients were admitted to the same room prior to their development of CRAB infection, and 2 case patients were admitted to the same room within 48 hours of admission. A fourth case patient was admitted to a different unit. Environmental sampling identified highly contaminated areas, and WGS of 5 environmental isolates revealed that they were highly related to the clinical cluster.Conclusions:We report a cluster of highly resistantAcinetobacter baumanniithat occurred in a burn ICU over 5 months and then spread to a separate ICU. Two case patients developed infections classified as community acquired under standard epidemiological definitions, but WGS revealed clonality, highlighting the risk of burn patients for early-onset nosocomial infections. An extensive investigation identified the role of environmental reservoirs.

Objective Create and validate diverticulitis surgical site infection prediction scale. Background Surgical site infections cause significant morbidity after colorectal surgery. An infection prediction scale could target infection prevention bundles to high-risk patients. Methods Prospectively collected National Surgical Quality Improvement Program and electronic medical record data obtained on diverticulitis colectomy patients across a Healthcare Network-wide Colorectal Surgery Collaborative (5 hospitals). Patients with and without surgical site infections were compared. Predictive variables were identified using logistic regression model; model estimates obtained through 1000 bootstrap replications for scale validation. Results A total of 1737 colectomies were performed (2010-2016): mean age 59.9 years (SD 12.7), 56.4% female; 93.4% Caucasian; smokers 16.3%, diabetics 7.7%, steroid use 6.0%. Two hundred thirty-one (13.3%) were presented to operating room emergently and 138 (7.9%) with abscess at time of disease admission. Two hundred ninety-six patients underwent Hartman procedures, and 113 (6.5%) received diverted primary anastomosis. Average length of stay was 6.9 days (standard deviation 7.01), 30-day mortality was 1.5%, anastomotic leak rate was 3.1%. Twenty-one percent of patients (n = 366) developed a surgical site infection. Several predictors for infection were identified: obesity (body mass index >30), advanced age (>70 years), diabetes mellitus, preoperative abscess, open surgery, emergent operations, and prolonged operations (>3 h). Creation of protected anastomosis in emergent settings was associated with increased infection rates. Presence of more than 5 risk factors was associated with infection rates of 45.8% (c = 0.69). Conclusions Patients with diverticulitis have high surgical site infection rates due to nonmodifiable risk factors. Our Prediction and Enaction of Prevention Treatments Trigger scale can risk stratify patients for targeting surgical site infection prevention bundles and outcomes risk adjustments.

BackgroundCarbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.MethodsTo overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem susceptible Enterobacterales, isolated from patients from four U.S. hospitals over nearly five years.ResultsOur CRE collection comprised a diverse range of species, lineages and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events.Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.ConclusionsCollectively, the framework we developed provides a clearer, high resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

Background Antimicrobial resistance is a significant concern to public health, and there is a pressing need to develop novel antimicrobial therapeutic modalities. Methods In this study, we investigated the capacity for quinine hydrochloride (Q-HCL) to enhance the antimicrobial effects of antimicrobial blue light ([aBL] 405 nm wavelength) against multidrug-resistant (MDR) Gram-negative bacteria in vitro and in vivo. Results Our findings demonstrated the significant improvement in the inactivation of MDR Pseudomonas aeruginosa and Acinetobacter baumannii (planktonic cells and biofilms) when aBL was illuminated during Q-HCL exposure. Furthermore, the addition of Q-HCL significantly potentiated the antimicrobial effects of aBL in a mouse skin abrasion infection model. In addition, combined exposure of aBL and Q-HCL did not result in any significant apoptosis when exposed to uninfected mouse skin. Conclusions In conclusion, aBL in combination with Q-HCL may offer a novel approach for the treatment of infections caused by MDR bacteria.

Background Through improved understanding of the structure-activity relationship attributes of fluoroquinolones, molecule development has improved efficacy, safety, and tolerability of the class. Adverse events (AEs) associated with the fluoroquinolones are well defined and a prospective part of the development process. However, not all fluoroquinolones have the same AE profile with different substitutions on the core molecule resulting in differences in side effects and spectrum of activity. Unique structural attributes of delafloxacin (DLX) may differentiate its AE profile compared to other fluoroquinolones. This analysis compared the incidence of AEs between DLX and vancomycin/aztreonam across two phase 3 ABSSSI studies in order to provide a broader overview of DLX safety. Methods Safety events occurring in all subjects in the pivotal phase 3 trials were pooled to provide a broad overview of DLX safety. Results DLX was safe and well-tolerated in the pooled phase 3 ABSSSI trial population of 741 subjects. Treatment-emergent AEs (TEAEs) were seen in the DLX group versus the comparator group at 45.1% and 47.7%, respectively. Most were mild or moderate in severity. Treatment-related TEAEs were reported in the DLX group versus the comparator group at rates of 22.1% and 26.1%, respectively. Conclusions Available data show DLX is well tolerated in both intravenous and oral formulation for the treatment of ABSSSI and does not appear to be associated with increased risk of AEs associated with other fluoroquinolones. It remains important to monitor for potential AEs that have been observed with other fluoroquinolones.

The worldwide distribution of qnr genes found on plasmids and their presence on the chromosomes of aquatic bacteria, such as Vibrio vulnificus, one of the suspected sources, suggests an origin before the development of synthetic quinolones. However, their native function remains unknown. Previous work indicated that expression of qnrVv in V. vulnificus was induced by cold shock. To investigate its role further, we constructed single in-frame deletion mutants in qnrVv and cspA (the gene for cold shock protein) and a double mutant in qnrVv and cspA in V. vulnificus ATCC 17562 to evaluate the response to different environmental conditions and stresses and to exposure to various DNA-damaging agents. We found that qnrVv is involved in resistance to ciprofloxacin, levofloxacin, and mitomycin C and in the cold shock response in V. vulnificus. Moreover, ΔqnrVv and ΔcspA mutants showed slower growth when they were treated with bile salts at 37°C and then shifted to 15°C (cold shock) without bile salts in the medium, with the effect being stronger in the double mutant. This transition may mimic what happens when V. vulnificus is ingested into the gastrointestinal tract and released in its natural environment. Cold shock and bile salts induced the expression of cspA and DNA gyrase and topoisomerase IV genes. However, no induction was found in the ΔqnrVv mutant, suggesting that the qnrVv gene is involved in the response to DNA damage and nucleic acid secondary structure.

Among hospitalized persons under investigation for coronavirus disease 2019 (COVID-19), more repeated severe acute respiratory syndrome coronavirus 2 nucleic acid amplification tests (NAATs) after a negative NAAT were positive from lower than from upper respiratory tract specimens (1.9% vs 1.0%, P = .033). Lower respiratory testing should be prioritized among patients displaying respiratory symptoms with moderate-to-high suspicion for COVID-19 after 1 negative upper respiratory NAAT.

The Qnr pentapeptide repeat proteins interact with DNA gyrase and protect it from quinolone inhibition. The two external loops, particularly the larger loop B, of Qnr proteins are essential for quinolone protection of DNA gyrase. The specific QnrB1 interaction sites on DNA gyrase are not known. In this study, we investigated the interaction between GyrA and QnrB1 using site-specific photo-cross-linking of QnrB1 loop B combined with mass spectrometry. We found that amino acid residues 286 to 298 on the tower domain of GyrA interact with QnrB1 and play a key role in QnrB1 protection of gyrase from quinolone inhibition. Alanine replacement of arginine at residue 293 and a small deletion of amino acids 286 to 289 of GyrA resulted in a decrease in the QnrB1-mediated increase in quinolone MICs and also abolished the QnrB1 protection of purified DNA gyrase from ciprofloxacin inhibition.

The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortium’s amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.

Antimicrobial resistance is a concern to public health, with methicillin resistant Staphylococcus aureus (MRSA) being particularly important. Blue light at 405 nm has demonstrated efficacy for the treatment of localized infections. With respect to MRSA, aBL is not effective enough to be developed into a stand-alone therapy. Findings demonstrated the antioxidant properties of the S. aureus pigment, staphyloxanthin (STX). We hypothesized that the efficacy of 405 nm light on MRSA may improve with STX photolysis using 460 nm light. We report an approach that exploits the STX photolysis effect of 460 nm light to sensitize MRSA to 405 nm light.

The Staphylococcus aureus Tet38 membrane protein has distinct functions, including drug efflux and host cell attachment and internalization mediated by interaction with host cell CD36. Using structural modeling and site-directed mutagenesis, we identified key amino acids involved in different functions. Tet38, a member of the major facilitator superfamily, is predicted to have 14 transmembrane segments (TMS), 6 cytoplasmic loops, and 7 external loops. Cysteine substitutions of arginine 106 situated at the junction of TMS 4 and external loop L2, and glycine 151 of motif C on TMS 5, resulted in complete or near-complete (8- to 16-fold) reductions in Tet38-mediated resistance to tetracycline, with minimal to no effect on A549 host cell internalization. In contrast, a three-amino-acid deletion, F(411)P(412)G(413), in external loop L7 situated between TMS 13 and 14 led to a decrease of 4-fold in S. aureus internalization by A549 cells and a partial effect on tetracycline resistance (4-fold reduction). A three-amino-acid deletion, D(38)D(39)L(40), in external loop L1 situated between TMS-1 and TMS-2, had a similar partial effect on tetracycline resistance but did not affect cell internalization. Using an Ni column retention assay, we showed further that the L7, but not the L1, deletion impaired binding to CD36. Thus, the L7 domain of Tet38 is key for interaction with CD36 and host cell internalization, and amino acids R(106) and G(151) (TMSs 4 and 5) are particularly important for tetracycline resistance without affecting internalization.

Phylogenetics of superspreading One important characteristic of coronavirus epidemiology is the occurrence of superspreading events. These are marked by a disproportionate number of cases originating from often-times asymptomatic individuals. Using a rich sequence dataset from the early stages of the Boston outbreak, Lemieux et al. identified superspreading events in specific settings and analyzed them phylogenetically (see the Perspective by Alizon). Using ancestral trait inference, the authors identified several importation events, further investigated the context and contribution of particular superspreading events to the establishment of local and wider SARS-CoV-2 transmission, and used viral phylogenies to describe sustained transmission. Science , this issue p. eabe3261 ; see also p. 574

Background Concerns about false-negative (FN) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification tests (NAATs) have prompted recommendations for repeat testing if suspicion for coronavirus disease 2019 (COVID-19) infection is moderate to high. However, the frequency of FNs and patient characteristics associated with FNs are poorly understood. Methods We retrospectively reviewed test results from 15 011 adults who underwent ≥1 SARS-CoV-2 NAATs; 2699 had an initial negative NAAT and repeat testing. We defined FNs as ≥1 negative NAATs followed by a positive NAAT within 14 days during the same episode of illness. We stratified subjects with FNs by duration of symptoms before the initial FN test (≤5 days versus >5 days) and examined their clinical, radiologic, and laboratory characteristics. Results Sixty of 2699 subjects (2.2%) had a FN result during the study period. The weekly frequency of FNs among subjects with repeat testing peaked at 4.4%, coinciding with peak NAAT positivity (38%). Most subjects with FNs had symptoms (52 of 60; 87%) and chest radiography (19 of 32; 59%) consistent with COVID-19. Of the FN NAATs, 18 of 60 (30%) were performed early (ie, ≤1 day of symptom onset), and 18 of 60 (30%) were performed late (ie, >7 days after symptom onset) in disease. Among 17 subjects with 2 consecutive FNs on NP NAATs, 9 (53%) provided lower respiratory tract (LRT) specimens for testing, all of which were positive. Conclusions Our findings support repeated NAATs among symptomatic patients, particularly during periods of higher COVID-19 incidence. The LRT testing should be prioritized to increase yield among patients with high clinical suspicion for COVID-19.

Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro. Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam–β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.

Key Points Question What is the prevalence of antibiotic therapy for possible pneumonia in hospitalized patients despite clinical signs within the reference range? Findings In this cohort study of 12 273 patients treated for possible pneumonia in 4 hospitals, all cardinal signs for pneumonia were within reference ranges in 18.6% of patients with possible community-acquired pneumonia and 13.5% of patients with possible hospital-acquired pneumonia. Antibiotics were continued for 3 days or longer after all clinical signs were normal in 34.8% of patients treated for community-acquired pneumonia and 38.4% treated for hospital-acquired pneumonia. Meaning Findings of this study suggest that antibiotics are prescribed frequently for suspected pneumonia in patients with clinical signs within reference ranges and continued for 3 days or longer after clinical signs normalize; these findings suggest potential targets to improve prescribing., Importance Antibiotics are frequently prescribed for suspected pneumonia, but overdiagnosis is common and fixed regimens are often used despite randomized trials suggesting it is safe to stop antibiotics once clinical signs are normalizing. Objective To quantify potential excess antibiotic prescribing by characterizing antibiotic use relative to patients’ initial clinical signs and subsequent trajectories. Design, Setting, and Participants An observational cohort study was conducted in 2 tertiary and 2 community hospitals in Eastern Massachusetts. All nonventilated adult patients admitted between May 1, 2017, and July 1, 2018 (194 521 hospitalizations), were included. Main Outcomes and Measures Identification of all antibiotic starts for possible community-acquired pneumonia (CAP) or hospital-acquired pneumonia (HAP) per clinicians’ stated indications. Potential excess antibiotic prescribing was quantified by characterizing the frequency of patients in whom all clinical signs were within reference ranges on the first day of antibiotic therapy and by how long antibiotic therapy was continued after all clinical signs were normal, including postdischarge antibiotics. Results Among 194 521 hospitalizations, 9540 patients were treated for possible CAP (4574 [48.0%] women; mean [SD] age, 67.6 [17.0] years) and 2733 for possible HAP (1211 [44.3%] women; mean [SD] age, 66.7 [16.2] years). Temperature, respiratory rate, oxygen saturation, and white blood cell count were all within reference ranges on the first day of antibiotics in 1779 of 9540 (18.6%) episodes of CAP and 370 of 2733 (13.5%) episodes of HAP. Antibiotics were continued for 3 days or longer after all clinical signs were normal in 3322 of 9540 (34.8%) episodes of CAP and 1050 of 2733 (38.4%) episodes of HAP. Up to 24 978 of 71 706 (34.8%) antibiotic-days prescribed for possible pneumonia may have been unnecessary. Conclusions and Relevance In this study, almost one-fifth of hospitalized patients treated for pneumonia did not have any of the cardinal signs of pneumonia on the first day of treatment and antibiotics were continued for 3 days or longer after all signs were normal in more than a third of patients. These observations suggest substantial opportunities to improve antibiotic prescribing., This cohort study examines the prescribing rates and duration of antibiotic therapy in patients with possible pneumonia whose clinical signs are within the reference ranges.

With the effectiveness of antimicrobials declining as antimicrobial resistance continues to threaten public health, we must look to alternative strategies for the treatment of infections. In this study, we investigated an innovative, drug-free, dual-wavelength irradiation approach that combines 2 wavelengths of light, 460 nm and 405 nm, against methicillin-resistant Staphylococcus aureus (MRSA). MRSA was initially irradiated with 460-nm light (90–360 J/cm(2)) and subsequently irradiated with aliquots of 405-nm light (54–324 J/cm(2)). For in vivo studies, mouse skin was abraded and infected with approximately 10(7) CFUs of MRSA and incubated for 3 hours before irradiating with 460 nm (360 J/cm(2)) and 405 nm (342 J/cm(2)). Naive mouse skin was also irradiated to investigate apoptosis. We found that staphyloxanthin, the carotenoid pigment in MRSA cells, promoted resistance to the antimicrobial effects of 405-nm light. In addition, we found that the photolytic effect of 460-nm light on staphyloxanthin attenuated resistance of MRSA to 405-nm light killing. Irradiation of 460 nm alone did not elicit any antimicrobial effect on MRSA. In a proof-of-principle mouse skin abrasion infection model, we observed significant killing of MRSA using the dual-wavelength irradiation approach. However, when either wavelength of light was administered alone, no significant decrease in bacterial viability was observed. Moreover, exposure of the dual-wavelength irradiation to naive mouse skin did not result in any visible apoptosis. In conclusion, a dual-wavelength irradiation strategy may offer an innovative, effective, and safe approach for the treatment of skin infections caused by MRSA.

To describe an investigation into 5 clinical cases of carbapenem-resistant Acinetobacter baumannii (CRAB).Epidemiological investigation supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates.A tertiary-care academic health center in Boston, Massachusetts.Individuals identified with CRAB clinical infections.A detailed review of patient demographic and clinical data was conducted. Clinical isolates underwent phenotypic antimicrobial susceptibility testing and WGS. Infection control practices were evaluated, and CRAB isolates obtained through environmental sampling were assessed by WGS. Genomic relatedness was measured by single-nucleotide polymorphism (SNP) analysis.Four clinical cases spanning 4 months were linked to a single index case; isolates differed by 1-7 SNPs and belonged to a single cluster. The index patient and 3 case patients were admitted to the same room prior to their development of CRAB infection, and 2 case patients were admitted to the same room within 48 hours of admission. A fourth case patient was admitted to a different unit. Environmental sampling identified highly contaminated areas, and WGS of 5 environmental isolates revealed that they were highly related to the clinical cluster.We report a cluster of highly resistant Acinetobacter baumannii that occurred in a burn ICU over 5 months and then spread to a separate ICU. Two case patients developed infections classified as community acquired under standard epidemiological definitions, but WGS revealed clonality, highlighting the risk of burn patients for early-onset nosocomial infections. An extensive investigation identified the role of environmental reservoirs.

The prevalence and effects of inappropriate empirical antibiotic therapy for bloodstream infections are unclear. We aimed to establish the population-level burden, predictors, and mortality risk of in-vitro susceptibility-discordant empirical antibiotic therapy among patients with bloodstream infections.Our retrospective cohort analysis of electronic health record data from 131 hospitals in the USA included patients with suspected-and subsequently confirmed-bloodstream infections who were treated empirically with systemic antibiotics between Jan 1, 2005, and Dec 31, 2014. We included all patients with monomicrobial bacteraemia caused by common bloodstream pathogens who received at least one systemic antibiotic either on the day blood cultures were drawn or the day after, and for whom susceptibility data were available. We calculated the prevalence of discordant empirical antibiotic therapy-which was defined as receiving antibiotics on the day blood culture samples were drawn to which the cultured isolate was not susceptible in vitro-overall and by hospital type by using regression tree analysis. We used generalised estimating equations to identify predictors of receiving discordant empirical antibiotic therapy, and used logistic regression to calculate adjusted odds ratios for the relationship between in-hospital mortality and discordant empirical antibiotic therapy.21 608 patients with bloodstream infections received empirical antibiotic therapy on the day of first blood culture collection. Of these patients, 4165 (19%) received discordant empirical antibiotic therapy. Discordant empirical antibiotic therapy was independently associated with increased risk of mortality (adjusted odds ratio 1·46 [95% CI, 1·28-1·66]; p0·0001), a relationship that was unaffected by the presence or absence of resistance or sepsis or septic shock. Infection with antibiotic-resistant species strongly predicted receiving discordant empirical therapy (adjusted odds ratio 9·09 [95% CI 7·68-10·76]; p0·0001). Most incidences of discordant empirical antibiotic therapy and associated deaths occurred among patients with bloodstream infections caused by Staphylococcus aureus or Enterobacterales.Approximately one in five patients with bloodstream infections in US hospitals received discordant empirical antibiotic therapy, receipt of which was closely associated with infection with antibiotic-resistant pathogens. Receiving discordant empirical antibiotic therapy was associated with increased odds of mortality overall, even in patients without sepsis. Early identification of bloodstream pathogens and resistance will probably improve population-level outcomes.US National Institutes of Health, US Centers for Disease Control and Prevention, and US Agency for Healthcare Research and Quality.

qnr genes are found in aquatic bacteria and preceded the development of synthetic quinolones. Their natural functions are unknown. We evaluated the expression of chromosomal qnr in Vibrio species in response to environmental stresses and DNA damaging agents. Sub-inhibitory concentrations of quinolones, but not other DNA damaging agents, induced the expression of chromosomal qnr by more than five times in Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio mytili Cold shock also induced the expression of qnr in V. parahaemolyticus, V. vulnificus, and V. mytili, as well as qnrS1 in Escherichia coli qnrS1 induction by cold shock was not altered in ΔihfA or ΔihfB mutants or in a strain over-expressing dnaA, that otherwise directly modulate qnrS1 induction by ciprofloxacin. In contrast, qnrS1 induction by cold shock was reduced in a ΔcspA mutant in the cold shock regulon compared to the wild type. In conclusion, cold shock as well as quinolones induce chromosomal qnr in Vibrio species, and the related qnrS1 in E. coli.

OBJECTIVETo validate a system to detect ventilator associated events (VAEs) autonomously and in real time.DESIGNRetrospective review of ventilated patients using a secure informatics platform to identify VAEs (ie, automated surveillance) compared to surveillance by infection control (IC) staff (ie, manual surveillance), including development and validation cohorts.SETTINGThe Massachusetts General Hospital, a tertiary-care academic health center, during January–March 2015 (development cohort) and January–March 2016 (validation cohort).PATIENTSVentilated patients in 4 intensive care units.METHODSThe automated process included (1) analysis of physiologic data to detect increases in positive end-expiratory pressure (PEEP) and fraction of inspired oxygen (FiO2); (2) querying the electronic health record (EHR) for leukopenia or leukocytosis and antibiotic initiation data; and (3) retrieval and interpretation of microbiology reports. The cohorts were evaluated as follows: (1) manual surveillance by IC staff with independent chart review; (2) automated surveillance detection of ventilator-associated condition (VAC), infection-related ventilator-associated complication (IVAC), and possible VAP (PVAP); (3) senior IC staff adjudicated manual surveillance–automated surveillance discordance. Outcomes included sensitivity, specificity, positive predictive value (PPV), and manual surveillance detection errors. Errors detected during the development cohort resulted in algorithm updates applied to the validation cohort.RESULTSIn the development cohort, there were 1,325 admissions, 479 ventilated patients, 2,539 ventilator days, and 47 VAEs. In the validation cohort, there were 1,234 admissions, 431 ventilated patients, 2,604 ventilator days, and 56 VAEs. With manual surveillance, in the development cohort, sensitivity was 40%, specificity was 98%, and PPV was 70%. In the validation cohort, sensitivity was 71%, specificity was 98%, and PPV was 87%. With automated surveillance, in the development cohort, sensitivity was 100%, specificity was 100%, and PPV was 100%. In the validation cohort, sensitivity was 85%, specificity was 99%, and PPV was 100%. Manual surveillance detection errors included missed detections, misclassifications, and false detections.CONCLUSIONSManual surveillance is vulnerable to human error. Automated surveillance is more accurate and more efficient for VAE surveillance.Infect Control Hosp Epidemiol 2018;826–833

Hospitalized patients are assigned to available staffed beds based on patient acuity and services required. In hospitals with double-occupancy rooms, patients must be additionally matched by gender. Patients with methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococcus (VRE) must be bedded in single-occupancy rooms or cohorted with other patients with similar MRSA/VRE flags.We developed a discrete event simulation (DES) model of patient flow through an acute care hospital. Patients are matched to beds based on acuity, service, gender, and known MRSA/VRE colonization. Outcomes included time to bed arrival, length of stay, patient-bed acuity mismatches, occupancy, idle beds, acuity-related transfers, rooms with discordant MRSA/VRE colonization, and transmission due to discordant colonization.Observed outcomes were well-approximated by model-generated outcomes for time-to-bed arrival (6.7 v. 6.2 to 6.5 h) and length of stay (3.3 v. 2.9 to 3.0 days), with overlapping 90% coverage intervals. Patient-bed acuity mismatches, where patient acuity exceeded bed acuity and where patient acuity was lower than bed acuity, ranged from 0.6 to 0.9 and 8.6 to 11.1 mismatches per h, respectively. Values for observed occupancy, total idle beds, and acuity-related transfers compared favorably to model-predicted values (91% v. 86% to 87% occupancy, 15.1 v. 14.3 to 15.7 total idle beds, and 27.2 v. 22.6 to 23.7 transfers). Rooms with discordant colonization status and transmission due to discordance were modeled without an observed value for comparison. One-way and multi-way sensitivity analyses were performed for idle beds and rooms with discordant colonization.We developed and validated a DES model of patient flow incorporating MRSA/VRE flags. The model allowed for quantification of the substantial impact of MRSA/VRE flags on hospital efficiency and potentially avoidable nosocomial transmission.

Background: Whole-genome sequencing (WGS) is well established as a high-resolution method for measuring bacterial relatedness to better understand infection transmission in cases of healthcare-associated infections (HAIs). However, sequencing is still rarely used in HAI investigations due to a lack of access to computational analysis platforms with actionable turnaround times. Single-nucleotide polymorphism (SNP) analysis is typically used to determine bacterial relatedness. However, SNP-based methods often require a suite of bioinformatics tools that can be difficult to use and interpret without the expertise of a trained computational biologist. These obstacles become more significant in the case of prospective, real-time surveillance of HAIs, which can require the analysis of a large number of isolates. To enable the use of WGS for proactive determination of infection outbreaks, a rapid, automated method that can scale to large data sets is needed. Methods: Here, we demonstrate the capabilities of ksim, a novel automated algorithm to determine the clonality of bacterial samples using WGS. ksim measures the number of shared kmers (genomic subsequences of length k) between bacterial samples to determine their relatedness. ksim also filters out accessory genomic regions, such as plasmids, that can confound genetic relatedness estimates. We benchmarked the accuracy and speed of ksim relative to an SNP-based pipeline on simulated data sets (with sequencing reads generated in silico) and on 9 clinical-cluster data sets (6 publicly available and 3 real-time data sets from Massachusetts General Hospital [MGH]). We also used ksim to determine the relatedness of >5,000 historical clinical bacterial isolates from MGH, collected between 2015 and 2019. Results: ksim first preprocesses raw sequencing data to generate a common data structure, after which it computes the genomic distance between bacterial samples in ∼0.2 seconds in simple cases and in ∼4 seconds in complex cases when accessory genome filtering is required. In simulations across 5 species, ksim determined clonality (defined as ksim performance on 9 clinical HAI data sets demonstrated its sensitivity (99.4%) and specificity (90.8%) compared to an SNP-based pipeline. ksim efficiently analyzed >5,000 clinical samples from MGH and found previously unidentified transmission clusters. Conclusions:ksim shows promise for rapid clonality determination in HAI outbreaks and has the potential to scale to tens of thousands of samples. This method could enable infection control teams to use WGS for prospective outbreak detection via an automated computational pipeline without the need for specialized computational biology training.Funding: Day Zero Diagnostics and the NIH provided Funding: for this study.Disclosures: Mohamad Sater reports salary from Day Zero Diagnostics.

Background: Delayed or in vitro inactive empiric antibiotic therapy may be detrimental to survival in patients with bloodstream infections (BSIs). Understanding the landscape of delayed or discordant empiric antibiotic therapy (DDEAT) across different patient, pathogen, and hospital types, as well as by their baseline resistance milieu, may enable providers, antimicrobial stewardship programs, and policy makers to optimize empiric prescribing. Methods: Inpatients with clinically suspected serious infection (based on sampling of blood cultures and receiving systemic antibiotic therapy on the same or next day) found to have BSI were identified in the Cerner Healthfacts EHR database. Patients were considered to have received DDEAT when, on culture sampling day, they received either no antibiotic(s) or none that displayed in vitro activity against the pathogenic bloodstream isolate. Antibiotic-resistant phenotypes were defined by in vitro resistance to taxon-specific prototype antibiotics (eg, methicillin/oxacillin resistance in S. aureus) and were used to estimate baseline resistance prevalence encountered by the hospital. The probability of DDEAT was examined by bacterial taxon, by time of BSI onset, and by presence versus absence of antibiotic-resistance phenotypes, sepsis or septic shock, hospital type, and baseline resistance. Results: Of 26,036 assessable patients with a BSI at 131 US hospitals between 2005 and 2014, 14,658 (56%) had sepsis, 3,623 (14%) had septic shock, 5,084 (20%) had antibiotic-resistant phenotypes, and 8,593 (33%) received DDEAT. Also, 4,428 (52%) recipients of DDEAT received no antibiotics on culture sampling day, whereas the remaining 4,165 (48%) received in vitro discordant therapy. DDEAT occurred most often in S. maltophilia (87%) and E. faecium (80%) BSIs; however, 75% of DDEAT cases and 76% of deaths among recipients of DDEAT collectively occurred among patients with S. aureus and Enterobacteriales BSIs. For every 8 bacteremic patients presenting with septic shock, 1 patient did not receive any antibiotics on culture day (Fig. 1A). Patients with BSIs of hospital (vs community) onset were twice as likely to receive no antibiotics on culture day, whereas those with bloodstream pathogens displaying antibiotic-resistant (vs susceptible) phenotypes were 3 times as likely to receive in vitro discordant therapy (Fig. 1B). The median proportion of DDEAT ranged between 25% (14, 37%) in eight Conclusions: Delayed or in vitro discordant empiric antibiotic therapy is common among patients with BSI in US hospitals regardless of hospital size, teaching status, or local resistance patterns. Prompt empiric antibiotic therapy in septic shock and hospital-onset BSI needs more support. Reliable detection of S. aureus and Enterobacteriales bloodstream pathogens and their resistance patterns earlier with rapid point-of-care diagnostics may mitigate the population-level impact of DDEAT in BSI.Funding: This study was funded in part by the National Institutes of Health Clinical Center, National Institutes of Allergy and Infectious Diseases, National Cancer Institute (NCI contract no. HHSN261200800001E) and the Agency for Healthcare Research and Quality.Disclosures: None

In a previous study, mutants with enhanced ciprofloxacin resistance (Cip r ) were selected from Escherichia coli J53/pMG252 carrying qnrA1 . Strain J53 Cip r 8-2 showed an increase in the copy number and transcription level of qnrA1 . We sequenced the plasmids on Illumina and MinION platforms.

Driven by applications in chemical sensing, biological imaging and material characterisation, Raman spectroscopies are attracting growing interest from a variety of scientific disciplines. The Raman effect originates from the inelastic scattering of light, and it can directly probe vibration/rotational-vibration states in molecules and materials. Despite numerous advantages over infrared spectroscopy, spontaneous Raman scattering is very weak, and consequently, a variety of enhanced Raman spectroscopic techniques have emerged. These techniques include stimulated Raman scattering and coherent anti-Stokes Raman scattering, as well as surface- and tip-enhanced Raman scattering spectroscopies. The present review provides the reader with an understanding of the fundamental physics that govern the Raman effect and its advantages, limitations and applications. The review also highlights the key experimental considerations for implementing the main experimental Raman spectroscopic techniques. The relevant data analysis methods and some of the most recent advances related to the Raman effect are finally presented. This review constitutes a practical introduction to the science of Raman spectroscopy; it also highlights recent and promising directions of future research developments.

Using an affinity column retention assay, we showed that the purified Tet38 membrane transporter of Staphylococcus aureus bound specifically to host cell CD36 and to the complex CD36–Toll-like receptor 2 (TLR-2), but not to TLR-2 alone or TLR-2 and S. aureus lipoteichoic acid (LTA). We tested the effect of LTA on the internalization of S. aureustet38 mutant QT7 versus RN6390 by A549 epithelial cells. Addition of anti-LTA antibody to the bacteria prior to adding to A549 cells reduced internalization of QT7 2-fold compared to that with nonspecific antibody treatment. QT7 internalized 4- to 6-fold less than RN6390 with or without anti-LTA antibody. These data suggested that Tet38 and LTA were independently involved in the invasion process. The wall teichoic acid (WTA) inhibitor tunicamycin had an 8-fold decrease in activity with overexpression of tet38 and a 2-fold increase in activity in QT7 (tet38). Reserpine (an inhibitor of efflux pumps) reduced the effect of tet38 overexpression on tunicamycin resistance 4-fold. In addition, tet38 affected growth in the presence of LTA inhibitor Congo red, with overexpression increasing growth and deletion of tet38 reducing growth. In conclusion, Tet38 contributes to S. aureus invasion of A549 via direct binding to CD36 of the complex CD36–TLR-2, and LTA independently bound to TLR-2. The reduction of tunicamycin resistance in the presence of reserpine and the survival ability of the tet38 overexpressor in the presence of Congo red suggest that Tet38 can also protect the synthesis of LTA and WTA in S. aureus against their inhibitors, possibly functioning as an efflux pump.

Antibiotic resistance is a major cause of treatment failure and leads to increased use of broad-spectrum agents, which begets further resistance. This vicious cycle is epitomized by uncomplicated urinary tract infection (UTI), which affects one in two women during their life and is associated with increasing antibiotic resistance and high rates of prescription for broad-spectrum second-line agents. To address this, we developed machine learning models to predict antibiotic susceptibility using electronic health record data and built a decision algorithm for recommending the narrowest possible antibiotic to which a specimen is susceptible. When applied to a test cohort of 3629 patients presenting between 2014 and 2016, the algorithm achieved a 67% reduction in the use of second-line antibiotics relative to clinicians. At the same time, it reduced inappropriate antibiotic therapy, defined as the choice of a treatment to which a specimen is resistant, by 18% relative to clinicians. For specimens where clinicians chose a second-line drug but the algorithm chose a first-line drug, 92% (1066 of 1157) of decisions ended up being susceptible to the first-line drug. When clinicians chose an inappropriate first-line drug, the algorithm chose an appropriate first-line drug 47% (183 of 392) of the time. Our machine learning decision algorithm provides antibiotic stewardship for a common infectious syndrome by maximizing reductions in broad-spectrum antibiotic use while maintaining optimal treatment outcomes. Further work is necessary to improve generalizability by training models in more diverse populations.

The light interacting on asymmetric nanostructures can give rise to the phenomenon called extrinsic chirality [1–3], even if the nanostructures are not chiral by themselves. In this cases, light can be manipulated in order to obtain interesting behaviour such as anomalous refraction [4] or circular dichroism [5].

Staphylococcus aureus exports staphylopine (StP), a broad-spectrum metallophore, via the CntE efflux pump. Here, the mechanism of the fitness defect in the ΔcntE mutant under metal depletion was investigated. Deletion of the StP exporter CntE results in a substantial growth defect, and disrupting the StP biosynthesis gene cntL restores growth of the ΔcntE mutant in metal-depleted media. High-resolution mass spectrometry revealed cytoplasmic accumulation of StP and absence of extracellular StP in the ΔcntE mutant. The fitness defect of the ΔcntE mutant in mouse subcutaneous abscesses is largely due to staphylopine accumulation. Expression of StP biosynthesis genes are upregulated in the ΔcntE mutant under metal starvation induction. In conclusion, failure to efflux StP results in intracellular StP accumulation and substantially impairs the fitness of S. aureus.