Last data update: Jun 03, 2024. (Total: 46935 publications since 2009)
Records 1-30 (of 40 Records) |
Query Trace: Limbago BM [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. |
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. |
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. |
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. |
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. |
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. |
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. |
Staphylococcus aureus colonization and strain type at various body sites among patients with a closed abscess and uninfected controls at U.S. emergency departments
Albrecht VS , Limbago BM , Moran GJ , Krishnadasan A , Gorwitz RJ , McDougal LK , Talan DA . J Clin Microbiol 2015 53 (11) 3478-84 INTRODUCTION: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a prevalent cause of skin and soft tissue infections (SSTI), but the association between CA-MRSA colonization and infection remains uncertain. We studied the carriage frequency at several body sites and the diversity of S. aureus strains from patients with and without SSTI. MATERIALS AND METHODS: Case-subjects with a closed skin abscess (i.e., without drainage) and matched control subjects without a skin infection (N=147 each) presenting to 10 U.S. emergency departments were cultured at the nares, throat, rectum, and groin using broth enrichment; wounds were cultured from abscess cases. Methicillin resistance testing and spa typing were performed for all S. aureus isolates. RESULTS: S. aureus was found in 85/147 (57.8%) of abscesses; 49 were MRSA, 36 were MSSA. MRSA colonization was more common among cases (59/147; 40.1%) than controls (27/147; 18.4%) overall (p<0.001), and at each body site; no differences were observed for MSSA. S. aureus-infected subjects were usually (75/85) colonized with the infecting strain; among MRSA-infected subjects this was most common in the groin. The CC8 lineage accounted for most of both infecting and colonizing isolates, although more than 16 distinct strains were identified. Nearly all MRSA infections were inferred as USA300. There was more diversity among colonizing than infecting isolates, and among those isolated from controls versus cases. CONCLUSIONS: CC8 S. aureus is a common colonizer of persons with and without skin infections. Detection of S. aureus colonization, and especially MRSA, may be enhanced by extra-nasal site culture. |
Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.
Bowers JR , Kitchel B , Driebe EM , MacCannell DR , Roe C , Lemmer D , de Man T , Rasheed JK , Engelthaler DM , Keim P , Limbago BM . PLoS One 2015 10 (7) e0133727 Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258. |
Draft Genome Sequence of a New Delhi Metallo-ß-Lactamase-5 (NDM-5)-Producing Multidrug-Resistant Escherichia coli Isolate.
de Man TJ , Perry KA , Avillan JJ , Rasheed JK , Limbago BM . Genome Announc 2015 3 (2) A multidrug-resistant Escherichia coli isolate from an abdominal lesion displayed resistance to all beta-lactams tested, including carbapenems, in addition to macrolides, fluoroquinolones, and tetracycline. Sequence analyses demonstrated the presence of blaNDM-5 in addition to at least 13 genes and 6 efflux pumps associated with antibiotic resistance. |
Burden of Clostridium difficile infection in the United States
Lessa FC , Mu Y , Bamberg WM , Beldavs ZG , Dumyati GK , Dunn JR , Farley MM , Holzbauer SM , Meek JI , Phipps EC , Wilson LE , Winston LG , Cohen JA , Limbago BM , Fridkin SK , Gerding DN , McDonald LC . N Engl J Med 2015 372 (9) 825-34 BACKGROUND: The magnitude and scope of Clostridium difficile infection in the United States continue to evolve. METHODS: In 2011, we performed active population- and laboratory-based surveillance across 10 geographic areas in the United States to identify cases of C. difficile infection (stool specimens positive for C. difficile on either toxin or molecular assay in residents ≥ 1 year of age). Cases were classified as community-associated or health care-associated. In a sample of cases of C. difficile infection, specimens were cultured and isolates underwent molecular typing. We used regression models to calculate estimates of national incidence and total number of infections, first recurrences, and deaths within 30 days after the diagnosis of C. difficile infection. RESULTS: A total of 15,461 cases of C. difficile infection were identified in the 10 geographic areas; 65.8% were health care-associated, but only 24.2% had onset during hospitalization. After adjustment for predictors of disease incidence, the estimated number of incident C. difficile infections in the United States was 453,000 (95% confidence interval [CI], 397,100 to 508,500). The incidence was estimated to be higher among females (rate ratio, 1.26; 95% CI, 1.25 to 1.27), whites (rate ratio, 1.72; 95% CI, 1.56 to 2.0), and persons 65 years of age or older (rate ratio, 8.65; 95% CI, 8.16 to 9.31). The estimated number of first recurrences of C. difficile infection was 83,000 (95% CI, 57,000 to 108,900), and the estimated number of deaths was 29,300 (95% CI, 16,500 to 42,100). The North American pulsed-field gel electrophoresis type 1 (NAP1) strain was more prevalent among health care-associated infections than among community-associated infections (30.7% vs. 18.8%, P<0.001). CONCLUSIONS: C. difficile was responsible for almost half a million infections and was associated with approximately 29,000 deaths in 2011. (Funded by the Centers for Disease Control and Prevention.). |
Prevalence of and risk factors for vancomycin-resistant Staphylococcus aureus precursor organisms in southeastern Michigan
Albrecht VS , Zervos MJ , Kaye KS , Tosh PK , Arshad S , Hayakawa K , Kallen AJ , McDougal LK , Limbago BM , Guh AY . Infect Control Hosp Epidemiol 2014 35 (12) 1531-4 We assessed for vancomycin-resistant Staphylococcus aureus (VRSA) precursor organisms in southeastern Michigan, an area known to have VRSA. The prevalence was 2.5% (pSK41-positive methicillin-resistant S. aureus, 2009-2011) and 1.5% (Inc18-positive vancomycin-resistant Enterococcus, 2006-2013); Inc18 prevalence significantly decreased after 2009 (3.7% to 0.82%). Risk factors for pSK41 included intravenous vancomycin exposure. |
New Delhi metallo-beta-lactamase-producing carbapenem-resistant Escherichia coli associated with exposure to duodenoscopes
Epstein L , Hunter JC , Arwady MA , Tsai V , Stein L , Gribogiannis M , Frias M , Guh AY , Laufer AS , Black S , Pacilli M , Moulton-Meissner H , Rasheed JK , Avillan JJ , Kitchel B , Limbago BM , MacCannell D , Lonsway D , Noble-Wang J , Conway J , Conover C , Vernon M , Kallen AJ . JAMA 2014 312 (14) 1447-55 IMPORTANCE: Carbapenem-resistant Enterobacteriaceae (CRE) producing the New Delhi metallo-beta-lactamase (NDM) are rare in the United States, but have the potential to add to the increasing CRE burden. Previous NDM-producing CRE clusters have been attributed to person-to-person transmission in health care facilities. OBJECTIVE: To identify a source for, and interrupt transmission of, NDM-producing CRE in a northeastern Illinois hospital. DESIGN, SETTING, AND PARTICIPANTS: Outbreak investigation among 39 case patients at a tertiary care hospital in northeastern Illinois, including a case-control study, infection control assessment, and collection of environmental and device cultures; patient and environmental isolate relatedness was evaluated with pulsed-field gel electrophoresis (PFGE). Following identification of a likely source, targeted patient notification and CRE screening cultures were performed. MAIN OUTCOMES AND MEASURES: Association between exposure and acquisition of NDM-producing CRE; results of environmental cultures and organism typing. RESULTS: In total, 39 case patients were identified from January 2013 through December 2013, 35 with duodenoscope exposure in 1 hospital. No lapses in duodenoscope reprocessing were identified; however, NDM-producing Escherichia coli was recovered from a reprocessed duodenoscope and shared more than 92% similarity to all case patient isolates by PFGE. Based on the case-control study, case patients had significantly higher odds of being exposed to a duodenoscope (odds ratio [OR], 78 [95% CI, 6.0-1008], P < .001). After the hospital changed its reprocessing procedure from automated high-level disinfection with ortho-phthalaldehyde to gas sterilization with ethylene oxide, no additional case patients were identified. CONCLUSIONS AND RELEVANCE: In this investigation, exposure to duodenoscopes with bacterial contamination was associated with apparent transmission of NDM-producing E coli among patients at 1 hospital. Bacterial contamination of duodenoscopes appeared to persist despite the absence of recognized reprocessing lapses. Facilities should be aware of the potential for transmission of bacteria including antimicrobial-resistant organisms via this route and should conduct regular reviews of their duodenoscope reprocessing procedures to ensure optimal manual cleaning and disinfection. |
Elevated Staphylococcus ceftriaxone MICs are an Etest artifact
Limbago BM , Pierce VM , Lonsway DR , Ferraro MJ . Clin Infect Dis 2014 60 (1) 162-3 The recent publication by Pickering et al [1] described a collection of methicillin-susceptible Staphylococcus aureus (MSSA) that displayed elevated ceftriaxone minimum inhibitory concentrations (MICs) when tested by Etest (bioMerieux, Durham, North Carolina) gradient diffusion and would have been called “Resistant” to ceftriaxone based on previous Clinical and Laboratory Standards Institute (CLSI) interpretive guidance. The authors reported that approximately 60% of MSSA tested at their institution would have been misclassified based on the current CLSI guidance, which recommends testing staphylococci only against penicillin and oxacillin or cefoxitin in order to infer susceptibility or resistance to other β-lactam agents. This article was available electronically ahead of print for several months. Although it was subsequently retracted as “an honest error in interpretation,” we believe a fuller explanation of the findings could improve understanding among Clinical Infectious Diseases readership. | We investigated the accuracy of the initial report by performing reference broth microdilution (BMD), disk diffusion, and Etest [both low (0.002–32 µg/mL) and high (0.016–256 µg/mL) range ceftriaxone Etest products] antimicrobial susceptibility testing on 8 pulsed field gel electrophoresis (PFGE)-matched pairs of MSSA from the Pickering study [1] reported to have mismatched ceftriaxone susceptibility. All 16 isolates were confirmed as oxacillin, cefoxitin, and ceftriaxone susceptible [2, 3] with BMD and disk methods. Ceftriaxone MICs obtained by both Etest products were typically higher than those obtained with BMD but were still in the susceptible range for 100% of isolates using the high concentration ceftriaxone Etest, and for 93.8% of isolates using the low concentration ceftriaxone Etest (1 isolate tested as intermediate). In addition, 30 consecutive, unique MSSA isolated from blood cultures during 2 months at a single hospital were tested against ceftriaxone byBMD, disk diffusion, and Etest using a single 0.5 McFarland inoculum. All isolates tested ceftriaxone susceptible by disk diffusion and BMD; 13 (43%) isolates tested nonsusceptible with Etest (Table 1). We also note that the Etest ceftriaxone package inserts do not list staphylococci as an organism group for which testing has been cleared [4, 5]. |
Transmission of methicillin-resistant Staphylococcus aureus infection through solid organ transplantation: confirmation via whole genome sequencing.
Wendt JM , Kaul D , Limbago BM , Ramesh M , Cohle S , Denison AM , Driebe EM , Rasheed JK , Zaki SR , Blau DM , Paddock CD , McDougal LK , Engelthaler DM , Keim PS , Roe CC , Akselrod H , Kuehnert MJ , Basavaraju SV . Am J Transplant 2014 14 (11) 2633-9 We describe two cases of donor-derived methicillin-resistant Staphylococcus aureus (MRSA) bacteremia that developed after transplantation of organs from a common donor who died from acute MRSA endocarditis. Both recipients developed recurrent MRSA infection despite appropriate antibiotic therapy, and required prolonged hospitalization and hospital readmission. Comparison of S. aureus whole genome sequence of DNA extracted from fixed donor tissue and recipients' isolates confirmed donor-derived transmission. Current guidelines emphasize the risk posed by donors with bacteremia from multidrug-resistant organisms. This investigation suggests that, particularly in the setting of donor endocarditis, even a standard course of prophylactic antibiotics may not be sufficient to prevent donor-derived infection. |
Epidemiology and prevention of carbapenem-resistant Enterobacteriaceae in the United States
Guh AY , Limbago BM , Kallen AJ . Expert Rev Anti Infect Ther 2014 12 (5) 565-80 Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug-resistant organisms with few treatment options that cause infections associated with substantial morbidity and mortality. CRE outbreaks have been increasingly reported worldwide and are mainly due to the emergence and spread of strains that produce carbapenemases. In the United States, transmission of CRE is primarily driven by the spread of organisms carrying the Klebsiella pneumoniae carbapenemase enzyme, but other carbapenemase enzymes, such as the New-Delhi metallo-beta-lactamase, have also emerged. Currently recommended control strategies for healthcare facilities include the detection of patients infected or colonized with CRE and implementation of measures to prevent further spread. In addition to efforts in individual facilities, effective CRE control requires coordination across all healthcare facilities in a region. This review describes the current epidemiology and surveillance of CRE in the United States and the recommended approach to prevention. |
Thirty-day laboratory-based surveillance for carbapenem-resistant enterobacteriaceae in the Minneapolis-St. Paul metropolitan area
Pereira EC , Shaw KM , Snippes Vagnone PM , Harper JE , Kallen AJ , Limbago BM , Lynfield R . Infect Control Hosp Epidemiol 2014 35 (4) 423-5 Carbapenem-resistant Enterobacteriaceae (CRE) are a growing problem in the United States. We explored the feasibility of active laboratory-based surveillance of CRE in a metropolitan area not previously considered to be an area of CRE endemicity. We provide a framework to address CRE surveillance and to monitor changes in the incidence of CRE infection over time. |
Carbapenem-resistant Klebsiella pneumoniae producing New Delhi metallo-ß-lactamase at an acute care hospital, Colorado, 2012.
Epson EE , Pisney LM , Wendt JM , Maccannell DR , Janelle SJ , Kitchel B , Rasheed JK , Limbago BM , Gould CV , Kallen AJ , Barron MA , Bamberg WM . Infect Control Hosp Epidemiol 2014 35 (4) 390-7 OBJECTIVE: To investigate an outbreak of New Delhi metallo-beta-lactamase (NDM)-producing carbapenem-resistant Enterobacteriaceae (CRE) and determine interventions to interrupt transmission. Design, Setting, and Patients. Epidemiologic investigation of an outbreak of NDM-producing CRE among patients at a Colorado acute care hospital. METHODS: Case patients had NDM-producing CRE isolated from clinical or rectal surveillance cultures (SCs) collected during the period January 1, 2012, through October 20, 2012. Case patients were identified through microbiology records and 6 rounds of SCs in hospital units where they had resided. CRE isolates were tested by real-time polymerase chain reaction for blaNDM. Medical records were reviewed for epidemiologic links; relatedness of isolates was evaluated by pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Infection control (IC) was assessed through staff interviews and direct observations. RESULTS: Two patients were initially identified with NDM-producing CRE during July-August 2012. A third case patient, admitted in May, was identified through microbiology records review. SC identified 5 additional case patients. Patients had resided in 11 different units before identification. All isolates were highly related by PFGE. WGS suggested 3 clusters of CRE. Combining WGS with epidemiology identified 4 units as likely transmission sites. NDM-producing CRE positivity in certain patients was not explained by direct epidemiologic overlap, which suggests that undetected colonized patients were involved in transmission. CONCLUSIONS: A 4-month outbreak of NDM-producing CRE occurred at a single hospital, highlighting the risk for spread of these organisms. Combined WGS and epidemiologic data suggested transmission primarily occurred on 4 units. Timely SC, combined with targeted IC measures, were likely responsible for controlling transmission. |
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