Karen Lolans

University of Chicago | UC · Medicine, Gastroenterology

Emerging and re-emerging respiratory viruses can spread rapidly and cause pandemics as demonstrated by the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The early human immune responses to respiratory viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory at the time of...

Background A crucial barrier to the routine application of whole-genome sequencing (WGS) for infection prevention is the insufficient criteria for determining whether a genomic linkage is consistent with transmission within the facility. We evaluated the use of single-nucleotide variant (SNV) thresholds, as well as a novel threshold-free approach,...

Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. The Ψ derivative, N1-methyl-Ψ, substitutes every U residue in the Pfizer/BioNTech and Moderna COVID mRNA vaccines. Previous research revealed that Ψ increases translation of...

To understand how a bacterium ultimately succeeds or fails in adapting to a new environment, it is essential to assess the temporal dynamics of its fitness over the course of colonization. The mammalian gut, into which exogenous microorganisms are regularly introduced, represents a biologically and clinically relevant system to explore microbial ad...

By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long‐read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long‐read sequencing experiments demand high concentrations of highly purified DNA of high mole...

Background ICU universal decolonization with daily chlorhexidine (CHG) baths plus mupirocin nasal decolonization reduces all-cause bloodstream infections (BSI) and MRSA clinical cultures. We assessed nasal iodophor, an antiseptic less susceptible to resistance, in place of mupirocin. Methods We conducted a cluster randomized non-inferiority trial...

Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training, machine learning modeling, and single-read linka...

Background: Identification of hospitalized patients with enteric multidrug-resistant organism (MDRO) carriage, combined with implementation of targeted infection control interventions, may help reduce MDRO transmission. However, the optimal surveillance approach has not been defined. We sought to determine whether daily serial rectal surveillance f...

A detailed understanding of gut microbial ecology is essential to engineer effective microbial therapeutics and to model microbial community assembly and succession in health and disease. However, establishing generalizable insights into the functional determinants of microbial fitness in the human gut has been a formidable challenge. Here we emplo...

By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long-read sequencing experiments demand high concentrations of highly purified DNA of high mole...

Background MDRO detection in colonized patients may be intermittent for reasons that are incompletely understood. We examined temporal patterns of gut MDRO colonization after initial MDRO detection by rectal swab screening, and determined the relationship of culture positivity to the relative abundance of corresponding MDRO operational taxonomic un...

Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that b...

Background: Long-term acute-care hospitals (LTACHs) are disproportionately burdened by multidrug-resistant organisms (MDROs) like KPC-Kp. Although cohorting KPC-Kp+ patients into rooms with other carriers can be an outbreak-control strategy and may protect negative patients from colonization, it is unclear whether cohorted patients are at unintende...

Background Carbapenem-resistant Enterobacteriaceae have been recognized as an urgent antibiotic resistance threat for more than a decade. Despite this attention, their prevalence has remained steady or increased in some settings, suggesting that transmission pathways remain uncontrolled by current prevention strategies. We hypothesized that these t...

Objective Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) protects uncolonized patients from acquiring MDROs in healthcare settings. The potential for cross transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits is...

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong t...

Objective: Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) has been demonstrated to protect uncolonized patients from acquiring MDROs in healthcare settings. A neglected aspect of cohorting is the potential for cross-transmission within the cohort and the possibility of colonized patients acquiring second...

Background Among hospitalized patients, underlying variation in gut microbiota may confer differential risk for gut MDRO acquisition. Methods Rectal swab samples were collected from patients ≤2 days of MICU admission and then daily in the 27-bed MICU of an acute care hospital in Chicago, IL over 1 year. Patients were screened for MDRO colonization...

Background CHG bathing is used to suppress patients’ microbial skin colonization, in order to prevent infections and transmission of multidrug-resistant organisms. Prior work has suggested that microbial growth is inhibited when CHG skin concentrations exceed threshold levels. Methods We conducted 6 single-day surveys from January 2018 to February...

Background Higher CHG skin levels may be needed to adequately control infection and transmission of pathogens in the ICU. We assessed whether measurement and feedback of patient CHG skin concentrations could improve CHG bathing quality and identified factors associated with higher CHG skin concentrations. Methods We conducted 6 one-day surveys fro...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Objective We assessed the impact of personal protective equipment (PPE) doffing errors on healthcare worker (HCW) contamination with multidrug-resistant organisms (MDROs). Design Prospective, observational study. Setting The study was conducted at 4 adult ICUs at 1 tertiary-care teaching hospital. Participants HCWs who cared for patients on cont...

Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia's unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the development of new vector control strategies. However,...

The original version of this Article contained an error in Fig. 1a, in which the sequences of the reverse and forward primers were swapped

Background Clinical culture results are sometimes used to estimate the burden of multidrug-resistant organisms (MDROs) in hospitals. The association between positive clinical culture results and prevalence of MDROs in the gut is incompletely understood. Methods Rectal swab or stool samples were collected daily from adult medical intensive care uni...

Background: An association between increased relative abundance of specific bacterial taxa in the intestinal microbiota and bacteremia has been reported in some high-risk patient populations. Methods: We collected weekly rectal swab samples from patients at one long-term acute care hospital (LTACH) in Chicago from May 2015 - May 2016. Samples we...

Background Identification of gut microbiota features associated with antibiotic-resistant bacterial colonization may reveal new infection prevention targets. Methods We conducted a matched, case-control study of long-term acute care hospital (LTACH) patients to identify gut microbiota and clinical features associated with colonization by Klebsiell...

BACKGROUND Bathing intensive care unit (ICU) patients with 2% chlorhexidine gluconate (CHG)–impregnated cloths decreases the risk of healthcare-associated bacteremia and multidrug-resistant organism transmission. Hospitals employ different methods of CHG bathing, and few studies have evaluated whether those methods yield comparable results. OBJECT...

Background: In 2007, Illinois became the first state in the United States to mandate active surveillance of methicillin-resistant Staphylococcus aureus (MRSA). The Illinois law applies to intensive care unit (ICU) patients; contact precautions are required for patients found to be MRSA-colonized. However, the effectiveness of a legislated "search...

Development of effective strategies to limit the proliferation of multidrug-resistant organisms requires a thorough understanding of how such organisms spread among health care facilities. We sought to uncover the chains of transmission underlying a 2008 U.S. regional outbreak of carbapenem-resistant Klebsiella pneumoniae by performing an integrate...

Background Colonization with KPC-Kp precedes infection and represents a potential target for intervention. To identify microbial signatures associated with KPC-Kp acquisition, we conducted a prospective, longitudinal study of the fecal microbiota in LTACH patients at risk of acquiring KPC-Kp. Methods We collected admission and weekly rectal swab s...

Background Two strains of influenza B virus, B/Yamagata and B/Victoria, co-circulate in the USA, typically appearing in late March. This year, influenza B virus (FluB) co-circulated consistently with influenza A virus (FluA). We hypothesized that this could be explained by an increased use of influenza trivalent vaccine, which lacks the B/Yamagata...

To compare two culture methods (nylon fiber flocked swabs with broth enrichment versus RODAC plates) for recovery of multidrug resistant organisms, 780 environmental surfaces in 63 rooms of patients on contact precautions in four intensive care units at one hospital were examined. Among sites that had at least one positive culture, swab culture wit...

Background Patients in long-term acute care hospitals (LTACHs) in the Chicago region have high prevalence of CPO carriage (in previous point prevalence surveys, ~30%). vSNFs care for a similarly ill population and often receive patient transfers from LTACHs. Based on these observations and our results from an earlier study, we hypothesized that vSN...

OBJECTIVE To identify modifiable risk factors for acquisition of Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC) colonization among long-term acute-care hospital (LTACH) patients. DESIGN Multicenter, matched case-control study. SETTING Four LTACHs in Chicago, Illinois. PARTICIPANTS Each case patient included in this study...

Abstract Background Sample collection for gut microbiota analysis from in-patients can be challenging. Collection method and storage conditions are potential sources of variability. In this study, we compared the bacterial microbiota from stool stored under different conditions, as well as stool and swab samples, to assess differences due to sample...

Background High prevalence of Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC) has been reported in long-term acute care hospitals (LTACHs), in part because of frequent readmissions of colonized patients. Knowledge of the duration of colonization with KPC is essential to identify patients at risk of KPC colonization upon readm...

Whether targeted or universal decolonization strategies for control of methicillin-resistant Staphylococcus aureus (MRSA) select for resistance to decolonizing agents is unresolved. The REDUCE MRSA trial provided an opportunity to investigate this question. REDUCE-MRSA was a 3-arm, cluster-randomized trial of screening and isolation without decolon...

There has been an increasing interest in the use of probiotic products for the prevention of Clostridium difficile infection (CDI). Bio-K+(®) is a commercial probiotic product comprising three strains of lactobacilli-Lactobacillus acidophilus CL1285(®), Lact. casei LBC80R(®) and Lact. rhamnosus CLR2(®)-that have been applied to prevent CDI. General...

Background: Routine skin cleansing with CHG is an effective strategy to prevent infection and cross-transmission of bacterial pathogens in healthcare settings. Whether daily CHG bathing selects for CHG resistance is unresolved. � Methods: We collected swab samples of patients' skin to monitor minimal inhibitory concentrations (MICs) of CHG for KPC-...

Background: Enterobacteriaceae that produce KPC often carry multiple β-lactamase genes, some conferring broad spectrum β-lactam resistance. Distinct β-lactamase resistome types may serve as markers of strain relatedness to identify potential outbreaks. Methods: We studied 363 KPC-producing Enterobacteriaceae recovered from 81 distinct hospital poin...

Background: LTACHs have high prevalence of KPC, but few studies have investigated the risk factors. Methods: We conducted a case-control study to determine risk factors for acquisition of KPC rectal colonization in patients at 4 LTACHs from 6/2012 - 6/2013 during a bundled KPC control intervention (KPC admission and biweekly screening; contact isol...

Background: Stool is the standard sample type for human gastrointestinal microbiota analysis. However, stool collection from in-patients can be challenging, making collection of rectal swabs a more feasible sampling approach. In this study, we compared the microbiota from stool and rectal swab samples to assess differences due to sample collection...

Background In theory, active surveillance of methicillin-resistant Staphylococcus aureus (MRSA) reduces MRSA spread by identifying all MRSA-colonized patients and placing them under contact precautions. In October 2007, Illinois mandated active MRSA surveillance in all intensive care units, including neonatal intensive care units (NICUs) and pediat...

OBJECTIVE Prevalence of bla KPC -encoding Enterobacteriaceae (KPC) in Chicago long-term acute care hospitals (LTACHs) rose rapidly after the first recognition in 2007. We studied the epidemiology and transmission capacity of KPC in LTACHs and the effect of patient cohorting. METHODS Data were available from 4 Chicago LTACHs from June 2012 to June...

Background: The CDC's Detect and Protect strategy encourages hospitals to be aware of CRE-positive patients; strategies include active surveillance and optimizing inter-facility communication for transfers. CRE detection approaches may vary among short-term & long term acute care hospitals (STACHs & LTACHs). Since Nov 2013, Illinois hospitals can q...

Background. Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC) are an increasing threat to healthcare institutions. Long-term acute care hospitals (LTACHs) have especially high prevalence of KPC. Methods. Using a stepped-wedge design, we tested whether a bundled intervention (screening patients for KPC rectal colonization upon a...

Background: Nosocomial outbreaks of Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC) are being reported increasingly. The first recognition of KPC in metropolitan Chicago, Illinois, USA, was in 2007. Prevalence rose rapidly thereafter, especially in long-term acute care hospitals (LTACHs). Using mathematical models we studied...

Background: Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC) are endemic in the USA and prevalence is especially high in long-term acute care hospitals (LTACHs). There, vulnerable patients are in close proximity to each other, allowing infections to spread easily. Another important aspect of LTACHs is the high readmission rate...