Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-24 (of 24 Records) |
Query Trace: Jacob JT[original query] |
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Carbapenem-resistant Acinetobacter baumannii complex in the United States - an epidemiological and molecular description of isolates collected through the Emerging Infections Program, 2019
Bulens SN , Campbell D , McKay SL , Vlachos N , Burgin A , Burroughs M , Padila J , Grass JE , Jacob JT , Smith G , Muleta DB , Maloney M , Macierowski B , Wilson LE , Vaeth E , Lynfield R , O'Malley S , Snippes Vagnone PM , Dale J , Janelle SJ , Czaja CA , Johnson H , Phipps EC , Flores KG , Dumyati G , Tsay R , Beldavs ZG , Maureen Cassidy P , Hall A , Walters MS , Guh AY , Magill SS , Lutgring JD . Am J Infect Control 2024 BACKGROUND: Understanding the epidemiology of carbapenem-resistant A. baumannii complex (CRAB) and the patients impacted is an important step towards informing better infection prevention and control practices and improving public health response. METHODS: Active, population-based surveillance was conducted for CRAB in 9 U.S. sites from January 1-December 31, 2019. Medical records were reviewed, isolates were collected and characterized including antimicrobial susceptibility testing and whole genome sequencing. RESULTS: Among 136 incident cases in 2019, 66 isolates were collected and characterized; 56.5% were from cases who were male, 54.5% were from persons of Black or African American race with non-Hispanic ethnicity, and the median age was 63.5 years. Most isolates, 77.2%, were isolated from urine, and 50.0% were collected in the outpatient setting; 72.7% of isolates harbored an acquired carbapenemase gene (aCP), predominantly bla(OXA-23) or bla(OXA-24/40); however, an isolate with bla(NDM) was identified. The antimicrobial agent with the most in vitro activity was cefiderocol (96.9% of isolates were susceptible). CONCLUSIONS: Our surveillance found that CRAB isolates in the U.S. commonly harbor an aCP, have an antimicrobial susceptibility profile that is defined as difficult-to-treat resistance, and epidemiologically are similar regardless of the presence of an aCP. |
Trends in incidence of carbapenem-resistant enterobacterales in 7 US sites, 2016─2020
Duffy N , Li R , Czaja CA , Johnston H , Janelle SJ , Jacob JT , Smith G , Wilson LE , Vaeth E , Lynfield R , O'Malley S , Vagnone PS , Dumyati G , Tsay R , Bulens SN , Grass JE , Pierce R , Cassidy PM , Hertzel H , Wilson C , Muleta D , Taylor J , Guh AY . Open Forum Infect Dis 2023 10 (12) ofad609 BACKGROUND: We described changes in 2016─2020 carbapenem-resistant Enterobacterales (CRE) incidence rates in 7 US sites that conduct population-based CRE surveillance. METHODS: An incident CRE case was defined as the first isolation of Escherichia coli, Klebsiella spp., or Enterobacter spp. resistant to ≥1 carbapenem from a sterile site or urine in a surveillance area resident in a 30-day period. We reviewed medical records and classified cases as hospital-onset (HO), healthcare-associated community-onset (HACO), or community-associated (CA) CRE based on healthcare exposures and location of disease onset. We calculated incidence rates using census data. We used Poisson mixed effects regression models to perform 2016─2020 trend analyses, adjusting for sex, race/ethnicity, and age. We compared adjusted incidence rates between 2016 and subsequent years using incidence rate ratios (RRs) and 95% confidence intervals (CIs). RESULTS: Of 4996 CRE cases, 62% were HACO, 21% CA, and 14% HO. The crude CRE incidence rate per 100 000 was 7.51 in 2016 and 6.08 in 2020 and was highest for HACO, followed by CA and HO. From 2016 to 2020, the adjusted overall CRE incidence rate decreased by 24% (RR, 0.76 [95% CI, .70-.83]). Significant decreases in incidence rates in 2020 were seen for HACO (RR, 0.75 [95% CI, .67-.84]) and CA (0.75 [.61-.92]) but not for HO CRE. CONCLUSIONS: Adjusted CRE incidence rates declined from 2016 to 2020, but changes over time varied by epidemiologic class. Continued surveillance and effective control strategies are needed to prevent CRE in all settings. |
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 |
Reductions in inpatient fluoroquinolone use and postdischarge Clostridioides difficile infection (CDI) from a systemwide antimicrobial stewardship intervention
Jones KA , Onwubiko UN , Kubes J , Albrecht B , Paciullo K , Howard-Anderson J , Suchindran S , Trible R , Jacob JT , Yi SH , Goodenough D , Fridkin SK , Sexton ME , Wiley Z . Antimicrob Steward Healthc Epidemiol 2021 1 (1) e32 OBJECTIVE: To determine the impact of an inpatient stewardship intervention targeting fluoroquinolone use on inpatient and postdischarge Clostridioides difficile infection (CDI). DESIGN: We used an interrupted time series study design to evaluate the rate of hospital-onset CDI (HO-CDI), postdischarge CDI (PD-CDI) within 12 weeks, and inpatient fluoroquinolone use from 2 years prior to 1 year after a stewardship intervention. SETTING: An academic healthcare system with 4 hospitals. PATIENTS: All inpatients hospitalized between January 2017 and September 2020, excluding those discharged from locations caring for oncology, bone marrow transplant, or solid-organ transplant patients. INTERVENTION: Introduction of electronic order sets designed to reduce inpatient fluoroquinolone prescribing. RESULTS: Among 163,117 admissions, there were 683 cases of HO-CDI and 1,104 cases of PD-CDI. In the context of a 2% month-to-month decline starting in the preintervention period (P < .01), we observed a reduction in fluoroquinolone days of therapy per 1,000 patient days of 21% after the intervention (level change, P < .05). HO-CDI rates were stable throughout the study period. In contrast, we also detected a change in the trend of PD-CDI rates from a stable monthly rate in the preintervention period to a monthly decrease of 2.5% in the postintervention period (P < .01). CONCLUSIONS: Our systemwide intervention reduced inpatient fluoroquinolone use immediately, but not HO-CDI. However, a downward trend in PD-CDI occurred. Relying on outcome measures limited to the inpatient setting may not reflect the full impact of inpatient stewardship efforts. |
Development of a broth microdilution method to characterize chlorhexidine mics among bacteria collected from 2005 to 2019 at three U.S. Sites
Lutgring JD , Grass JE , Lonsway D , Yoo BB , Epson E , Crumpler M , Galliher K , O'Donnell K , Zahn M , Evans E , Jacob JT , Page A , Satola SW , Smith G , Kainer M , Muleta D , Wilson CD , Hayden MK , Reddy S , Elkins CA , Rasheed JK , Karlsson M , Magill SS , Guh AY . Microbiol Spectr 2023 11 (3) e0413422 Chlorhexidine bathing to prevent transmission of multidrug-resistant organisms has been adopted by many U.S. hospitals, but increasing chlorhexidine use has raised concerns about possible emergence of resistance. We sought to establish a broth microdilution method for determining chlorhexidine MICs and then used the method to evaluate chlorhexidine MICs for bacteria that can cause health care-associated infections. We adapted a broth microdilution method for determining chlorhexidine MICs, poured panels, established quality control ranges, and tested Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae complex isolates collected at three U.S. sites. Chlorhexidine MICs were determined for 535 isolates including 129 S. aureus, 156 E. coli, 142 K. pneumoniae, and 108 E. cloacae complex isolates. The respective MIC distributions for each species ranged from 1 to 8 mg/L (MIC(50) = 2 mg/L and MIC(90) = 4 mg/L), 1 to 64 mg/L (MIC(50) = 2 mg/L and MIC(90) = 4 mg/L), 4 to 64 mg/L (MIC(50) = 16 mg/L and MIC(90) = 32 mg/L), and 1 to >64 mg/L (MIC(50) = 16 mg/L and MIC(90) = 64 mg/L). We successfully adapted a broth microdilution procedure that several laboratories were able to use to determine the chlorhexidine MICs of bacterial isolates. This method could be used to investigate whether chlorhexidine MICs are increasing. IMPORTANCE Chlorhexidine bathing to prevent transmission of multidrug-resistant organisms and reduce health care-associated infections has been adopted by many hospitals. There is concern about the possible unintended consequences of using this agent widely. One possible unintended consequence is decreased susceptibility to chlorhexidine, but there are not readily available methods to perform this evaluation. We developed a method for chlorhexidine MIC testing that can be used to evaluate for possible unintended consequences. |
Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018.
Stanton RA , Campbell D , McAllister GA , Breaker E , Adamczyk M , Daniels JB , Lutgring JD , Karlsson M , Schutz K , Jacob JT , Wilson LE , Vaeth E , Li L , Lynfield R , Snippes Vagnone PM , Phipps EC , Hancock EB , Dumyati G , Tsay R , Cassidy PM , Mounsey J , Grass JE , Bulens SN , Walters MS , Halpin AL . Antimicrob Agents Chemother 2022 66 (9) e0049622 The CDC's Emerging Infections Program (EIP) conducted population- and laboratory-based surveillance of US carbapenem-resistant Pseudomonas aeruginosa (CRPA) from 2016 through 2018. To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. Both chromosomal and horizontally transmitted mechanisms of carbapenem resistance were assessed. There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. Mutations associated with dysfunction of the porin OprD were found in 888 (87.1%) of the genomes and were correlated with carbapenem resistance, and a machine learning model incorporating hundreds of genetic variations among the chromosomal mechanisms of resistance was able to classify resistant genomes. While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase β-lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. The genetic diversity demonstrates that the pathotype includes a variety of strains, and clones previously identified as high-risk make up only a minority of CRPA strains in the United States. The increased carbapenem resistance in isolates with acquired non-carbapenemase β-lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa. |
Carbapenem-Resistant enterobacterales in individuals with and without health care risk factors -Emerging infections program, United States, 2012-2015.
Bulens SN , Reses HE , Ansari UA , Grass JE , Carmon C , Albrecht V , Lawsin A , McAllister G , Daniels J , Lee YK , Yi S , See I , Jacob JT , Bower CW , Wilson L , Vaeth E , Lynfield R , Vagnone PS , Shaw KM , Dumyati G , Tsay R , Phipps EC , Bamberg W , Janelle SJ , Beldavs ZG , Cassidy PM , Kainer M , Muleta D , Mounsey JT , Laufer-Halpin A , Karlsson M , Lutgring JD , Walters MS . Am J Infect Control 2022 51 (1) 70-77 BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) are usually healthcare-associated but are also emerging in the community. METHODS: Active, population-based surveillance was conducted to identify case-patients with cultures positive for Enterobacterales not susceptible to a carbapenem (excluding ertapenem) and resistant to all third-generation cephalosporins tested at 8 US sites from January 2012 to December 2015. Medical records were used to classify cases as health care-associated, or as community-associated (CA) if a patient had no known health care risk factors and a culture was collected <3 days after hospital admission. Enterobacterales isolates from selected cases were submitted to CDC for whole genome sequencing. RESULTS: We identified 1499 CRE cases in 1194 case-patients; 149 cases (10%) in 139 case-patients were CA. The incidence of CRE cases per 100,000 population was 2.96 (95% CI: 2.81, 3.11) overall and 0.29 (95% CI: 0.25, 0.35) for CA-CRE. Most CA-CRE cases were in White persons (73%), females (84%) and identified from urine cultures (98%). Among the 12 sequenced CA-CRE isolates, 5 (42%) harbored a carbapenemase gene. CONCLUSIONS: Ten percent of CRE cases were CA; some isolates from CA-CRE cases harbored carbapenemase genes. Continued CRE surveillance in the community is critical to monitor emergence outside of traditional health care settings. |
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. |
Epidemiology of extended-spectrum β-lactamase-producing Enterobacterales in five US sites participating in the Emerging Infections Program, 2017.
Duffy N , Karlsson M , Reses HE , Campbell D , Daniels J , Stanton RA , Janelle SJ , Schutz K , Bamberg W , Rebolledo PA , Bower C , Blakney R , Jacob JT , Phipps EC , Flores KG , Dumyati G , Kopin H , Tsay R , Kainer MA , Muleta D , Byrd-Warner B , Grass JE , Lutgring JD , Rasheed JK , Elkins CA , Magill SS , See I . Infect Control Hosp Epidemiol 2022 43 (11) 1-9 OBJECTIVE: The incidence of infections from extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-E) is increasing in the United States. We describe the epidemiology of ESBL-E at 5 Emerging Infections Program (EIP) sites. METHODS: During October-December 2017, we piloted active laboratory- and population-based (New York, New Mexico, Tennessee) or sentinel (Colorado, Georgia) ESBL-E surveillance. An incident case was the first isolation from normally sterile body sites or urine of Escherichia coli or Klebsiella pneumoniae/oxytoca resistant to ≥1 extended-spectrum cephalosporin and nonresistant to all carbapenems tested at a clinical laboratory from a surveillance area resident in a 30-day period. Demographic and clinical data were obtained from medical records. The Centers for Disease Control and Prevention (CDC) performed reference antimicrobial susceptibility testing and whole-genome sequencing on a convenience sample of case isolates. RESULTS: We identified 884 incident cases. The estimated annual incidence in sites conducting population-based surveillance was 199.7 per 100,000 population. Overall, 800 isolates (96%) were from urine, and 790 (89%) were E. coli. Also, 393 cases (47%) were community-associated. Among 136 isolates (15%) tested at the CDC, 122 (90%) met the surveillance definition phenotype; 114 (93%) of 122 were shown to be ESBL producers by clavulanate testing. In total, 111 (97%) of confirmed ESBL producers harbored a blaCTX-M gene. Among ESBL-producing E. coli isolates, 52 (54%) were ST131; 44% of these cases were community associated. CONCLUSIONS: The burden of ESBL-E was high across surveillance sites, with nearly half of cases acquired in the community. EIP has implemented ongoing ESBL-E surveillance to inform prevention efforts, particularly in the community and to watch for the emergence of new ESBL-E strains. |
Occupational risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among healthcare personnel: A 6-month prospective analysis of the COVID-19 Prevention in Emory Healthcare Personnel (COPE) Study.
Howard-Anderson J , Adams C , Dube WC , Smith TC , Sherman AC , Edupuganti N , Mendez M , Chea N , Magill SS , Espinoza DO , Zhu Y , Phadke VK , Edupuganti S , Steinberg JP , Lopman BA , Jacob JT , Fridkin SK , Collins MH . Infect Control Hosp Epidemiol 2022 43 (11) 1-30 OBJECTIVE: Determine the incidence of SARS-CoV-2 infection among healthcare personnel (HCP) and assess occupational risks for SARS-CoV-2 infection. DESIGN: Prospective cohort of HCP followed for 6-months from May-December 2020. SETTING: Large academic healthcare system including four hospitals and affiliated clinics in Atlanta, GA. PARTICIPANTS: HCP, including those with and without direct patient care activities, working during the COVID-19 pandemic. METHODS: Incident SARS-CoV-2 infections were determined through serologic testing for SARS-CoV-2 IgG at enrollment, 3 and 6 months. HCP completed monthly surveys regarding occupational activities. Multivariable logistic regression was used to identify occupational factors that increased the risk of SARS-CoV-2 infection. RESULTS: Of the 304 evaluable HCP that were seronegative at enrollment, 26 (9%) seroconverted for SARS-CoV-2 IgG by 6 months. Participants self-identified predominantly as White (n=219, 73%), nurses (n=119, 40%), and working in inpatient medical/surgical floors (n=121, 40%). In a multivariable analysis, HCP who identified as Black were more likely to seroconvert than HCP who identified as White (odds ratio 4.5, 95% confidence interval 1.3-14.2). Increased risk for SARS-CoV-2 infection was not identified for any occupational activity, including spending >50% of a typical shift at a patient's bedside, working in COVID-19 units, or performing/being present for aerosol generating procedures (AGPs). CONCLUSIONS: In our study cohort of HCP working in an academic healthcare system, <10% had evidence of SARS-CoV-2 infection over six months. No specific occupational activities were identified as increasing risk for SARS-CoV-2 infection. |
Development and evaluation of a structured guide to assess the preventability of hospital-onset bacteremia and fungemia
Schrank GM , Sick-Samuels A , Bleasdale SC , Jacob JT , Dantes R , Gokhale RH , Mayer J , Mehrotra P , Mehta SA , MenaLora AJ , Ray SM , Rhee C , Salinas JL , Seo SK , Shane AL , Nadimpalli G , Milstone AM , Robinson G , Brown CH , Harris AD , Leekha S . Infect Control Hosp Epidemiol 2022 43 (10) 1-7 OBJECTIVE: To assess preventability of hospital-onset bacteremia and fungemia (HOB), we developed and evaluated a structured rating guide accounting for intrinsic patient and extrinsic healthcare-related risks. DESIGN: HOB preventability rating guide was compared against a reference standard expert panel. PARTICIPANTS: A 10-member panel of clinical experts was assembled as the standard of preventability assessment, and 2 physician reviewers applied the rating guide for comparison. METHODS: The expert panel independently rated 82 hypothetical HOB scenarios using a 6-point Likert scale collapsed into 3 categories: preventable, uncertain, or not preventable. Consensus was defined as concurrence on the same category among 70% experts. Scenarios without consensus were deliberated and followed by a second round of rating.Two reviewers independently applied the rating guide to adjudicate the same 82 scenarios in 2 rounds, with interim revisions. Interrater reliability was evaluated using the (kappa) statistic. RESULTS: Expert panel consensus criteria were met for 52 scenarios (63%) after 2 rounds.After 2 rounds, guide-based rating matched expert panel consensus in 40 of 52 (77%) and 39 of 52 (75%) cases for reviewers 1 and 2, respectively. Agreement rates between the 2 reviewers were 84% overall (, 0.76; 95% confidence interval [CI], 0.64-0.88]) and 87% (, 0.79; 95% CI, 0.65-0.94) for the 52 scenarios with expert consensus. CONCLUSIONS: Preventability ratings of HOB scenarios by 2 reviewers using a rating guide matched expert consensus in most cases with moderately high interreviewer reliability. Although diversity of expert opinions and uncertainty of preventability merit further exploration, this is a step toward standardized assessment of HOB preventability. |
Distinctive Features of Ertapenem-Mono-Resistant Carbapenem-Resistant Enterobacterales in the United States: A Cohort Study.
Adelman MW , Bower CW , Grass JE , Ansari UA , Soda EA , See I , Lutgring JD , Jacob JT . Open Forum Infect Dis 2022 9 (1) ofab643 BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) are highly antibiotic-resistant bacteria. Whether CRE resistant only to ertapenem among carbapenems (ertapenem "mono-resistant") represent a unique CRE subset with regards to risk factors, carbapenemase genes, and outcomes is unknown. METHODS: We analyzed surveillance data from 9 CDC Emerging Infections Program (EIP) sites. A case was the first isolation of a carbapenem-resistant Enterobacter cloacae complex, Escherichia coli, Klebsiella aerogenes, K. oxytoca, K. pneumoniae, or K. variicola from a normally sterile site or urine in an EIP catchment area resident in 2016-2017. We compared risk factors, carbapenemase genes, antibiotic susceptibility, and mortality of ertapenem "mono-resistant" cases to "other" CRE cases (resistant to1 carbapenem other than ertapenem) and analyzed risk factors for mortality. RESULTS: Of 2009 cases, 1249 (62.2%) were ertapenem-mono-resistant and 760 (37.8%) were other CRE. Ertapenem-mono-resistant CRE cases were more frequently80 years old (29.1% vs 19.5%; P<.0001) and female (67.9% vs 59.0%; P<.0001). Ertapenem-mono-resistant isolates were more likely to be Enterobacter cloacae complex (48.4% vs 15.4%; P<.0001) but less likely to be isolated from a normally sterile site (7.1% vs 11.7%; P<.01) or to have a carbapenemase gene (2.4% vs 47.4%; P<.0001). Ertapenem-mono-resistance was not associated with 90-day mortality in logistic regression models. Carbapenemase-positive isolates were associated with mortality (odds ratio, 1.93; 95% CI, 1.30-2.86). CONCLUSIONS: Ertapenem-mono-resistant CRE rarely have carbapenemase genes and have distinct clinical and microbiologic characteristics from other CRE. These findings may inform antibiotic choice and infection prevention practices, particularly when carbapenemase testing is not available. |
Risk Factors Associated With SARS-CoV-2 Seropositivity Among US Health Care Personnel.
Jacob JT , Baker JM , Fridkin SK , Lopman BA , Steinberg JP , Christenson RH , King B , Leekha S , O'Hara LM , Rock P , Schrank GM , Hayden MK , Hota B , Lin MY , Stein BD , Caturegli P , Milstone AM , Rock C , Voskertchian A , Reddy SC , Harris AD . JAMA Netw Open 2021 4 (3) e211283 IMPORTANCE: Risks for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health care personnel (HCP) are unclear. OBJECTIVE: To evaluate the risk factors associated with SARS-CoV-2 seropositivity among HCP with the a priori hypothesis that community exposure but not health care exposure was associated with seropositivity. DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study was conducted among volunteer HCP at 4 large health care systems in 3 US states. Sites shared deidentified data sets, including previously collected serology results, questionnaire results on community and workplace exposures at the time of serology, and 3-digit residential zip code prefix of HCP. Site-specific responses were mapped to a common metadata set. Residential weekly coronavirus disease 2019 (COVID-19) cumulative incidence was calculated from state-based COVID-19 case and census data. EXPOSURES: Model variables included demographic (age, race, sex, ethnicity), community (known COVID-19 contact, COVID-19 cumulative incidence by 3-digit zip code prefix), and health care (workplace, job role, COVID-19 patient contact) factors. MAIN OUTCOME AND MEASURES: The main outcome was SARS-CoV-2 seropositivity. Risk factors for seropositivity were estimated using a mixed-effects logistic regression model with a random intercept to account for clustering by site. RESULTS: Among 2 749 HCP, most were younger than 50 years (17 233 [69.6%]), were women (19 361 [78.2%]), were White individuals (15 157 [61.2%]), and reported workplace contact with patients with COVID-19 (12 413 [50.2%]). Many HCP worked in the inpatient setting (8893 [35.9%]) and were nurses (7830 [31.6%]). Cumulative incidence of COVID-19 per 10 000 in the community up to 1 week prior to serology testing ranged from 8.2 to 275.6; 20 072 HCP (81.1%) reported no COVID-19 contact in the community. Seropositivity was 4.4% (95% CI, 4.1%-4.6%; 1080 HCP) overall. In multivariable analysis, community COVID-19 contact and community COVID-19 cumulative incidence were associated with seropositivity (community contact: adjusted odds ratio [aOR], 3.5; 95% CI, 2.9-4.1; community cumulative incidence: aOR, 1.8; 95% CI, 1.3-2.6). No assessed workplace factors were associated with seropositivity, including nurse job role (aOR, 1.1; 95% CI, 0.9-1.3), working in the emergency department (aOR, 1.0; 95% CI, 0.8-1.3), or workplace contact with patients with COVID-19 (aOR, 1.1; 95% CI, 0.9-1.3). CONCLUSIONS AND RELEVANCE: In this cross-sectional study of US HCP in 3 states, community exposures were associated with seropositivity to SARS-CoV-2, but workplace factors, including workplace role, environment, or contact with patients with known COVID-19, were not. These findings provide reassurance that current infection prevention practices in diverse health care settings are effective in preventing transmission of SARS-CoV-2 from patients to HCP. |
Occupational Risk Factors for SARS-CoV-2 Infection among Healthcare Personnel: A Cross-Sectional Analysis of Subjects Enrolled in the COPE Study.
Howard-Anderson J , Adams C , Sherman AC , Dube WC , Smith TC , Edupuganti N , Chea N , Magill SS , Espinoza DO , Zhu Y , Phadke VK , Edupuganti S , Steinberg JP , Lopman BA , Jacob JT , Collins MH , Fridkin SK . Infect Control Hosp Epidemiol 2021 43 (3) 1-20 Among 353 healthcare personnel in a longitudinal cohort in four hospitals in Atlanta, GA (May-June 2020), 23 (6.5%) had SARS-CoV-2 antibodies. Spending >50% of a typical shift at bedside (OR 3.4, 95% CI: 1.2-10.5) and Black race (OR 8.4, 95% CI: 2.7-27.4) were associated with SARS-CoV-2 seropositivity. |
Evaluating movement of patients with Carbapenem-Resistant Enterobacteriaceae infections in the Greater Atlanta Metropolitan Area using social network analysis
Bower CW , Fridkin DW , Wolford HM , Slayton RB , Kubes JN , Jacob JT , Ray SM , Fridkin SK . Clin Infect Dis 2019 70 (1) 75-81 BACKGROUND: Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent threat with potential for rapid spread. We evaluated the role of Medicare patient movement between facilities to model the spread of CRE within a region. METHODS: Through population-based CRE surveillance in the 8-county Atlanta Metropolitan area (population 4.1 million), all Escherichiacoli, Enterobacter spp, or Klebsiella spp. resistant to >/=1 carbapenem collected from urine or a normally sterile site were reported from residents. CRE was attributed to a facility based on timing of culture and facility exposures in the previous year; centrality metrics were calculated from 2016 Medicare data and compared to CRE-transfer derived centrality metrics by Spearman correlation. RESULTS: During 2016, 283 incident CRE cases with concurrent or prior year facility stays were identified; cases were attributed mostly to acute care hospitals (ACH: 141, 50%) and skilled nursing facilities (SNF: 113, 40%), and less frequently to long term acute care hospitals (LTACH: 29, 10%). Attribution was widespread, originating at 17 of 20 ACH (85%), 7 of 8 (88%) LTACH, but only 35 of 65 (54%) SNFs. Betweenness of Medicare patient-transfers strongly correlated with betweenness of CRE case-transfer data in ACHs (r=0.75; P<.01) and LTACHs (r=0.77; P=.03), but not in SNFs (r=0.02; p=0.85). We note six SNFs with high CRE-derived betweenness but low Medicare-derived betweenness. CONCLUSION: CRE infections originate from almost all ACHs and about half of SNFs. We identified a subset of SNFs very central to the CRE transfer network but not the Medicare transfer network; other factors may better explain CRE patient movement in these facilities. |
Preventability of hospital onset bacteremia and fungemia: A pilot study of a potential healthcare-associated infection outcome measure
Dantes RB , Rock C , Milstone AM , Jacob JT , Chernetsky-Tejedor S , Harris AD , Leekha S . Infect Control Hosp Epidemiol 2019 40 (3) 1-4 Hospital-onset bacteremia and fungemia (HOB), a potential measure of healthcare-associated infections, was evaluated in a pilot study among 60 patients across 3 hospitals. Two-thirds of all HOB events and half of nonskin commensal HOB events were judged as potentially preventable. Follow-up studies are needed to further develop this measure. |
Carbapenem-nonsusceptible Acinetobacter baumannii, 8 US Metropolitan Areas, 2012-2015
Bulens SN , Yi SH , Walters MS , Jacob JT , Bower C , Reno J , Wilson L , Vaeth E , Bamberg W , Janelle SJ , Lynfield R , Vagnone PS , Shaw K , Kainer M , Muleta D , Mounsey J , Dumyati G , Concannon C , Beldavs Z , Cassidy PM , Phipps EC , Kenslow N , Hancock EB , Kallen AJ . Emerg Infect Dis 2018 24 (4) 727-734 In healthcare settings, Acinetobacter spp. bacteria commonly demonstrate antimicrobial resistance, making them a major treatment challenge. Nearly half of Acinetobacter organisms from clinical cultures in the United States are nonsusceptible to carbapenem antimicrobial drugs. During 2012-2015, we conducted laboratory- and population-based surveillance in selected metropolitan areas in Colorado, Georgia, Maryland, Minnesota, New Mexico, New York, Oregon, and Tennessee to determine the incidence of carbapenem-nonsusceptible A. baumannii cultured from urine or normally sterile sites and to describe the demographic and clinical characteristics of patients and cases. We identified 621 cases in 537 patients; crude annual incidence was 1.2 cases/100,000 persons. Among 598 cases for which complete data were available, 528 (88.3%) occurred among patients with exposure to a healthcare facility during the preceding year; 506 (84.6%) patients had an indwelling device. Although incidence was lower than for other healthcare-associated pathogens, cases were associated with substantial illness and death. |
Diagnostic importance of hyphae on heart valve tissue in Histoplasma endocarditis and treatment with isavuconazole
Wiley Z , Woodworth MH , Jacob JT , Lockhart SR , Rouphael NG , Gullett JC , Guarner J , Workowski K . Open Forum Infect Dis 2017 4 (4) ofx241 A patient who never resided in an endemic area for dimorphic fungi was diagnosed with Histoplasma capsulatum endocarditis. His diagnosis was suggested by yeast and hyphae on cardiac valve tissue pathology. Isavuconazole was an optimal therapeutic option due to renal dysfunction and anticoagulation with warfarin for mechanical valve replacement. |
Case diagnosis and characterization of suspected paralytic shellfish poisoning in Alaska.
Knaack JS , Porter KA , Jacob JT , Sullivan K , Forester M , Wang RY , Trainer VL , Morton S , Eckert G , McGahee E , Thomas J , McLaughlin J , Johnson RC . Harmful Algae 2016 57 45-50 Clinical cases of paralytic shellfish poisoning (PSP) are common in Alaska, and result from human consumption of shellfish contaminated with saxitoxin (STX) and its analogues. Diagnosis of PSP is presumptive and based on recent ingestion of shellfish and presence of manifestations consistent with symptoms of PSP; diagnosis is confirmed by detection of paralytic shellfish toxins in a clinical specimen or food sample. A clinical diagnostic analytical method using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was used to evaluate the diagnosis of saxitoxin-induced PSP (STX-PSP) in 11 Alaskan patients using urine specimens collected between June 2010 and November 2011. Concentrations of urinary STX were corrected for creatinine concentrations to account for dilution or concentration of urine from water intake or restriction, respectively. Of the 11 patients with suspected PSP, four patients were confirmed to have STX-PSP by urine testing (24-364 ng STX/g creatinine). Five patients had clinical manifestations of PSP though no STX was detected in their urine. Two patients were ruled out for STX-PSP based on non-detected urinary STX and the absence of clinical findings. Results revealed that dysphagia and dysarthria may be stronger indicators of PSP than paresthesia and nausea, which are commonly used to clinically diagnose patients with PSP. PSP can also occur from exposure to a number of STX congeners, such as gonyautoxins, however their presence in urine was not assessed in this investigation. In addition, meal remnants obtained from six presumptive PSP cases were analyzed using the Association of Official Analytical Chemists' mouse bioassay. All six samples tested positive for PSP toxins. In the future, the clinical diagnostic method can be used in conjunction with the mouse bioassay or HPLC-MS/MS to assess the extent of STX-PSP in Alaska where it has been suggested that PSP is underreported. |
Assessment of the overall and multidrug-resistant organism bioburden on environmental surfaces in healthcare facilities
Shams AM , Rose LJ , Edwards JR , Cali S , Harris AD , Jacob JT , LaFae A , Pineles LL , Thom KA , McDonald LC , Arduino MJ , Noble-Wang JA . Infect Control Hosp Epidemiol 2016 37 (12) 1-7 OBJECTIVE To determine the typical microbial bioburden (overall bacterial and multidrug-resistant organisms [MDROs]) on high-touch healthcare environmental surfaces after routine or terminal cleaning. DESIGN Prospective 2.5-year microbiological survey of large surface areas (>1,000 cm2). SETTING MDRO contact-precaution rooms from 9 acute-care hospitals and 2 long-term care facilities in 4 states. PARTICIPANTS Samples from 166 rooms (113 routine cleaned and 53 terminal cleaned rooms). METHODS Using a standard sponge-wipe sampling protocol, 2 composite samples were collected from each room; a third sample was collected from each Clostridium difficile room. Composite 1 included the TV remote, telephone, call button, and bed rails. Composite 2 included the room door handle, IV pole, and overbed table. Composite 3 included toileting surfaces. Total bacteria and MDROs (ie, methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci [VRE], Acinetobacter baumannii, Klebsiella pneumoniae, and C. difficile) were quantified, confirmed, and tested for drug resistance. RESULTS The mean microbial bioburden and range from routine cleaned room composites were higher (2,700 colony-forming units [CFU]/100 cm2; ≤1-130,000 CFU/100 cm2) than from terminal cleaned room composites (353 CFU/100 cm2; ≤1-4,300 CFU/100 cm2). MDROs were recovered from 34% of routine cleaned room composites (range ≤1-13,000 CFU/100 cm2) and 17% of terminal cleaned room composites (≤1-524 CFU/100 cm2). MDROs were recovered from 40% of rooms; VRE was the most common (19%). CONCLUSIONS This multicenter bioburden summary provides a first step to determining microbial bioburden on healthcare surfaces, which may help provide a basis for developing standards to evaluate cleaning and disinfection as well as a framework for studies using an evidentiary hierarchy for environmental infection control. Infect Control Hosp Epidemiol 2016;1-7. |
Epidemiology of carbapenem-resistant Enterobacteriaceae in 7 US communities, 2012-2013
Guh AY , Bulens SN , Mu Y , Jacob JT , Reno J , Scott J , Wilson LE , Vaeth E , Lynfield R , Shaw KM , Vagnone PM , Bamberg WM , Janelle SJ , Dumyati G , Concannon C , Beldavs Z , Cunningham M , Cassidy PM , Phipps EC , Kenslow N , Travis T , Lonsway D , Rasheed JK , Limbago BM , Kallen AJ . JAMA 2015 314 (14) 1479-1487 IMPORTANCE: Carbapenem-resistant Enterobacteriaceae (CRE) are increasingly reported worldwide as a cause of infections with high-mortality rates. Assessment of the US epidemiology of CRE is needed to inform national prevention efforts. OBJECTIVE: To determine the population-based CRE incidence and describe the characteristics and resistance mechanism associated with isolates from 7 US geographical areas. DESIGN, SETTING, AND PARTICIPANTS: Population- and laboratory-based active surveillance of CRE conducted among individuals living in 1 of 7 US metropolitan areas in Colorado, Georgia, Maryland, Minnesota, New Mexico, New York, and Oregon. Cases of CRE were defined as carbapenem-nonsusceptible (excluding ertapenem) and extended-spectrum cephalosporin-resistant Escherichia coli, Enterobacter aerogenes, Enterobacter cloacae complex, Klebsiella pneumoniae, or Klebsiella oxytoca that were recovered from sterile-site or urine cultures during 2012-2013. Case records were reviewed and molecular typing for common carbapenemases was performed. EXPOSURES: Demographics, comorbidities, health care exposures, and culture source and location. MAIN OUTCOMES AND MEASURES: Population-based CRE incidence, site-specific standardized incidence ratios (adjusted for age and race), and clinical and microbiological characteristics. Results: Among 599 CRE cases in 481 individuals, 520 (86.8%; 95% CI, 84.1%-89.5%) were isolated from urine and 68 (11.4%; 95% CI, 8.8%-13.9%) from blood. The median age was 66 years (95% CI, 62.1-65.4 years) and 284 (59.0%; 95% CI, 54.6%-63.5%) were female. The overall annual CRE incidence rate per 100000 population was 2.93 (95% CI, 2.65-3.23). The CRE standardized incidence ratio was significantly higher than predicted for the sites in Georgia (1.65 [95% CI, 1.20-2.25]; P < .001), Maryland (1.44 [95% CI, 1.06-1.96]; P = .001), and New York (1.42 [95% CI, 1.05-1.92]; P = .048), and significantly lower than predicted for the sites in Colorado (0.53 [95% CI, 0.39-0.71]; P < .001), New Mexico (0.41 [95% CI, 0.30-0.55]; P = .01), and Oregon (0.28 [95% CI, 0.21-0.38]; P < .001). Most cases occurred in individuals with prior hospitalizations (399/531 [75.1%; 95% CI, 71.4%-78.8%]) or indwelling devices (382/525 [72.8%; 95% CI, 68.9%-76.6%]); 180 of 322 (55.9%; 95% CI, 50.0%-60.8%) admitted cases resulted in a discharge to a long-term care setting. Death occurred in 51 (9.0%; 95% CI, 6.6%-11.4%) cases, including in 25 of 91 cases (27.5%; 95% CI, 18.1%-36.8%) with CRE isolated from normally sterile sites. Of 188 isolates tested, 90 (47.9%; 95% CI, 40.6%-55.1%) produced a carbapenemase. CONCLUSIONS AND RELEVANCE: In this population- and laboratory-based active surveillance system in 7 states, the incidence of CRE was 2.93 per 100000 population. Most CRE cases were isolated from a urine source, and were associated with high prevalence of prior hospitalizations or indwelling devices, and discharge to long-term care settings. |
Severity of rhinovirus infection in hospitalized adults is unrelated to genotype.
McCulloch DJ , Sears MH , Jacob JT , Lyon GM , Burd EM , Caliendo AM , Hill CE , Nix WA , Oberste MS , Kraft CS . Am J Clin Pathol 2014 142 (2) 165-72 OBJECTIVES: To determine whether rhinovirus (RV) species is associated with more severe clinical illness in adults. METHODS: Seventy-two RV-positive viral respiratory samples from adult patients were sequenced and analyzed phylogenetically after reverse transcriptase polymerase chain reaction of the region spanning the VP4 gene and 5' terminus of the VP2 gene. The clinical features and severity of illness associated with the different RV species were compared. RESULTS: Phylogenetic analysis identified three distinct clusters as RV-A (54%), B (11%), or C (35%) species. In an unadjusted model, patients with RV-B infection were significantly more likely to have the composite outcome variable of death or intensive care unit admission (P = .03), but this effect diminished when controlling for patient sex. A logistic model of the relationship between RV species and adverse outcomes produced nonsignificant odds ratios when controlling for patient sex. CONCLUSIONS: Infection with RV-A or RV-B was associated with greater severity of illness in our adult population; however, the association disappeared after controlling for confounders. |
Microbial biofilms on needleless connectors for central venous catheters: a comparison of standard and silver-coated devices collected from patients in an acute care hospital
Perez E , Williams M , Jacob JT , Reyes MD , Chernetsky Tejedor S , Steinberg JP , Rowe L , Ganakammal SR , Changayil S , Weil MR , Donlan RM . J Clin Microbiol 2013 52 (3) 823-31 Microorganisms may colonize needleless connectors (NCs) on intravascular catheters, forming biofilms and predisposing patients to catheter- associated infection (CAI). Standard and silver-coated NCs were collected from catheterized intensive care unit patients to characterize biofilm formation using culture-dependent and culture-independent methods and to investigate association between NC usage and biofilm characteristics. Viable microorganisms were detected by plate count (PC) from 46% of standard and 59% of silver-coated NCs (p=0.11). There were no significant associations (p>0.05, chi-squared test) between catheter type, side of catheter placement, number of catheter lumens, site of catheter placement, or NC duration, and positive NC. There was an association (p=0.04, chi-squared test) between infusion type and positive standard NCs. Viable microorganisms exhibiting intracellular esterase activity were detected on >90% of both NC types (p=0.751), suggesting that a large percentage of organisms were not culturable using the conditions provided in this study. Amplification of the 16S ribosomal RNA gene from selected NCs provided a substantially larger number of operational taxonomic units per NC than PC (26-43 vs 1-4), suggesting that culture-dependent methods may substantially underestimate microbial diversity on NCs. NC bacterial communities were clustered by patient and venous access type and may reflect the composition of the patient's local microbiome but may also contain organisms from the healthcare environment. NCs provide a portal of entry for a wide diversity of opportunistic pathogens to colonize the catheter lumen, forming a biofilm and increasing the potential for CAI, highlighting the importance of catheter maintenance practices to reduce microbial contamination. |
A high-throughput diagnostic method for measuring human exposure to organophosphorus nerve agents
Knaack JS , Zhou Y , Abney CW , Jacob JT , Prezioso SM , Hardy K , Lemire SW , Thomas J , Johnson RC . Anal Chem 2012 84 (21) 9470-7 An automated high-throughput immunomagnetic separation (IMS) method for diagnosing exposure to the organophosphorus nerve agents (OPNAs) sarin (GB), cyclohexylsarin (GF), VX, and Russian VX (RVX) was developed to increase sample processing capacity for emergency response applications. Diagnosis of exposure to OPNAs was based on the formation of OPNA adducts to butyrylcholinesterase (BuChE). Data reported with this method represent a ratio of the agent-specific BuChE adduct concentration, relative to the total BuChE peptide concentration that provides a nonactivity measurement expressed as percent adducted. All magnetic bead transfer steps and washes were performed using instrumentation in a 96-well format allowing for simultaneous extraction of 86 clinical samples plus reference materials. Automating extractions increased sample throughput 50-fold, as compared to a previously reported manual method. The limits of detection, determined using synthetic peptides, were 1 ng/mL for unadducted BuChE and GB-, GF-, VX-, and RVX-adducted BuChE. The automated method was characterized using unexposed serum and serum pools exposed to GB, GF, VX, or RVX. Variation for the measurement of percent adducted was <12% for all characterized quality control serum pools. Twenty-six (26) serum samples from individuals asymptomatic for cholinesterase inhibitor exposure were analyzed using this method, and no background levels of OPNA exposure were observed. Unexposed BuChE serum concentrations measured using this method ranged from 2.8 mcg/mL to 10.6 mcg/mL, with an average concentration of 6.4 mcg/mL. |
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