Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 70 Records) |
Query Trace: Limbago B[original query] |
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Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators
Lutgring JD , Kent AG , Bowers JR , Jasso-Selles DE , Albrecht V , Stevens VA , Pfeiffer A , Barnes R , Engelthaler DM , Johnson JK , Gargis AS , Rasheed JK , Limbago BM , Elkins CA , Karlsson M , Halpin AL . Microb Genom 2023 9 (11) Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community. |
Multiplex Real-Time Reverse Transcription PCR for Influenza A Virus, Influenza B Virus, and Severe Acute Respiratory Syndrome Coronavirus 2.
Shu B , Kirby MK , Davis WG , Warnes C , Liddell J , Liu J , Wu KH , Hassell N , Benitez AJ , Wilson MM , Keller MW , Rambo-Martin BL , Camara Y , Winter J , Kondor RJ , Zhou B , Spies S , Rose LE , Winchell JM , Limbago BM , Wentworth DE , Barnes JR . Emerg Infect Dis 2021 27 (7) 1821-1830 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 10(2.0), influenza B virus at 10(2.2), and SARS-CoV-2 at 10(0.3) 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2. |
Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020-May 2021.
Paul P , France AM , Aoki Y , Batra D , Biggerstaff M , Dugan V , Galloway S , Hall AJ , Johansson MA , Kondor RJ , Halpin AL , Lee B , Lee JS , Limbago B , MacNeil A , MacCannell D , Paden CR , Queen K , Reese HE , Retchless AC , Slayton RB , Steele M , Tong S , Walters MS , Wentworth DE , Silk BJ . MMWR Morb Mortal Wkly Rep 2021 70 (23) 846-850 SARS-CoV-2, the virus that causes COVID-19, is constantly mutating, leading to new variants (1). Variants have the potential to affect transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. In November 2020, CDC established national surveillance for SARS-CoV-2 variants using genomic sequencing. As of May 6, 2021, sequences from 177,044 SARS-CoV-2-positive specimens collected during December 20, 2020-May 6, 2021, from 55 U.S. jurisdictions had been generated by or reported to CDC. These included 3,275 sequences for the 2-week period ending January 2, 2021, compared with 25,000 sequences for the 2-week period ending April 24, 2021 (0.1% and 3.1% of reported positive SARS-CoV-2 tests, respectively). Because sequences might be generated by multiple laboratories and sequence availability varies both geographically and over time, CDC developed statistical weighting and variance estimation methods to generate population-based estimates of the proportions of identified variants among SARS-CoV-2 infections circulating nationwide and in each of the 10 U.S. Department of Health and Human Services (HHS) geographic regions.* During the 2-week period ending April 24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. SARS-CoV-2 infections, respectively, demonstrating the rise to predominance of the B.1.1.7 variant of concern(†) (VOC) and emergence of the P.1 VOC in the United States. Using SARS-CoV-2 genomic surveillance methods to analyze surveillance data produces timely population-based estimates of the proportions of variants circulating nationally and regionally. Surveillance findings demonstrate the potential for new variants to emerge and become predominant, and the importance of robust genomic surveillance. Along with efforts to characterize the clinical and public health impact of SARS-CoV-2 variants, surveillance can help guide interventions to control the COVID-19 pandemic in the United States. |
Epidemiologic characteristics associated with SARS-CoV-2 antigen-based test results, rRT-PCR cycle threshold values, subgenomic RNA, and viral culture results from university testing.
Ford L , Lee C , Pray IW , Cole D , Bigouette JP , Abedi GR , Bushman D , Delahoy MJ , Currie DW , Cherney B , Kirby M , Fajardo G , Caudill M , Langolf K , Kahrs J , Zochert T , Kelly P , Pitts C , Lim A , Aulik N , Tamin A , Harcourt JL , Queen K , Zhang J , Whitaker B , Browne H , Medrzycki M , Shewmaker P , Bonenfant G , Zhou B , Folster J , Bankamp B , Bowen MD , Thornburg NJ , Goffard K , Limbago B , Bateman A , Tate JE , Gieryn D , Kirking HL , Westergaard R , Killerby M . Clin Infect Dis 2021 73 (6) e1348-e1355 BACKGROUND: Real-time reverse transcription polymerase chain reaction (rRT-PCR) and antigen tests are important diagnostics for SARS-CoV-2. Sensitivity of antigen tests has been shown to be lower than that of rRT-PCR; however, data to evaluate epidemiologic characteristics that affect test performance are limited. METHODS: Paired mid-turbinate nasal swabs were collected from university students and staff and tested for SARS-CoV-2 using both Quidel Sofia SARS Antigen Fluorescent Immunoassay (FIA) and rRT-PCR assay. Specimens positive by either rRT-PCR or antigen FIA were placed in viral culture and tested for subgenomic RNA (sgRNA). Logistic regression models were used to evaluate characteristics associated with antigen results, rRT-PCR cycle threshold (Ct) values, sgRNA, and viral culture. RESULTS: Antigen FIA sensitivity was 78.9% and 43.8% among symptomatic and asymptomatic participants respectively. Among rRT-PCR positive participants, negative antigen results were more likely among asymptomatic participants (OR 4.6, CI:1.3-15.4) and less likely among participants reporting nasal congestion (OR 0.1, CI:0.03-0.8). rRT-PCR-positive specimens with higher Ct values (OR 0.5, CI:0.4-0.8) were less likely, and specimens positive for sgRNA (OR 10.2, CI:1.6-65.0) more likely, to yield positive virus isolation. Antigen testing was >90% positive in specimens with Ct values <29. Positive predictive value of antigen test for positive viral culture (57.7%) was similar to that of rRT-PCR (59.3%). CONCLUSIONS: SARS-CoV-2 antigen test advantages include low cost, wide availability and rapid turnaround time, making them important screening tests. The performance of antigen tests may vary with patient characteristics, so performance characteristics should be accounted for when designing testing strategies and interpreting results. |
Evaluation of methods for detection of β-lactamase production in MSSA.
Skov R , Lonsway DR , Larsen J , Larsen AR , Samulioniené J , Limbago BM . J Antimicrob Chemother 2021 76 (6) 1487-1494 OBJECTIVES: Correct determination of penicillin susceptibility is pivotal for using penicillin in the treatment of Staphylococcus aureus infections. This study examines the performance of MIC determination, disc diffusion and a range of confirmatory tests for detection of penicillin susceptibility in S. aureus. METHODS: A total of 286 consecutive penicillin-susceptible S. aureus blood culture isolates as well as a challenge set of 62 MSSA isolates were investigated for the presence of the blaZ gene by PCR and subjected to penicillin-susceptibility testing using broth microdilution MIC determination, disc diffusion including reading of the zone edge, two nitrocefin tests and the cloverleaf test. RESULTS: Using PCR-based detection of blaZ as the gold standard, both broth microdilution MIC testing and disc diffusion testing resulted in a relatively low accuracy (82%-93%) with a sensitivity ranging from 49%-93%. Among the confirmatory tests, the cloverleaf test performed with 100% accuracy, while zone edge interpretation and nitrocefin-based tests increased the sensitivity of β-lactamase detection to 96%-98% and 82%-96% when using MIC determination or disc diffusion as primary test, respectively. CONCLUSIONS: This investigation showed that reliable and accurate detection of β-lactamase production in S. aureus can be obtained by MIC determination or penicillin disc diffusion followed by interpretation of the zone edge as a confirmatory test for apparently penicillin-susceptible isolates. The more cumbersome cloverleaf test can also be used. Nitrocefin-based tests should not be used as the only test for confirmation of a presumptive β-lactamase-negative isolate. |
Performance of an Antigen-Based Test for Asymptomatic and Symptomatic SARS-CoV-2 Testing at Two University Campuses - Wisconsin, September-October 2020.
Pray IW , Ford L , Cole D , Lee C , Bigouette JP , Abedi GR , Bushman D , Delahoy MJ , Currie D , Cherney B , Kirby M , Fajardo G , Caudill M , Langolf K , Kahrs J , Kelly P , Pitts C , Lim A , Aulik N , Tamin A , Harcourt JL , Queen K , Zhang J , Whitaker B , Browne H , Medrzycki M , Shewmaker P , Folster J , Bankamp B , Bowen MD , Thornburg NJ , Goffard K , Limbago B , Bateman A , Tate JE , Gieryn D , Kirking HL , Westergaard R , Killerby M . MMWR Morb Mortal Wkly Rep 2021 69 (5152) 1642-1647 Antigen-based tests for SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), are inexpensive and can return results within 15 minutes (1). Antigen tests have received Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for use in asymptomatic and symptomatic persons within the first 5-12 days after symptom onset (2). These tests have been used at U.S. colleges and universities and other congregate settings (e.g., nursing homes and correctional and detention facilities), where serial testing of asymptomatic persons might facilitate early case identification (3-5). However, test performance data from symptomatic and asymptomatic persons are limited. This investigation evaluated performance of the Sofia SARS Antigen Fluorescent Immunoassay (FIA) (Quidel Corporation) compared with real-time reverse transcription-polymerase chain reaction (RT-PCR) for SARS-CoV-2 detection among asymptomatic and symptomatic persons at two universities in Wisconsin. During September 28-October 9, a total of 1,098 paired nasal swabs were tested using the Sofia SARS Antigen FIA and real-time RT-PCR. Virus culture was attempted on all antigen-positive or real-time RT-PCR-positive specimens. Among 871 (79%) paired swabs from asymptomatic participants, the antigen test sensitivity was 41.2%, specificity was 98.4%, and in this population the estimated positive predictive value (PPV) was 33.3%, and negative predictive value (NPV) was 98.8%. Antigen test performance was improved among 227 (21%) paired swabs from participants who reported one or more symptoms at specimen collection (sensitivity = 80.0%; specificity = 98.9%; PPV = 94.1%; NPV = 95.9%). Virus was isolated from 34 (46.6%) of 73 antigen-positive or real-time RT-PCR-positive nasal swab specimens, including two of 18 that were antigen-negative and real-time RT-PCR-positive (false-negatives). The advantages of antigen tests such as low cost and rapid turnaround might allow for rapid identification of infectious persons. However, these advantages need to be balanced against lower sensitivity and lower PPV, especially among asymptomatic persons. Confirmatory testing with an FDA-authorized nucleic acid amplification test (NAAT), such as RT-PCR, should be considered after negative antigen test results in symptomatic persons, and after positive antigen test results in asymptomatic persons (1). |
Evaluation of viral co-infections among patients with community-associated Clostridioides difficile infection
Korhonen L , Cohen J , Gregoricus N , Farley MM , Perlmutter R , Holzbauer SM , Dumyati G , Beldavs Z , Paulick A , Vinjé J , Limbago BM , Lessa FC , Guh AY . PLoS One 2020 15 (10) e0240549 We assessed viral co-infections in 155 patients with community-associated Clostridioides difficile infection in five U.S. sites during December 2012-February 2013. Eighteen patients (12%) tested positive for norovirus (n = 10), adenovirus (n = 4), rotavirus (n = 3), or sapovirus (n = 1). Co-infected patients were more likely than non-co-infected patients to have nausea or vomiting (56% vs 31%; p = 0.04), suggesting that viral co-pathogens contributed to symptoms in some patients. There were no significant differences in prior healthcare or medication exposures or in CDI complications. |
Multispecies Outbreak of Verona Integron-Encoded Metallo-ß-Lactamase-Producing Multidrugresistant Bacteria Driven by a Promiscuous Incompatibility Group A/C2.
de Man TJB , Yaffee AQ , Zhu W , Batra D , Alyanak E , Rowe LA , McAllister G , Moulton-Meissner H , Boyd S , Flinchum A , Slayton RB , Hancock S , Spalding Walters M , Laufer Halpin A , Rasheed JK , Noble-Wang J , Kallen AJ , Limbago BM . Clin Infect Dis 2020 72 (3) 414-420 BACKGROUND: Antibiotic resistance is often spread through bacterial populations via conjugative plasmids. However, plasmid transfer is not well recognized in clinical settings because of technical limitations, and health care-associated infections are usually caused by clonal transmission of a single pathogen. In 2015, multiple species of carbapenem-resistant Enterobacteriaceae (CRE), all producing a rare carbapenemase, were identified among patients in an intensive care unit. This observation suggested a large, previously unrecognized plasmid transmission chain and prompted our investigation. METHODS: Electronic medical record reviews, infection control observations, and environmental sampling completed the epidemiologic outbreak investigation. A laboratory analysis, conducted on patient and environmental isolates, included long-read whole-genome sequencing to fully elucidate plasmid DNA structures. Bioinformatics analyses were applied to infer plasmid transmission chains and results were subsequently confirmed using plasmid conjugation experiments. RESULTS: We identified 14 Verona integron-encoded metallo-ss-lactamase (VIM)-producing CRE in 12 patients, and 1 additional isolate was obtained from a patient room sink drain. Whole-genome sequencing identified the horizontal transfer of blaVIM-1, a rare carbapenem resistance mechanism in the United States, via a promiscuous incompatibility group A/C2 plasmid that spread among 5 bacterial species isolated from patients and the environment. CONCLUSIONS: This investigation represents the largest known outbreak of VIM-producing CRE in the United States to date, which comprises numerous bacterial species and strains. We present evidence of in-hospital plasmid transmission, as well as environmental contamination. Our findings demonstrate the potential for 2 types of hospital-acquired infection outbreaks: those due to clonal expansion and those due to the spread of conjugative plasmids encoding antibiotic resistance across species. |
Qualitative Variation Among Commercial Immunoassays to Detect Measles-Specific IgG.
Latner DR , Sowers SB , Anthony K , Colley H , Badeau C , Coates J , Wong P , Fakile Y , Interiano C , Pannell KB , Leung-Pineda V , Patel MM , Rota PA , Limbago BM , Hickman CJ . J Clin Microbiol 2020 58 (6) Measurement of measles virus-specific IgG is used to assess presumptive evidence of immunity among immunocompetent individuals with uncertain immune or vaccination status. False-negative test results may lead to unnecessary quarantine and exclusion from activities such as employment, education, and travel or result in unnecessary re-vaccination. In contrast, false-positive results may fail to identify susceptible individuals and promote spread of disease by those who are exposed and unprotected. To better understand the performance characteristics of tests to detect measles IgG, we compared five widely used, commercially available measles IgG test platforms using a set of 223 well characterized serum samples. Measles virus neutralizing antibodies were also measured by in vitro plaque reduction neutralization (PRN), the gold standard method and compared to IgG test results. Discrepant results were observed for samples in the low-positive ranges of the most sensitive tests, but there was good agreement across platforms for IgG negative sera and for samples with intermediate to high levels of IgG. False negative test results occurred in approximately 11% of sera, which had low levels of neutralizing antibody. |
Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages.
Frisch MB , Castillo-Ramirez S , Petit RA3rd , Farley MM , Ray SM , Albrecht VS , Limbago BM , Hernandez J , See I , Satola SW , Read TD . mSphere 2018 3 (3) USA500 isolates are clonal complex 8 (CC8) Staphylococcus aureus strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant S. aureus (MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasive S. aureus surveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS256 insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term "USA500" should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.IMPORTANCE In this work, we have removed some of the confusion surrounding the use of the name "USA500," placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years. |
Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis.
Bowers JR , Driebe EM , Albrecht V , McDougal LK , Granade M , Roe CC , Lemmer D , Rasheed JK , Engelthaler DM , Keim P , Limbago BM . mSphere 2018 3 (3) Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described "Canadian epidemic MRSA" strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen.IMPORTANCEStaphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus. |
Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase-48-Like Carbapenemases, United States.
Lutgring JD , Zhu W , de Man TJB , Avillan JJ , Anderson KF , Lonsway DR , Rowe LA , Batra D , Rasheed JK , Limbago BM . Emerg Infect Dis 2018 24 (4) 700-709 Oxacillinase (OXA)-48-like carbapenemases remain relatively uncommon in the United States. We performed phenotypic and genotypic characterization of 30 Enterobacteriaceae producing OXA-48-like carbapenemases that were recovered from patients during 2010-2014. Isolates were collected from 12 states and not associated with outbreaks, although we could not exclude limited local transmission. The alleles beta-lactamase OXA-181 (blaOXA-181) (43%), blaOXA-232 (33%), and blaOXA-48 (23%) were found. All isolates were resistant to ertapenem and showed positive results for the ertapenem and meropenem modified Hodge test and the modified carbapenem inactivation method; 73% showed a positive result for the Carba Nordmann-Poirel test. Whole-genome sequencing identified extended-spectrum beta-lactamase genes in 93% of isolates. In all blaOXA-232 isolates, the gene was on a ColKP3 plasmid. A total of 12 of 13 isolates harboring blaOXA-181 contained the insertion sequence DeltaISEcp1. In all isolates with blaOXA-48, the gene was located on a TN1999 transposon; these isolates also carried IncL/M plasmids. |
Carbapenemase-Producing Organisms: A Global Scourge!
Bonomo RA , Burd EM , Conly J , Limbago BM , Poirel L , Segre JA , Westblade LF . Clin Infect Dis 2017 66 (8) 1290-1297 The dramatic increase in the prevalence and clinical impact of infections caused by bacteria producing carbapenemases is a global health concern. Carbapenemase production is especially problematic when encountered in members of the family Enterobacteriaceae. Due to their ability to readily spread and colonize patients in health care environments, preventing the transmission of these organisms is a major public health initiative and coordinated international effort is needed to contain the risk of infection. Central to the treatment and control of Carbapenemase-producing organisms (CPO) are phenotypic- (growth-/biochemical-dependent) and nucleic acid-based carbapenemase detection tests that identify carbapenemase activity directly or their associated molecular determinants. Importantly, bacterial isolates harboring carbapenemases are often resistant to multiple antibiotic classes resulting in limited therapy options. Emerging agents, novel antibiotic combinations and treatment regimens offer promise for management of these infections. This review highlights our current understanding of CPO with emphasis on their epidemiology, detection, treatment, and control. |
Multicenter Evaluation of the Modified Carbapenem Inactivation Method and the Carba NP for Detection of Carbapenemase-Producing Pseudomonas aeruginosa and Acinetobacter baumannii.
Simner PJ , Johnson JK , Brasso WB , Anderson K , Lonsway DR , Pierce VM , Bobenchik AM , Lockett ZC , Charnot-Katsikas A , Westblade LF , Yoo BB , Jenkins SG , Limbago BM , Das S , Roe-Carpenter DE . J Clin Microbiol 2017 56 (1) The purpose of this study was to develop the modified Carbapenem Inactivation Method (mCIM) for the detection of carbapenemase-producing (CP) Pseudomonas aeruginosa (PA) and Acinetobacter baumannii (AB) and perform a multicenter evaluation of the mCIM and Carba NP tests for these non-fermenters. Thirty P. aeruginosa and 30 A. baumannii isolates previously characterized by whole genome sequencing from the CDC-FDA Antibiotic Resistance Isolate Bank were evaluated, including carbapenemase-producers (CP; Ambler Class A, B, and D), non-carbapenemase-producing (non-CP) carbapenem-resistant isolates, and carbapenem-susceptible isolates. Initial comparison of a 1 microl versus 10 microl loop inoculum for the mCIM was performed by two testing sites and showed that 10 microl was required for reliable detection of carbapenemase production among PA and AB. Ten testing sites then evaluated the mCIM using a 10 microl loop inoculum. Overall, the mean sensitivity and specificity of the mCIM for detection of CP-PA across all ten sites were 98.0% (95% CI: 94.3-99.6; range: 86.7-100) and 95% (95% CI: 89.8-97.7; range: 93.3-100), whereas the mean sensitivity and specificity among CP-AB were 79.8% (95% CI: 74.0-84.9; range: 36.3-95.7) and 52.9% (95% CI: 40.6- 64.9; range: 28.6-100), respectively. At three sites that evaluated the performance of the Carba NP using the same set of isolates, the mean sensitivity and specificity of the Carba NP were 97.8% (95% CI: 88.2-99.9; range: 93.3-100) and 97.8% (95% CI: 88.2-99.9; range: 93.3-100) for PA and 18.8% (95%CI: 10.4-30.1; range: 8.7-26.1) and 100% (95% CI: 83.9-100; range: 100) for AB. Overall, we found both the mCIM and the Carba NP to be accurate for detection of carbapenemases among PA and less reliable for use with AB isolates. |
Multicenter performance assessment of the Carba NP Test
Cunningham SA , Limbago B , Traczewski M , Anderson K , Hackel M , Hindler J , Sahm D , Alyanak E , Lawsin A , Gulvik CA , de Man TJ , Mandrekar JN , Schuetz AN , Jenkins S , Humphries R , Palavecino E , Vasoo S , Patel R . J Clin Microbiol 2017 55 (6) 1954-1960 Eighty Gram-negative bacilli (54 Enterobacteriaceae and 26 non-fermenting Gram-negative bacilli), obtained from multiple institutions in the United States were distributed in a blinded manner to seven testing laboratories to compare the performance of a test for detection of carbapenemase production, the Carba NP test. The Carba NP test was performed by all laboratories, following the Clinical and Laboratory Standards Institute (CLSI) procedure. Site-versus-site comparisons demonstrated a high level of consistency for the Carba NP assay with just 3/21 site comparisons yielding a difference in sensitivity (p<0.05). Previously described limitations with blaOXA-48-like carbapenemases and blaOXA carbapenemases associated with Acinetobacter baumannii were noted. Based on these data, we demonstrate that the Carba NP test, when implemented with the standardized CLSI methodology, provides reproducible results across multiple sites for detection of carbapenemases. |
Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemase Production among Enterobacteriaceae
Pierce VM , Simner PJ , Lonsway DR , Roe-Carpenter DE , Johnson JK , Brasso WB , Bobenchik AM , Lockett ZC , Charnot-Katsikas A , Ferraro MJ , Thomson RB Jr , Jenkins SG , Limbago BM , Das S . J Clin Microbiol 2017 55 (8) 2321-2333 The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. Existing methods each have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended. A validation study was performed in a single clinical laboratory to determine the accuracy of the mCIM, followed by a nine-laboratory study to verify the reproducibility of these results and define the zone size cut-off that best discriminated between CP-CRE and Enterobacteriaceae that do not produce carbapenemases. Bacterial isolates previously characterized through whole genome sequencing or targeted PCR as to the presence or absence of carbapenemase genes were tested for carbapenemase production using the mCIM; isolates with Ambler class A, B, and D carbapenemases, non-CP-CRE isolates, and carbapenem-susceptible isolates were included. The sensitivity of the mCIM observed in the validation study was 99% (95% confidence interval [CI], 93 to 100) and the specificity was 100% (95% CI, 82 to 100). In the second stage of the study, the range of sensitivities observed across nine laboratories was 93% to 100%, with a mean of 97%; the range of specificities was 97% to 100%, with a mean of 99%. The mCIM was easy to perform and interpret for Enterobacteriaceae, with results in less than 24 hours and excellent reproducibility across laboratories. |
Notes from the Field: New Delhi metallo-beta-lactamase-producing carbapenem-resistant Enterobacteriaceae identified in patients without known health care risk factors - Colorado, 2014-2016
Janelle SJ , Kallen A , de Man T , Limbago B , Walters M , Halpin A , Xavier K , Knutsen J , Badolato E , Bamberg WM . MMWR Morb Mortal Wkly Rep 2016 65 (49) 1414-1415 Carbapenem-resistant Enterobacteriaceae (CRE) are considered an urgent threat in the United States because they are associated with high morbidity and mortality, limited treatment options, and potential for rapid spread among patients (1). Carbapenemases, enzymes that confer resistance to the carbapenem class of antibiotics, are believed to contribute to increasing transmission and regional spread of CRE because the genes encoding these enzymes can reside on mobile plasmids and can be transferred among bacterial species. Klebsiella pneumoniae carbapenemase (KPC) is the most common carbapenemase seen in the United States, but isolates with the New Delhi metallo-β-lactamase (NDM) are emerging. Known risk factors for carbapenemase-producing CRE, including NDM, include health care exposures such as hospitalization outside the United States, recent overnight admissions to short-stay and long-term acute care hospitals, residence in long-term care facilities, surgical procedures, and having indwelling devices. Community-associated CRE lack these health care exposures and are rare in the United States (2). During 2014–2016, NDM-producing CRE were isolated from patients in Colorado without known health care risk factors. | The Colorado Department of Public Health and Environment (CDPHE) has conducted statewide laboratory-based surveillance of CRE since November 2012. CRE isolates that are resistant to two or more carbapenems are tested for the KPC and NDM genes by polymerase-chain reaction at the CDPHE laboratory. As of April 2016, Colorado had reported the second highest number of NDM-producing CRE in the United States (3). NDM was first detected in Colorado in 2012 in eight patients during a hospital outbreak (4). Ten additional patients with NDM-producing CRE were identified in Colorado during 2014–2016. Among these 10 patients, the mean age was 64 years (range = 20–85 years); isolates from nine patients were from urine, and in one patient, from bile. Five patients had traveled internationally in the 2 months before specimen collection (two of whom had known hospitalizations during international travel) (Figure). In six patients, the isolate was detected from cultures collected in outpatient settings and lacked the known CRE risk factors of overnight stays in health care settings, dialysis, or surgery in the preceding 12 months, and had no invasive devices in the preceding 2 days (i.e., the isolates were community-associated). |
Vaginal and Rectal Clostridium sordellii and Clostridium perfringens Presence Among Women in the United States
Chong E , Winikoff B , Charles D , Agnew K , Prentice JL , Limbago BM , Platais I , Louie K , Jones HE , Shannon C , NCT01283828 Study Team , Avillan J , Kitchel B , Hubbard A , MacCannell D , Rasheed JK , Callaghan WM , McDonald LC . Obstet Gynecol 2016 127 (2) 360-8 OBJECTIVE: To characterize the presence of Clostridium sordellii and Clostridium perfringens in the vagina and rectum, identify correlates of presence, and describe strain diversity and presence of key toxins. METHODS: We conducted an observational cohort study in which we screened a diverse cohort of reproductive-aged women in the United States up to three times using vaginal and rectal swabs analyzed by molecular and culture methods. We used multivariate regression models to explore predictors of presence. Strains were characterized by pulsed-field gel electrophoresis and tested for known virulence factors by polymerase chain reaction assays. RESULTS: Of 4,152 participants enrolled between 2010 and 2013, 3.4% (95% confidence interval [CI] 2.9-4.0) were positive for C sordellii and 10.4% (95% CI 9.5-11.3) were positive for C perfringens at baseline. Among the 66% with follow-up data, 94.7% (95% CI 88.0-98.3) of those positive for C sordellii and 74.4% (95% CI 69.0-79.3) of those positive for C perfringens at baseline were negative at follow-up. At baseline, recent gynecologic surgery was associated with C sordellii presence, whereas a high body mass index was associated with C perfringens presence in adjusted models. Two of 238 C sordellii isolates contained the lethal toxin gene, and none contained the hemorrhagic toxin gene. Substantial strain diversity was observed in both species with few clusters and no dominant clones identified. CONCLUSION: The relatively rare and transient nature of C sordellii and C perfringens presence in the vagina and rectum makes it inadvisable to use any screening or prophylactic approach to try to prevent clostridial infection. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, www.clinicaltrials.gov, NCT01283828. |
Antimicrobial-resistant pathogens associated with healthcare-associated infections: Summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011-2014
Weiner LM , Webb AK , Limbago B , Dudeck MA , Patel J , Kallen AJ , Edwards JR , Sievert DM . Infect Control Hosp Epidemiol 2016 37 (11) 1-14 OBJECTIVE To describe antimicrobial resistance patterns for healthcare-associated infections (HAIs) that occurred in 2011-2014 and were reported to the Centers for Disease Control and Prevention's National Healthcare Safety Network. METHODS Data from central line-associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated pneumonias, and surgical site infections were analyzed. These HAIs were reported from acute care hospitals, long-term acute care hospitals, and inpatient rehabilitation facilities. Pooled mean proportions of pathogens that tested resistant (or nonsusceptible) to selected antimicrobials were calculated by year and HAI type. RESULTS Overall, 4,515 hospitals reported that at least 1 HAI occurred in 2011-2014. There were 408,151 pathogens from 365,490 HAIs reported to the National Healthcare Safety Network, most of which were reported from acute care hospitals with greater than 200 beds. Fifteen pathogen groups accounted for 87% of reported pathogens; the most common included Escherichia coli (15%), Staphylococcus aureus (12%), Klebsiella species (8%), and coagulase-negative staphylococci (8%). In general, the proportion of isolates with common resistance phenotypes was higher among device-associated HAIs compared with surgical site infections. Although the percent resistance for most phenotypes was similar to earlier reports, an increase in the magnitude of the resistance percentages among E. coli pathogens was noted, especially related to fluoroquinolone resistance. CONCLUSION This report represents a national summary of antimicrobial resistance among select HAIs and phenotypes. The distribution of frequent pathogens and some resistance patterns appear to have changed from 2009-2010, highlighting the need for continual, careful monitoring of these data across the spectrum of HAI types. Infect Control Hosp Epidemiol 2016;1-14. |
SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor.
de Man TJ , Limbago BM . mSphere 2016 1 (1) We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included. Unique about this tool is the ability to easily detect putative new alleles and truncated versions of existing AR genes. Variants and potential new alleles are brought to the attention of the user for further investigation. For instance, SSTAR is able to identify modified or truncated versions of porins, which may be of great importance in carbapenemase-negative carbapenem-resistant Enterobacteriaceae. SSTAR is written in Java and is therefore platform independent and compatible with both Windows and Unix operating systems. SSTAR and its manual, which includes a simple installation guide, are freely available from https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance -SSTAR-. IMPORTANCE Whole-genome sequencing (WGS) is quickly becoming a routine method for identifying genes associated with antimicrobial resistance (AR). However, for many microbiologists, the use and analysis of WGS data present a substantial challenge. We developed SSTAR, software with a graphical user interface that enables the identification of known AR genes from WGS and has the unique capacity to easily detect new variants of known AR genes, including truncated protein variants. Current software solutions do not notify the user when genes are truncated and, therefore, likely nonfunctional, which makes phenotype predictions less accurate. SSTAR users can apply any AR database of interest as a reference comparator and can manually add genes that impact resistance, even if such genes are not resistance determinants per se (e.g., porins and efflux pumps). |
Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.
de Man TJ , Perry KA , Lawsin A , Coulliette AD , Jensen B , Toney NC , Limbago BM , Noble-Wang J . Genome Announc 2016 4 (2) Mycobacterium wolinskyi is a nonpigmented, rapidly growing nontuberculous mycobacterium species that is associated with bacteremia, peritonitis, infections associated with implants/prostheses, and skin and soft tissue infections often following surgical procedures in humans. Here, we report the first functionally annotated draft genome sequence of M. wolinskyi CDC_01. |
Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention.
Halpin AL , de Man TJ , Kraft CS , Perry KA , Chan AW , Lieu S , Mikell J , Limbago BM , McDonald LC . Am J Infect Control 2016 44 (7) 830-6 BACKGROUND: Composition and diversity of intestinal microbial communities (microbiota) are generally accepted as a risk factor for poor outcomes; however, we cannot yet use this information to prevent adverse outcomes. METHODS: Stool was collected from 8 long-term acute care hospital patients experiencing diarrhea and 2 fecal microbiota transplant donors; 16S rDNA V1-V2 hypervariable regions were sequenced. Composition and diversity of each sample were described. Stool was also tested for Clostridium difficile, vancomycin-resistant enterococci (VRE), and carbapenem-resistant Enterobacteriaceae. Associations between microbiota diversity and demographic and clinical characteristics, including antibiotic use, were analyzed. RESULTS: Antibiotic exposure and Charlson Comorbidity Index were inversely correlated with diversity (Spearman = -0.7). Two patients were positive for VRE; both had microbiomes dominated by Enterococcus faecium, accounting for 67%-84% of their microbiome. CONCLUSIONS: Antibiotic exposure correlated with diversity; however, other environmental and host factors not easily obtainable in a clinical setting are also known to impact the microbiota. Therefore, direct measurement of microbiome disruption by sequencing, rather than reliance on surrogate markers, might be most predictive of adverse outcomes. If and when microbiome characterization becomes a standard diagnostic test, improving our understanding of microbiome dynamics will allow for interpretation of results to improve patient outcomes. |
What's in a name? The impact of accurate Staphylococcus pseudintermedius identification on appropriate antimicrobial susceptibility testing
Limbago BM . J Clin Microbiol 2016 54 (3) 516-7 Bacteria in the Staphylococcus intermedius, including Staphylococcus pseudintermedius, often encode mecA-mediated methicillin resistance. Reliable detection of this phenotype for proper treatment and infection control decisions requires that these coagulase-positive staphylococci are accurately identified, and specifically that they are not misidentified as S. aureus. As correct species-level bacterial identification becomes more commonplace in clinical laboratories, one can expect to see changes in guidance for antimicrobial susceptibility testing and interpretation. The study by Wu et al. (J Clin Microbiol, 54:XXXXXX, 2016, http://dx.doi.org/10.1128/JCM.02864-15) in this issue highlights the impact of robust identification of Staphylococcus intermedius group organisms on the selection of appropriate antimicrobial susceptibility testing methods and interpretation. |
The problem of carbapenemase producing carbapenem-resistant Enterobacteriaceae detection
Lutgring JD , Limbago BM . J Clin Microbiol 2016 54 (3) 529-34 The emergence and spread of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is a significant clinical and public health concern. Reliable detection of CP-CRE is the first step in combating this problem. There are both phenotypic and molecular methods available for CP-CRE detection. There is no single detection method that is ideal for all situations. |
Evaluation of an immunochromatographic assay for rapid detection of penicillin-binding protein 2a in human and animal Staphylococcus intermedius group, Staphylococcus lugdunensis, and Staphylococcus schleiferi clinical isolates
Arnold AR , Burham CD , Ford BA , Lawhon SD , McAllister SK , Lonsway D , Albrecht V , Jerris RC , Rasheed JK , Limbago B , Burd EM , Westblade LF . J Clin Microbiol 2015 54 (3) 745-8 The performance of a rapid penicillin-binding protein 2a (PBP2a) detection assay, the Alere PBP2a Culture Colony Test, was evaluated for identification of PBP2a-mediated beta-lactam resistance in human and animal clinical isolates of Staphylococcus intermedius group, Staphylococcus lugdunensis, and Staphylococcus schleiferi. The assay was sensitive and specific, with all PBP2a-negative and -positive strains testing negative and positive, respectively. |
Notes from the field: Carbapenem-resistant Enterobacteriaceae producing OXA-48-like carbapenemases - United States, 2010-2015
Lyman M , Walters M , Lonsway D , Rasheed K , Limbago B , Kallen A . MMWR Morb Mortal Wkly Rep 2015 64 (47) 1315-6 Carbapenem-resistant Enterobacteriaceae (CRE) are bacteria that are often resistant to most classes of antibiotics and cause health care-associated infections with high mortality rates Among CRE, strains that carry plasmid-encoded carbapenemase enzymes that inactivate carbapenem antibiotics are of greatest public health concern because of their potential for rapid global dissemination, as evidenced by the increasing distribution of CRE that produce the Klebsiella pneumoniae carbapenemase and the New Delhi metallo-beta-lactamase. Newly described resistance in Enterobacteriaceae, such as plasmid-mediated resistance to the last-line antimicrobial colistin, recently detected in China, and resistance to the newly approved antimicrobial, ceftazidime-avibactam, identified from a U.S. K. pneumoniae carbapenemase-producing isolate, highlight the continued urgency to delay spread of CRE. Monitoring the emergence of carbapenemases is crucial to limiting their spread; identification of patients carrying carbapenemase-producing CRE should result in the institution of transmission-based precautions and enhanced environmental cleaning to prevent transmission. The OXA-48 carbapenemase was first identified in Enterobacteriaceae in Turkey in 2001, and OXA-48-like variants have subsequently been reported around the world. The first U.S. reports of OXA-48-like carbapenemases were published in 2013 and included retrospectively identified isolates from 2009 and two isolates collected in 2012 from patients in Virginia who had recently been hospitalized outside the United States. Although there are limited additional published reports from the United States, CDC continues to receive reports of these organisms. This report describes patients identified as carrying CRE producing OXA-48-like carbapenemases in the United States during June 2010-August 2015. |
Investigation of a cluster of Clostridium difficile infections in a pediatric oncology setting
Dantes R , Epson EE , Dominguez SR , Dolan S , Wang F , Hurst A , Parker SK , Johnston H , West K , Anderson L , Rasheed JK , Moulton-Meissner H , Noble-Wang J , Limbago B , Dowell E , Hilden JM , Guh A , Pollack LA , Gould CV . Am J Infect Control 2015 44 (2) 138-45 BACKGROUND: We investigated an increase in Clostridium difficile infection (CDI) among pediatric oncology patients. METHODS: CDI cases were defined as first C difficile positive stool tests between December 1, 2010, and September 6, 2012, in pediatric oncology patients receiving inpatient or outpatient care at a single hospital. A case-control study was performed to identify CDI risk factors, infection prevention and antimicrobial prescribing practices were assessed, and environmental sampling was conducted. Available isolates were strain-typed by pulsed-field gel electrophoresis. RESULTS: An increase in hospital-onset CDI cases was observed from June-August 2012. Independent risk factors for CDI included hospitalization in the bone marrow transplant ward and exposure to computerized tomography scanning or cefepime in the prior 12 weeks. Cefepime use increased beginning in late 2011, reflecting a practice change for patients with neutropenic fever. There were 13 distinct strain types among 22 available isolates. Hospital-onset CDI rates decreased to near-baseline levels with enhanced infection prevention measures, including environmental cleaning and prolonged contact isolation. CONCLUSION: C difficile strain diversity associated with a cluster of CDI among pediatric oncology patients suggests a need for greater understanding of modes and sources of transmission and strategies to reduce patient susceptibility to CDI. Further research is needed on the risk of CDI with cefepime and its use as primary empirical treatment for neutropenic fever. |
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. |
Vancomycin-resistant Staphylococcus aureus - Delaware, 2015
Walters MS , Eggers P , Albrecht V , Travis T , Lonsway D , Hovan G , Taylor D , Rasheed K , Limbago B , Kallen A . MMWR Morb Mortal Wkly Rep 2015 64 (37) 1056 Vancomycin-resistant Staphylococcus aureus (VRSA) is a rare, multidrug-resistant bacterium of public health concern that emerged in the United States in 2002. VRSA (S. aureus with vancomycin minimum inhibitory concentration [MIC] ≥16 µg/mL) arises when vancomycin resistance genes (e.g., the vanA operon, which codes for enzymes that result in modification or elimination of the vancomycin binding site) from vancomycin-resistant enterococci (VRE) are transferred to S. aureus (1). To date, all VRSA strains have arisen from methicillin-resistant S. aureus (MRSA). The fourteenth VRSA isolate (VRSA 14) identified in the United States was reported to CDC in February 2015. | VRSA 14 was cultured from the chronic toe wound of a patient in Delaware with diabetes mellitus and end-stage renal disease requiring hemodialysis; vancomycin-resistant Enterococcus faecalis was also isolated from this culture. The wound was first noted during an inpatient admission in April 2014. MRSA was isolated in August and October 2014, and MRSA and VRE were isolated in January 2015; these isolates are not available for further characterization. No antibiotic use was reported in the 4 months before VRSA isolation. | The VRSA and VRE toe wound isolates (February 2015) and an MRSA isolate from a nasal swab from the patient (March 2015) were sent to CDC for further characterization. The VRSA and VRE were confirmed to be resistant to vancomycin (MICs = 512 µg/mL for both); polymerase chain reaction testing confirmed the presence of vanA in both isolates. Pulsed-field gel electrophoresis and S. aureus protein A (spa) typing identified both the VRSA and MRSA as types USA100 and t002, placing them in staphylococcal clonal complex 5. This indicates that VRSA 14 has a health care–associated strain background, as do VRSA 1–12. Among VRSA isolated in the United States, only VRSA 13 had a community-associated strain background (2). |
Improved Phenotype-Based Definition for Identifying Carbapenemase Producers among Carbapenem-Resistant Enterobacteriaceae.
Chea N , Bulens SN , Kongphet-Tran T , Lynfield R , Shaw KM , Vagnone PS , Kainer MA , Muleta DB , Wilson L , Vaeth E , Dumyati G , Concannon C , Phipps EC , Culbreath K , Janelle SJ , Bamberg WM , Guh AY , Limbago B , Kallen AJ . Emerg Infect Dis 2015 21 (9) 1611-6 Preventing transmission of carbapenemase-producing, carbapenem-resistant Enterobacteriaceae (CP-CRE) is a public health priority. A phenotype-based definition that reliably identifies CP-CRE while minimizing misclassification of non-CP-CRE could help prevention efforts. To assess possible definitions, we evaluated enterobacterial isolates that had been tested and deemed nonsusceptible to >1 carbapenem at US Emerging Infections Program sites. We determined the number of non-CP isolates that met (false positives) and CP isolates that did not meet (false negatives) the Centers for Disease Control and Prevention CRE definition in use during our study: 30% (94/312) of CRE had carbapenemase genes, and 21% (14/67) of Klebsiella pneumoniae carbapenemase-producing Klebsiella isolates had been misclassified as non-CP. A new definition requiring resistance to 1 carbapenem rarely missed CP strains, but 55% of results were false positive; adding the modified Hodge test to the definition decreased false positives to 12%. This definition should be considered for use in carbapenemase-producing CRE surveillance and prevention. |
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