Last data update: May 20, 2024. (Total: 46824 publications since 2009)
Records 1-15 (of 15 Records) |
Query Trace: Babiker A [original query] |
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High-level colonization with antibiotic-resistant enterobacterales among individuals in a semi-urban setting in South India: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study
Kumar CPG , Bhatnagar T , Sathya Narayanan G , Swathi SS , Sindhuja V , Siromany VA , VanderEnde D , Malpiedi P , Smith RM , Bollinger S , Babiker A , Styczynski A . Clin Infect Dis 2023 77 S111-7 BACKGROUND: Antimicrobial resistance poses a significant threat to public health globally. We studied the prevalence of colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), carbapenem-resistant Enterobacterales (CRE), and colistin-resistant Enterobacterales (Col-RE) in hospitals and the surrounding community in South India. METHODS: Adults from 2 hospitals and the catchment community who consented to provide stool specimens were enrolled. Stools were plated on CHROMagar selective for ESCrE, CRE, and Col-RE. Bacterial identification and antibiotic susceptibility testing were done using Vitek 2 Compact and disc diffusion testing. Colistin broth microdilution was performed for a subset of isolates. Prevalence estimates were calculated with 95% confidence intervals (CIs), and differences were compared across populations using the Pearson χ(2) or Fisher exact test. RESULTS: Between November 2020 and March 2022, 757 adults in the community and 556 hospitalized adults were enrolled. ESCrE colonization prevalence was 71.5% (95% CI, 68.1%–74.6%) in the community and 81.8% (95% CI, 78.4%–84.8%) in the hospital, whereas CRE colonization prevalence was 15.1% (95% CI, 12.7%–17.8%) in the community and 22.7% (95% CI, 19.4%–26.3%) in the hospital. Col-RE colonization prevalence was estimated to be 1.1% (95% CI, .5%–2.1%) in the community and 0.5% (95% CI, .2%–1.6%) in the hospital. ESCrE and CRE colonization in hospital participants was significantly higher compared with community participants (P < .001 for both). CONCLUSIONS: High levels of colonization with antibiotic-resistant Enterobacterales were found in both community and hospital settings. This study highlights the importance of surveillance of colonization in these settings for understanding the burden of antimicrobial resistance. |
Unrecognized introductions of SARS-CoV-2 into the state of Georgia shaped the early epidemic (preprint)
Babiker A , Martin MA , Marvil C , Bellman S , Petit Iii RA , Bradley HL , Stittleburg VD , Ingersoll J , Kraft CS , Read TD , Waggoner JJ , Koelle K , Piantadosi A . medRxiv 2021 2021.09.19.21262615 In early 2020, as SARS-CoV-2 diagnostic and surveillance responses ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the U.S. by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single introduction from Asia at least two weeks prior to the state’s first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely-related viruses in multiple U.S. states by the end of March 2020. Our findings indicate that the early attention directed towards identifying SARS-CoV-2 in returning international travelers may have led to a failure to recognize locally circulating infections for several weeks, and points towards a critical need for rapid and broadly-targeted surveillance efforts in the future.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis study was supported by the CDC contract 75D30121C10084 under BAA ERR 20-15-2997 the Pediatric Research Alliance Center for Childhood Infections and Vaccines and Childrens Healthcare of Atlanta and the Emory WHSC COVID-19 Urgent Research Engagement (CURE) Center made possible by generous philanthropic support from the O. Wayne Rollins Foundation and the William Randolph Hearst Foundation. AP is supported by NIH K08 AI139348. The Yerkes NHP Genomics Core is supported in part by NIH P51 OD011132 and sequence data was acquired on an Illumina NovaSeq6000 funded by NIH S10 OD 026799. Sample collection was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1TR002378. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:This study was approved by the Emory University institutional review boardAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesPublicly-available SARS-CoV-2 sequences from Georgia were generously contributed by Mayo Clinic Laboratories, Quest Diagnostics, and the U.S. Air Force School of Aerospace Medicine. We gratefully acknowledge the authors from the originating laboratories responsible for obtaining the specimens, as well as the submitting laboratories where the genome data were generated and shared via GISAID, on which this research is based (Supplementary Table 10). All Submitters of data may be contacted directly via www.gisaid.org.All the data will be publicly released upon publication. |
Clinical and genomic epidemiology of mcr-9-carrying carbapenem-resistant Enterobacterales isolates in Metropolitan Atlanta, 2012-2017 (preprint)
Babiker A , Bower C , Lutgring JD , Howard-Anderson J , Ansari U , McAllister G , Adamczyk M , Breaker E , Satola SW , Jacob JT , Woodworth MH . medRxiv 2021 2021.10.13.21264308 Colistin is a last-resort antibiotic for multidrug-resistant gram-negative infections. Recently, the ninth allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, was reported. However, its clinical and public health significance remains unclear. We queried genomes of carbapenem-resistant Enterobacterales (CRE) for mcr-9 from a convenience sample of clinical isolates collected between 2012-2017 through the Georgia Emerging Infections Program, a population- and laboratory-based surveillance program. Isolates underwent phenotypic characterization and whole genome sequencing. Phenotypic characteristics, genomic features, and clinical outcomes of mcr-9 positive and negative CRE cases were then compared. Among 235 sequenced CRE genomes, thirteen (6%) were found to harbor mcr-9, all of which were Enterobacter cloacae complex. The median MIC, rates of heteroresistance and inducible resistance to colistin were similar between mcr-9 positive and negative isolates. However, rates of resistance were higher among mcr-9 positive isolates across most antibiotic classes. All cases had significant healthcare exposures. The 90-day mortality was similarly high in both mcr-9 positive (31%) and negative (7%) CRE cases. Nucleotide identity and phylogenetic analysis did not reveal geo-temporal clustering. mcr-9 positive isolates had a significantly higher number of median [range] AMR genes (16 [4-22] vs. 6 [2-15]; p <0.001) compared to mcr-9 negative isolates. Pan genome tests confirmed a significant association of mcr-9 detection with mobile genetic element and heavy metal resistance genes. Overall, the presence of mcr-9 was not associated with significant changes in colistin resistance or clinical outcomes but continued genomic surveillance to monitor for emergence of AMR genes is warranted.Competing Interest StatementThe authors have declared no competing interest.Funding StatementEIP Surveillance of the Multi-site Gram-Negative Surveillance Initiative (MuGSI) was funded through the Centers for Disease Control and Preventions Emerging Infections Program [U50CK000485].Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Georgia EIP surveillance activities are reviewed and approved by the Emory University Institutional Review Board.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors |
Maternal colonization versus nosocomial transmission as the source of drug-resistant bloodstream infection in an Indian neonatal intensive care unit: A prospective cohort study
Robinson ML , Johnson J , Naik S , Patil S , Kulkarni R , Kinikar A , Dohe V , Mudshingkar S , Kagal A , Smith RM , Westercamp M , Randive B , Kadam A , Babiker A , Kulkarni V , Karyakarte R , Mave V , Gupta A , Milstone AM , Manabe YC . Clin Infect Dis 2023 77 S38-s45 BACKGROUND: Drug-resistant gram-negative (GN) pathogens are a common cause of neonatal sepsis in low- and middle-income countries. Identifying GN transmission patterns is vital to inform preventive efforts. METHODS: We conducted a prospective cohort study, 12 October 2018 to 31 October 2019 to describe the association of maternal and environmental GN colonization with bloodstream infection (BSI) among neonates admitted to a neonatal intensive care unit (NICU) in Western India. We assessed rectal and vaginal colonization in pregnant women presenting for delivery and colonization in neonates and the environment using culture-based methods. We also collected data on BSI for all NICU patients, including neonates born to unenrolled mothers. Organism identification, antibiotic susceptibility testing, and next-generation sequencing (NGS) were performed to compare BSI and related colonization isolates. RESULTS: Among 952 enrolled women who delivered, 257 neonates required NICU admission, and 24 (9.3%) developed BSI. Among mothers of neonates with GN BSI (n = 21), 10 (47.7%) had rectal, 5 (23.8%) had vaginal, and 10 (47.7%) had no colonization with resistant GN organisms. No maternal isolates matched the species and resistance pattern of associated neonatal BSI isolates. Thirty GN BSI were observed among neonates born to unenrolled mothers. Among 37 of 51 BSI with available NGS data, 21 (57%) showed a single nucleotide polymorphism distance of ≤5 to another BSI isolate. CONCLUSIONS: Prospective assessment of maternal GN colonization did not demonstrate linkage to neonatal BSI. Organism-relatedness among neonates with BSI suggests nosocomial spread, highlighting the importance of NICU infection prevention and control practices to reduce GN BSI. |
Remdesivir for the Treatment of Covid-19 - Final Report
Beigel JH , Tomashek KM , Dodd LE , Mehta AK , Zingman BS , Kalil AC , Hohmann E , Chu HY , Luetkemeyer A , Kline S , Lopez de Castilla D , Finberg RW , Dierberg K , Tapson V , Hsieh L , Patterson TF , Paredes R , Sweeney DA , Short WR , Touloumi G , Lye DC , Ohmagari N , Oh MD , Ruiz-Palacios GM , Benfield T , Fätkenheuer G , Kortepeter MG , Atmar RL , Creech CB , Lundgren J , Babiker AG , Pett S , Neaton JD , Burgess TH , Bonnett T , Green M , Makowski M , Osinusi A , Nayak S , Lane HC , ACTT-1 Study Group Members , Uyeki Timothy . N Engl J Med 2020 383 (19) 1813-1826 BACKGROUND: Although several therapeutic agents have been evaluated for the treatment of coronavirus disease 2019 (Covid-19), no antiviral agents have yet been shown to be efficacious. METHODS: We conducted a double-blind, randomized, placebo-controlled trial of intravenous remdesivir in adults who were hospitalized with Covid-19 and had evidence of lower respiratory tract infection. Patients were randomly assigned to receive either remdesivir (200 mg loading dose on day 1, followed by 100 mg daily for up to 9 additional days) or placebo for up to 10 days. The primary outcome was the time to recovery, defined by either discharge from the hospital or hospitalization for infection-control purposes only. RESULTS: A total of 1062 patients underwent randomization (with 541 assigned to remdesivir and 521 to placebo). Those who received remdesivir had a median recovery time of 10 days (95% confidence interval [CI], 9 to 11), as compared with 15 days (95% CI, 13 to 18) among those who received placebo (rate ratio for recovery, 1.29; 95% CI, 1.12 to 1.49; P<0.001, by a log-rank test). In an analysis that used a proportional-odds model with an eight-category ordinal scale, the patients who received remdesivir were found to be more likely than those who received placebo to have clinical improvement at day 15 (odds ratio, 1.5; 95% CI, 1.2 to 1.9, after adjustment for actual disease severity). The Kaplan-Meier estimates of mortality were 6.7% with remdesivir and 11.9% with placebo by day 15 and 11.4% with remdesivir and 15.2% with placebo by day 29 (hazard ratio, 0.73; 95% CI, 0.52 to 1.03). Serious adverse events were reported in 131 of the 532 patients who received remdesivir (24.6%) and in 163 of the 516 patients who received placebo (31.6%). CONCLUSIONS: Our data show that remdesivir was superior to placebo in shortening the time to recovery in adults who were hospitalized with Covid-19 and had evidence of lower respiratory tract infection. (Funded by the National Institute of Allergy and Infectious Diseases and others; ACTT-1 ClinicalTrials.gov number, NCT04280705.). |
Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient with Meningoencephalitis.
Al-Heeti O , Wu EL , Ison MG , Saluja RK , Ramsey G , Matkovic E , Ha K , Hall S , Banach B , Wilson MR , Miller S , Chiu CY , McCabe M , Bari C , Zimler RA , Babiker H , Freeman D , Popovitch J , Annambhotla P , Lehman JA , Fitzpatrick K , Velez JO , Davis EH , Hughes HR , Panella A , Brault A , Erin Staples J , Gould CV , Tanna S . Clin Infect Dis 2022 76 (3) e1320-e1327 BACKGROUND: Cache Valley virus (CVV) is a mosquito-borne virus that is a rare cause of disease in humans. In the Fall of 2020, a patient developed encephalitis six weeks following kidney transplantation and receipt of multiple blood transfusions. METHODS: After ruling out more common etiologies, metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) was performed. We reviewed the medical histories of the index kidney recipient, organ donor, and recipients of other organs from the same donor and conducted a blood traceback investigation to evaluate blood transfusion as a possible source of infection in the kidney recipient. We tested patient specimens by reverse transcription-polymerase chain reaction (RT-PCR), plaque reduction neutralization test (PRNT), cell culture, and whole genome sequencing. RESULTS: CVV was detected in CSF from the index patient by mNGS, and this result was confirmed by RT-PCR, viral culture, and additional whole genome sequencing. The organ donor and other organ recipients had no evidence of infection with CVV by molecular or serologic testing. Neutralizing antibodies against CVV were detected in serum from a donor of red blood cells received by the index patient immediately prior to transplant. CVV neutralizing antibodies were also detected in serum from a patient who received the co-component plasma from the same blood donation. CONCLUSION: Our investigation demonstrates probable CVV transmission through blood transfusion. Clinicians should consider arboviral infections in unexplained meningoencephalitis after blood transfusion or organ transplantation. The use of mNGS testing might facilitate detection of rare, unexpected infections, particularly in immunocompromised patients. |
Clinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017.
Babiker A , Bower C , Lutgring JD , Petit RA3rd , Howard-Anderson J , Ansari U , McAllister G , Adamczyk M , Breaker E , Satola SW , Jacob JT , Woodworth MH . Microbiol Spectr 2022 10 (4) e0252221 Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. Recently, the ninth allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, was reported. However, its clinical and public health significance remains unclear. We queried genomes of carbapenem-resistant Enterobacterales (CRE) for mcr-9 from a convenience sample of clinical isolates collected between 2012 and 2017 through the Georgia Emerging Infections Program, a population- and laboratory-based surveillance program. Isolates underwent phenotypic characterization and whole-genome sequencing. Phenotypic characteristics, genomic features, and clinical outcomes of mcr-9-positive and -negative CRE cases were then compared. Among 235 sequenced CRE genomes, 13 (6%) were found to harbor mcr-9, all of which were Enterobacter cloacae complex. The median MIC and rates of heteroresistance and inducible resistance to colistin were similar between mcr-9-positive and -negative isolates. However, rates of resistance were higher among mcr-9-positive isolates across most antibiotic classes. All cases had significant health care exposures. The 90-day mortality was similarly high in both mcr-9-positive (31%) and -negative (7%) CRE cases. Nucleotide identity and phylogenetic analysis did not reveal geotemporal clustering. mcr-9-positive isolates had a significantly higher number of median [range] antimicrobial resistance (AMR) genes (16 [4 to 22] versus 6 [2 to 15]; P < 0.001) than did mcr-9-negative isolates. Pangenome tests confirmed a significant association of mcr-9 detection with mobile genetic element and heavy metal resistance genes. Overall, the presence of mcr-9 was not associated with significant changes in colistin resistance or clinical outcomes, but continued genomic surveillance to monitor for emergence of AMR genes is warranted. IMPORTANCE Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. A recently described allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, has been widely reported among Enterobacterales species. However, its clinical and public health significance remains unclear. We compared characteristics and outcomes of mcr-9-positive and -negative CRE cases. All cases were acquired in the health care setting and associated with a high rate of mortality. The presence of mcr-9 was not associated with significant changes in colistin resistance, heteroresistance, or inducible resistance but was associated with resistance to other antimicrobials and antimicrobial resistance (AMR), virulence, and heavy metal resistance (HMR) genes. Overall, the presence of mcr-9 was not associated with significant phenotypic changes or clinical outcomes. However, given the increase in AMR and HMR gene content and potential clinical impact, continued genomic surveillance of multidrug-resistant organisms to monitor for emergence of AMR genes is warranted. |
Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic.
Babiker A , Martin MA , Marvil C , Bellman S , Petit Iii RA , Bradley HL , Stittleburg VD , Ingersoll J , Kraft CS , Li Y , Zhang J , Paden CR , Read TD , Waggoner JJ , Koelle K , Piantadosi A . Virus Evol 2022 8 (1) veac011 In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics. |
Association Between Caseload Surge and COVID-19 Survival in 558 U.S. Hospitals, March to August 2020.
Kadri SS , Sun J , Lawandi A , Strich JR , Busch LM , Keller M , Babiker A , Yek C , Malik S , Krack J , Dekker JP , Spaulding AB , Ricotta E , Powers Iii JH , Rhee C , Klompas M , Athale J , Boehmer TK , Gundlapalli AV , Bentley W , Datta SD , Danner RL , Demirkale CY , Warner S . Ann Intern Med 2021 174 (9) 1240-1251 BACKGROUND: Several U.S. hospitals had surges in COVID-19 caseload, but their effect on COVID-19 survival rates remains unclear, especially independent of temporal changes in survival. OBJECTIVE: To determine the association between hospitals' severity-weighted COVID-19 caseload and COVID-19 mortality risk and identify effect modifiers of this relationship. DESIGN: Retrospective cohort study. (ClinicalTrials.gov: NCT04688372). SETTING: 558 U.S. hospitals in the Premier Healthcare Database. PARTICIPANTS: Adult COVID-19-coded inpatients admitted from March to August 2020 with discharge dispositions by October 2020. MEASUREMENTS: Each hospital-month was stratified by percentile rank on a surge index (a severity-weighted measure of COVID-19 caseload relative to pre-COVID-19 bed capacity). The effect of surge index on risk-adjusted odds ratio (aOR) of in-hospital mortality or discharge to hospice was calculated using hierarchical modeling; interaction by surge attributes was assessed. RESULTS: Of 144 116 inpatients with COVID-19 at 558 U.S. hospitals, 78 144 (54.2%) were admitted to hospitals in the top surge index decile. Overall, 25 344 (17.6%) died; crude COVID-19 mortality decreased over time across all surge index strata. However, compared with nonsurging (<50th surge index percentile) hospital-months, aORs in the 50th to 75th, 75th to 90th, 90th to 95th, 95th to 99th, and greater than 99th percentiles were 1.11 (95% CI, 1.01 to 1.23), 1.24 (CI, 1.12 to 1.38), 1.42 (CI, 1.27 to 1.60), 1.59 (CI, 1.41 to 1.80), and 2.00 (CI, 1.69 to 2.38), respectively. The surge index was associated with mortality across ward, intensive care unit, and intubated patients. The surge-mortality relationship was stronger in June to August than in March to May (slope difference, 0.10 [CI, 0.033 to 0.16]) despite greater corticosteroid use and more judicious intubation during later and higher-surging months. Nearly 1 in 4 COVID-19 deaths (5868 [CI, 3584 to 8171]; 23.2%) was potentially attributable to hospitals strained by surging caseload. LIMITATION: Residual confounding. CONCLUSION: Despite improvements in COVID-19 survival between March and August 2020, surges in hospital COVID-19 caseload remained detrimental to survival and potentially eroded benefits gained from emerging treatments. Bolstering preventive measures and supporting surging hospitals will save many lives. PRIMARY FUNDING SOURCE: Intramural Research Program of the National Institutes of Health Clinical Center, the National Institute of Allergy and Infectious Diseases, and the National Cancer Institute. |
Bioaerosol sampling for SARS-CoV-2 in a referral center with critically ill COVID-19 patients March-May 2020.
Lane MA , Brownsword EA , Babiker A , Ingersoll JM , Waggoner J , Ayers M , Klopman M , Uyeki TM , Lindsley WG , Kraft CS . Clin Infect Dis 2021 73 (7) e1790-e1794 BACKGROUND: Previous research has shown that rooms of patients with COVID-19 present the potential for healthcare-associated transmission through aerosols containing SARS-CoV-2. However, data on the presence of these aerosols outside of patient rooms are limited. We investigated whether virus-containing aerosols were present in nursing stations and patient room hallways in a referral center with critically ill COVID-19 patients. METHODS: Eight National Institute for Occupational Safety and Health BC 251 two-stage cyclone samplers were set up throughout six units, including nursing stations and visitor corridors in intensive care units and general medical units, for six hours each sampling period. Samplers were placed on tripods which held two samplers positioned 102 cm and 152 cm above the floor. Units were sampled for three days. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid and the housekeeping gene human RNase P as an internal control. RESULTS: The units sampled varied in the number of laboratory-confirmed COVID-19 patients present on the days of sampling. Some of the units included patient rooms under negative pressure, while most were maintained at a neutral pressure. Of 528 aerosol samples collected, none were positive for SARS-CoV-2 RNA by the estimated limit of detection of 8 viral copies/m 3 of air. CONCLUSION: Aerosolized SARS-CoV-2 outside of patient rooms was undetectable. While healthcare personnel should avoid unmasked close contact with each other, these findings may provide reassurance for the use of alternatives to tight-fitting respirators in areas outside of patient rooms during the current pandemic. |
Inappropriate empirical antibiotic therapy for bloodstream infections based on discordant in-vitro susceptibilities: a retrospective cohort analysis of prevalence, predictors, and mortality risk in US hospitals
Kadri SS , Lai YL , Warner S , Strich JR , Babiker A , Ricotta EE , Demirkale CY , Dekker JP , Palmore TN , Rhee C , Klompas M , Hooper DC , Powers JH3rd , Srinivasan A , Danner RL , Adjemian J . Lancet Infect Dis 2020 21 (2) 241-251 BACKGROUND: 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. METHODS: 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. FINDINGS: 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]; p<0·0001), 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]; p<0·0001). Most incidences of discordant empirical antibiotic therapy and associated deaths occurred among patients with bloodstream infections caused by Staphylococcus aureus or Enterobacterales. INTERPRETATION: 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. FUNDING: US National Institutes of Health, US Centers for Disease Control and Prevention, and US Agency for Healthcare Research and Quality. |
Bioaerosol sampling of a ventilated patient with COVID-19.
Lane MA , Brownsword EA , Morgan JS , Babiker A , Vanairsdale SA , Lyon GM , Mehta AK , Ingersoll JM , Lindsley WG , Kraft CS . Am J Infect Control 2020 48 (12) 1540-1542 Bioaerosol samples were collected in an airborne infection isolation room, bathroom and anteroom of a ventilated patient with coronavirus disease 2019. Twenty-eight samples were negative for SARS-CoV-2 nucleic acid, possibly due to the patient being on a closed-circuit ventilator or the efficiency of the air exchanges in the room. |
Assessing the potential for unintended microbial consequences of routine chlorhexidine bathing for prevention of healthcare associated infections
Babiker A , Lutgring JD , Frikdin S , Hayden MK . Clin Infect Dis 2020 72 (5) 891-898 Chlorhexidine gluconate (CHG) is an antiseptic that is widely used in healthcare due to its excellent safety profile and wide spectrum of activity. Daily bathing with CHG has proven to be effective in the prevention of healthcare-associated infections and multi-drug resistant pathogen decolonization. Despite the proven benefits of CHG use, there remain concerns and unanswered questions about the potential for unintended microbial consequences of routine CHG bathing. This review aims to explore some of these questions. |
Phylogenetic and ecologic perspectives of a monkeypox outbreak, southern Sudan, 2005.
Nakazawa Y , Emerson GL , Carroll DS , Zhao H , Li Y , Reynolds MG , Karem KL , Olson VA , Lash RR , Davidson WB , Smith SK , Levine RS , Regnery RL , Sammons SA , Frace MA , Mutasim EM , Karsani ME , Muntasir MO , Babiker AA , Opoka L , Chowdhary V , Damon IK . Emerg Infect Dis 2013 19 (2) 237-45 Identification of human monkeypox cases during 2005 in southern Sudan (now South Sudan) raised several questions about the natural history of monkeypox virus (MPXV) in Africa. The outbreak area, characterized by seasonally dry riverine grasslands, is not identified as environmentally suitable for MPXV transmission. We examined possible origins of this outbreak by performing phylogenetic analysis of genome sequences of MPXV isolates from the outbreak in Sudan and from differing localities. We also compared the environmental suitability of study localities for monkeypox transmission. Phylogenetically, the viruses isolated from Sudan outbreak specimens belong to a clade identified in the Congo Basin. This finding, added to the political instability of the area during the time of the outbreak, supports the hypothesis of importation by infected animals or humans entering Sudan from the Congo Basin, and person-to-person transmission of virus, rather than transmission of indigenous virus from infected animals to humans. |
Human monkeypox outbreak caused by novel virus belonging to Congo Basin clade, Sudan, 2005
Formenty P , Muntasir MO , Damon I , Chowdhary V , Opoka ML , Monimart C , Mutasim EM , Manuguerra JC , Davidson WB , Karem KL , Cabeza J , Wang S , Malik MR , Durand T , Khalid A , Rioton T , Kuong-Ruay A , Babiker AA , Karsani ME , Abdalla MS . Emerg Infect Dis 2010 16 (10) 1539-1545 To determine the outbreak source of monkeypox virus (MPXV) infections in Unity State, Sudan, in November 2005, we conducted a retrospective investigation. MPXV was identified in a sub-Sahelian savannah environment. Three case notification categories were used: suspected, probable, and confirmed. Molecular, virologic, and serologic assays were used to test blood specimens, vesicular swabs, and crust specimens obtained from symptomatic and recovering persons. Ten laboratory-confirmed cases and 9 probable cases of MPXV were reported during September-December 2005; no deaths occurred. Human-to-human transmission up to 5 generations was described. Our investigation could not fully determine the source of the outbreak. Preliminary data indicate that the MPXV strain isolated during this outbreak was a novel virus belonging to the Congo Basin clade. Our results indicate that MPXV should be considered endemic to the wetland areas of Unity State. This finding will enhance understanding of the ecologic niche for this virus. |
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