Publications by authors named "Evan S Snitkin"

44 Publications

Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection.

mSystems 2021 Mar 16;6(2). Epub 2021 Mar 16.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

Carbapenem-resistant (CRKP) is a critical-priority antibiotic resistance threat that has emerged over the past several decades, spread across the globe, and accumulated resistance to last-line antibiotic agents. While CRKP infections are associated with high mortality, only a subset of patients acquiring CRKP extraintestinal colonization will develop clinical infection. Here, we sought to ascertain the relative importance of patient characteristics and CRKP genetic background in determining patient risk of infection. Machine learning models classifying colonization versus infection were built using whole-genome sequences and clinical metadata from a comprehensive set of 331 CRKP extraintestinal isolates collected across 21 long-term acute-care hospitals over the course of a year. Model performance was evaluated based on area under the receiver operating characteristic curve (AUROC) on held-out test data. We found that patient and genomic features were predictive of clinical CRKP infection to similar extents (AUROC interquartile ranges [IQRs]: patient = 0.59 to 0.68, genomic = 0.55 to 0.61, combined = 0.62 to 0.68). Patient predictors of infection included the presence of indwelling devices, kidney disease, and length of stay. Genomic predictors of infection included presence of the ICEKp10 mobile genetic element carrying the yersiniabactin iron acquisition system and disruption of an O-antigen biosynthetic gene in a sublineage of the epidemic ST258 clone. Altered O-antigen biosynthesis increased association with the respiratory tract, and subsequent ICEKp10 acquisition was associated with increased virulence. These results highlight the potential of integrated models including both patient and microbial features to provide a more holistic understanding of patient clinical trajectories and ongoing within-lineage pathogen adaptation. Multidrug-resistant organisms, such as carbapenem-resistant (CRKP), colonize alarmingly large fractions of patients in regions of endemicity, but only a subset of patients develop life-threatening infections. While patient characteristics influence risk for infection, the relative contribution of microbial genetic background to patient risk remains unclear. We used machine learning to determine whether patient and/or microbial characteristics can discriminate between CRKP extraintestinal colonization and infection across multiple health care facilities and found that both patient and microbial factors were predictive. Examination of informative microbial genetic features revealed variation within the ST258 epidemic lineage that was associated with respiratory tract colonization and increased rates of infection. These findings indicate that circulating genetic variation within a highly prevalent epidemic lineage of CRKP influences patient clinical trajectories. In addition, this work supports the need for future studies examining the microbial genetic determinants of clinical outcomes in human populations, as well as epidemiologic and experimental follow-ups of identified features to discern generalizability and biological mechanisms.
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http://dx.doi.org/10.1128/mSystems.00177-21DOI Listing
March 2021

cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets.

BMC Bioinformatics 2021 Feb 15;22(1):70. Epub 2021 Feb 15.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA.

Background: The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis.

Results: We illustrate that cognac is able to rapidly identify phylogenetic marker genes using a data driven approach and efficiently generate concatenated gene alignments for very large genomic datasets. To benchmark our tool, we generated core gene alignments for eight unique genera of bacteria, including a dataset of over 11,000 genomes from the genus Escherichia producing an alignment with 1353 genes, which was constructed in less than 17 h.

Conclusions: We demonstrate that cognac presents an efficient method for generating concatenated gene alignments for phylogenetic analysis. We have released cognac as an R package ( https://github.com/rdcrawford/cognac ) with customizable parameters for adaptation to diverse applications.
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http://dx.doi.org/10.1186/s12859-021-03981-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7885345PMC
February 2021

Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail.

Clin Infect Dis 2021 Jan 4. Epub 2021 Jan 4.

Section of Infectious Diseases, Rush University Medical Center/Cook County Health, Chicago, IL, USA.

Background: Congregate settings, such as jails, may be a location where colonized detainees transmit MRSA. We examined MRSA acquisition during incarceration and characterized the genomic epidemiology of MRSA entering the jail and isolated during incarceration.

Methods: Males incarcerated at the Cook County Jail were enrolled within 72 hours of intake and MRSA surveillance cultures collected. Detainees in jail at Day30 were re-cultured to determine MRSA acquisition. A survey was administered to identify acquisition predictors. Genomic sequencing of surveillance and clinical isolates was integrated with epidemiologic and jail location data to track MRSA transmission pathways.

Results: 800 males were enrolled; 19% MRSA colonized at intake. Of 184 who reached Day30 visit, 12 acquired MRSA. Heroin use before entering (OR 3.67,p=0.05) and sharing personal items during incarceration (OR=4.92,p=.01) were predictors of acquisition. Sequenced clinical USA300 isolates (n=112) were more genetically similar than diverse intake USA300 strains (p<0.001), suggesting jail transmission. Four acquired colonization isolates were within 20 SNVs of other isolates; 4 were within 20SNVs of an intake isolate, 2 for an acquisition isolate, and 1 for a clinical isolate. Individuals with genetically similar isolates were more likely to have had overlapping stays in the same buildings.

Conclusion: There was a high MRSA burden entering jail. Genomic analysis of acquisition and clinical isolates suggests potential spread of incoming strains and networks of spread during incarceration, with spread often occurring among detainees housed in similar locations. Sharing personal items during incarceration is associated with MRSA acquisition and could be a focus for intervention.
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http://dx.doi.org/10.1093/cid/ciaa1937DOI Listing
January 2021

Homologous Recombination in Mediates Diversification of Cell Surface Features and Transport Systems.

mSphere 2020 11 18;5(6). Epub 2020 Nov 18.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA

Illness caused by the pathogen is widespread and can range in severity from mild diarrhea to sepsis and death. Strains of isolated from human infections exhibit great genetic diversity, leading to the hypothesis that the genetic background of the infecting strain at least partially determines a patient's clinical course. However, although certain strains of have been suggested to be associated with increased severity, strain typing alone has proved insufficient to explain infection severity. The limited explanatory power of strain typing has been hypothesized to be due to genetic variation within strain types, as well as genetic elements shared between strain types. Homologous recombination is an evolutionary mechanism that can result in large genetic differences between two otherwise clonal isolates, and also lead to convergent genotypes in distantly related strains. More than 400 genomes were analyzed here to assess the effect of homologous recombination within and between clades. Almost three-quarters of single nucleotide variants in the phylogeny are predicted to be due to homologous recombination events. Furthermore, recombination events were enriched in genes previously reported to be important to virulence and host-pathogen interactions, such as flagella, cell wall proteins, and sugar transport and metabolism. Thus, by exploring the landscape of homologous recombination in , we identified genetic loci whose elevated rates of recombination mediated diversification, making them strong candidates for being mediators of host-pathogen interaction in diverse strains of Infections with result in up to half a million illnesses and tens of thousands of deaths annually in the United States. The severity of illness is dependent on both host and bacterial factors. Studying the evolutionary history of pathogens is important for understanding the variation in pathogenicity of these bacteria. This study examines the extent and targets of homologous recombination, a mechanism by which distant strains of bacteria can share genetic material, in hundreds of strains and identifies hot spots of realized recombination events. The results of this analysis reveal the importance of homologous recombination in the diversification of genetic loci in that are significant in its pathogenicity and host interactions, such as flagellar construction, cell wall proteins, and sugar transport and metabolism.
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http://dx.doi.org/10.1128/mSphere.00799-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677006PMC
November 2020

Hogwash: three methods for genome-wide association studies in bacteria.

Microb Genom 2020 11;6(11)

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

Bacterial genome-wide association studies (bGWAS) capture associations between genomic variation and phenotypic variation. Convergence-based bGWAS methods identify genomic mutations that occur independently multiple times on the phylogenetic tree in the presence of phenotypic variation more often than is expected by chance. This work introduces hogwash, an open source R package that implements three algorithms for convergence-based bGWAS. Hogwash additionally contains two burden testing approaches to perform gene or pathway analysis to improve power and increase convergence detection for related but weakly penetrant genotypes. To identify optimal use cases, we applied hogwash to data simulated with a variety of phylogenetic signals and convergence distributions. These simulated data are publicly available and contain the relevant metadata regarding convergence and phylogenetic signal for each phenotype and genotype. Hogwash is available for download from GitHub.
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http://dx.doi.org/10.1099/mgen.0.000469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725327PMC
November 2020

Cohorting KPC+ (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH).

Infect Control Hosp Epidemiol 2020 10 23;41(10):1162-1168. Epub 2020 Jun 23.

Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan.

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 often neglected. We searched for evidence of cross transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute-care hospital (LTACH), and we evaluated the impact of secondary acquisitions on resistance potential.

Design: Genomic epidemiological investigation.

Setting: A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp-positive patients.

Methods: Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross transmission between cohorted patients.

Results: Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient's isolate than to their own admission isolate. Of these 19 cases, 14 showed strong genomic evidence for cross transmission (<10 single nucleotide variants or SNVs), and most of these patients occupied shared cohort floors (12 patients) or rooms (4 patients) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.

Conclusions: Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and they indicate the need for future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.
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http://dx.doi.org/10.1017/ice.2020.261DOI Listing
October 2020

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron.

Nat Microbiol 2020 09 29;5(9):1170-1181. Epub 2020 Jun 29.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

A variety of cell surface structures dictate interactions between bacteria and their environment, including their viruses (bacteriophages). Members of the human gut Bacteroidetes characteristically produce several phase-variable capsular polysaccharides (CPSs), but their contributions to bacteriophage interactions are unknown. To begin to understand how CPSs have an impact on Bacteroides-phage interactions, we isolated 71 Bacteroides thetaiotaomicron-infecting bacteriophages from two locations in the United States. Using B. thetaiotaomicron strains that express defined subsets of CPSs, we show that CPSs dictate host tropism for these phages and that expression of non-permissive CPS variants is selected under phage predation, enabling survival. In the absence of CPSs, B. thetaiotaomicron escapes bacteriophage predation by altering expression of eight distinct phase-variable lipoproteins. When constitutively expressed, one of these lipoproteins promotes resistance to multiple bacteriophages. Our results reveal important roles for Bacteroides CPSs and other cell surface structures that allow these bacteria to persist under bacteriophage predation, and hold important implications for using bacteriophages therapeutically to target gut symbionts.
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http://dx.doi.org/10.1038/s41564-020-0746-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482406PMC
September 2020

MRSA transmission in ICUs: Genomic analysis of patients, their environments and healthcare workers.

Clin Infect Dis 2020 Jun 6. Epub 2020 Jun 6.

Rush University Medical Center/Cook County Health.

Background: MRSA-and now USA300 MRSA-is a significant ICU pathogen; healthcare worker (HCW) contamination may lead to patient cross-transmission.

Methods: From 9/2015-2/2016, to study spread of MRSA, we enrolled HCWs in 4 adult ICUs caring for patients on MRSA contact precautions. Samples were collected from patient body sites and high-touch surfaces in patient rooms. HCW hands, gloves, and personal protective equipment were sampled pre/post-patient encounter. Whole genome sequencing (WGS) was used to compare isolates from patients, HCW, and environment.

Results: There were 413 MRSA isolates sequenced (38% USA300, 52% USA100) from 66 patient encounters. Six of 66 HCWs were contaminated with MRSA prior to room entry. Isolates from a single patient encounter were typically either USA100 or USA300; in 8 (12%) encounters both USA300 and USA100 were isolated. WGS demonstrated that isolates from patient, HCW, and environment often were genetically similar, while there was substantial between-encounter diversity. Strikingly, there were 5 USA100 and 1 USA300 clusters that contained similar strains (<22 SNVs, with most <10 SNVs) within the cluster despite coming from different encounters, suggesting intra- and inter-ICU spread of strains, i.e., 4 of these genomic clusters were from encounters in the same ICU; 5 of 6 clusters occurred within 1 week.

Conclusion: We demonstrated frequent spread of MRSA USA300 and USA100 strains among patients, environment, and HCWs. WGS identified possible spread within and even between ICUs. Future analysis with detailed contact tracing in conjunction with genomic data may further elucidate pathways of MRSA spread and points for intervention.
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http://dx.doi.org/10.1093/cid/ciaa731DOI Listing
June 2020

Gut Microbiota Features on Nursing Home Admission Are Associated With Subsequent Acquisition of Antibiotic-resistant Organism Colonization.

Clin Infect Dis 2020 Dec;71(12):3244-3247

Division of Infectious Diseases, Department of Medicine, University of Michigan, Medical School, Ann Arbor, Michigan, USA.

Nursing home (NH) patients often acquire colonization with antibiotic-resistant organisms (AROs). We show that patients exposed to broad-spectrum antibiotics during previous hospitalizations have elevated enterococcal relative abundances on NH admission and higher risk of subsequent ARO acquisition. Our findings suggest that interventions preventing ARO spread should extend beyond NH doors.
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http://dx.doi.org/10.1093/cid/ciaa662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7819526PMC
December 2020

prewas: data pre-processing for more informative bacterial GWAS.

Microb Genom 2020 05 20;6(5). Epub 2020 Apr 20.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior to their use in bacterial genome-wide association studies (bGWAS). Three nuances of variant pre-processing that impact downstream identification of genetic associations include the separation of variants at multiallelic sites, separation of variants in overlapping genes, and referencing of variants relative to ancestral alleles. Here we demonstrate the importance of these variant pre-processing steps on diverse bacterial genomic datasets and present prewas, an R package, that standardizes the pre-processing of multiallelic sites, overlapping genes, and reference alleles before bGWAS. This package facilitates improved reproducibility and interpretability of bGWAS results. prewas enables users to extract maximal information from bGWAS by implementing multi-line representation for multiallelic sites and variants in overlapping genes. prewas outputs a binary SNP matrix that can be used for SNP-based bGWAS and will prevent the masking of minor alleles during bGWAS analysis. The optional binary gene matrix output can be used for gene-based bGWAS, which will enable users to maximize the power and evolutionary interpretability of their bGWAS studies. prewas is available for download from GitHub.
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http://dx.doi.org/10.1099/mgen.0.000368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371116PMC
May 2020

Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages.

Clin Infect Dis 2020 Dec;71(10):e642-e649

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Background: Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species across regional NFs and evaluated patient-level characteristics and transfer acute care hospitals (ACHs) as risk factors for colonization.

Methods: Patients from 6 NFs (n = 584) were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm), and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined.

Results: The majority of ARO isolates belonged to major healthcare-associated lineages: MRSA (sequence type [ST] 5); VREfc (ST6); CipREc (ST131), and VREfm (clade A). While the genomic similarity of strains between NF pairs was positively associated with overlap in their feeder ACHs (P < .05 for MRSA, VREfc, and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status and recent exposure to glycopeptides (adjusted odds ratio [aOR], > 2 for MRSA and VREfc/VREfm) or third-/fourth-generation cephalosporins (aOR, > 2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only 1 ARO/ACH pair (VREfm/ACH19: aOR, 2.48).

Conclusions: In this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.
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http://dx.doi.org/10.1093/cid/ciaa364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7745002PMC
December 2020

Interplay Between Patient Colonization and Environmental Contamination With Vancomycin-Resistant Enterococci and Their Association With Patient Health Outcomes in Postacute Care.

Open Forum Infect Dis 2020 Jan 11;7(1):ofz519. Epub 2019 Dec 11.

Division of Geriatrics and Palliative Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Background: The clinical utility of patient and environmental surveillance screening for vancomycin-resistant enterococci (VRE) in the postacute care setting has not been definitively clarified. We assessed the longitudinal relationship between patient colonization and room contamination, and we established their association with unfavorable health outcomes.

Methods: Four hundred sixty-three postacute care patients were followed longitudinally from enrollment to discharge for up to 6 months. Multiple body and environmental sites were sampled at regular intervals to establish correlation between environmental contamination and patient colonization and with longer than expected stay, unplanned hospitalization, and infections adjusting for sex, age, race, Charlson's comorbidity index, and physical self-maintenance score.

Results: New VRE acquisition was more likely in patients residing in contaminated rooms (multivariable odds ratio [OR] = 3.75; 95% confidence interval [CI], 1.98-7.11) and vice versa (OR = 3.99; 95% CI, 2.16-7.51). New acquisition and new contamination were associated with increased length of stay (OR = 4.36, 95% CI = 1.86-10.2 and OR = 4.61, 95% CI = 1.92-11.0, respectively) and hospitalization (OR = 2.42, 95% CI = 1.39-4.22 and OR = 2.80, 95% CI = 1.52-5.12). New-onset infections were more common with higher VRE burdens (15% in the absence of VRE, 20% when after VRE isolation only on the patient or only in the room, and 29% after VRE isolation in both the patient and the room).

Conclusions: Room contamination with VRE is a risk factor for patient colonization, and both are associated with future adverse health outcomes in our postacute care patients. Further research is warranted to establish whether VRE screening may contribute to better understanding of risk assessment and adverse outcome prevention in postacute care.
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http://dx.doi.org/10.1093/ofid/ofz519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976341PMC
January 2020

Genetic Determinants of Trehalose Utilization Are Not Associated With Severe Infection Outcome.

Open Forum Infect Dis 2020 Jan 4;7(1):ofz548. Epub 2020 Jan 4.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.

In a case-control study of patients with infection, we found no statistically significant association between the presence of trehalose utilization variants in infecting strains and development of severe infection outcome. These results do not support trehalose utilization conferring enhanced virulence in the context of human infections.
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http://dx.doi.org/10.1093/ofid/ofz548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966243PMC
January 2020

Genetically diverse uropathogenic adopt a common transcriptional program in patients with UTIs.

Elife 2019 10 21;8. Epub 2019 Oct 21.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States.

Uropathogenic (UPEC) is the major causative agent of uncomplicated urinary tract infections (UTIs). A common virulence genotype of UPEC strains responsible for UTIs is yet to be defined, due to the large variation of virulence factors observed in UPEC strains. We hypothesized that studying UPEC functional responses in patients might reveal universal UPEC features that enable pathogenesis. Here we identify a transcriptional program shared by genetically diverse UPEC strains isolated from 14 patients during uncomplicated UTIs. Strikingly, this in vivo gene expression program is marked by upregulation of translational machinery, providing a mechanism for the rapid growth within the host. Our analysis indicates that switching to a more specialized catabolism and scavenging lifestyle in the host allows for the increased translational output. Our study identifies a common transcriptional program underlying UTIs and illuminates the molecular underpinnings that likely facilitate the fast growth rate of UPEC in infected patients.
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http://dx.doi.org/10.7554/eLife.49748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6802966PMC
October 2019

Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals.

Antimicrob Agents Chemother 2019 11 22;63(11). Epub 2019 Oct 22.

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA

Carbapenem-resistant (CRKP) is an antibiotic resistance threat of the highest priority. Given the limited treatment options for this multidrug-resistant organism (MDRO), there is an urgent need for targeted strategies to prevent transmission. Here, we applied whole-genome sequencing to a comprehensive collection of clinical isolates to reconstruct regional transmission pathways and analyzed this transmission network in the context of statewide patient transfer data and patient-level clinical data to identify drivers of regional transmission. We found that high regional CRKP burdens were due to a small number of regional introductions, with subsequent regional proliferation occurring via patient transfers among health care facilities. While CRKP was predicted to have been imported into each facility multiple times, there was substantial variation in the ratio of intrafacility transmission events per importation, indicating that amplification occurs unevenly across regional facilities. While myriad factors likely influence intrafacility transmission rates, an understudied one is the potential for clinical characteristics of colonized and infected patients to influence their propensity for transmission. Supporting the contribution of high-risk patients to elevated transmission rates, we observed that patients colonized and infected with CRKP in high-transmission facilities had higher rates of carbapenem use, malnutrition, and dialysis and were older. This report highlights the potential for regional infection prevention efforts that are grounded in genomic epidemiology to identify the patients and facilities that make the greatest contribution to regional MDRO prevalence, thereby facilitating the design of precision interventions of maximal impact.
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http://dx.doi.org/10.1128/AAC.01622-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811406PMC
November 2019

Frequent Methicillin-Resistant Staphylococcus aureus Introductions Into an Inner-city Jail: Indications of Community Transmission Networks.

Clin Infect Dis 2020 07;71(2):323-331

Division of Infectious Diseases, Rush University Medical Center/Cook County Health, Chicago, Illinois, USA.

Background: Jails may facilitate spread of methicillin-resistant Staphylococcus aureus (MRSA) in urban areas. We examined MRSA colonization upon entrance to a large urban jail to determine if there are MRSA transmission networks preceding incarceration.

Methods: Males incarcerated in Cook County Jail (Chicago) were enrolled, with enrichment for people living with human immunodeficiency virus (PLHIV), within 72 hours of intake. Surveillance cultures assessed prevalence of MRSA colonization. Whole-genome sequencing (WGS) identified preincarceration transmission networks.We examined methicillin-resistant Staphylococcus aureus (MRSA) isolates to determine if there are transmission networks that precede incarceration. A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to community reservoirs for MRSA.

Results: There were 718 individuals (800 incarcerations) enrolled; 58% were PLHIV. The prevalence of MRSA colonization at intake was 19%. In multivariate analysis, methamphetamine use, unstable housing, current/recent skin infection, and recent injection drug use were predictors of MRSA. Among PLHIV, recent injection drug use, current skin infection, and HIV care at outpatient clinic A that emphasizes comprehensive care to the lesbian, gay, bisexual, transgender community were predictors of MRSA. Fourteen (45%) of 31 detainees with care at clinic A had colonization. WGS revealed that this prevalence was not due to clonal spread in clinic but rather to an intermingling of distinct community transmission networks. In contrast, genomic analysis supported spread of USA500 strains within a network. Members of this USA500 network were more likely to be PLHIV (P < .01), men who have sex with men (P < .001), and methamphetamine users (P < .001).

Conclusions: A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to identify colonized detainees entering jail and potential community reservoirs of MRSA.
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http://dx.doi.org/10.1093/cid/ciz818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353325PMC
July 2020

Outbreak of Murine Infection with Associated with the Administration of a Pre- and Perinatal Methyl Donor Diet.

mSphere 2019 03 20;4(2). Epub 2019 Mar 20.

Division of Geriatric and Palliative Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA

Between October 2016 and June 2017, a C57BL/6J mouse colony that was undergoing a pre- and perinatal methyl donor supplementation diet intervention to study the impact of parental nutrition on offspring susceptibility to disease was found to suffer from an epizootic of unexpected deaths. Necropsy revealed the presence of severe colitis, and further investigation linked these outbreak deaths to a strain of ribotype 027 that we term 16N203. infection (CDI) is associated with antibiotic use in humans. Current murine models of CDI rely on antibiotic pretreatment to establish clinical phenotypes. In this report, the outbreak occurs in F1 mice linked to alterations in the parental diet. The diagnosis of CDI in the affected mice was confirmed by cecal/colonic histopathology, the presence of bacteria in fecal/colonic culture, and detection of toxins. F1 mice from parents fed the methyl supplementation diet also had significantly reduced survival ( < 0.0001) compared with F1 mice from parents fed the control diet. When we tested the 16N203 outbreak strain in an established mouse model of antibiotic-induced CDI, we confirmed that this strain is pathogenic. Our serendipitous observations from this spontaneous outbreak of in association with a pre- and perinatal methyl donor diet suggest the important role that diet may play in host defense and CDI risk factors. infection (CDI) has become the leading cause of infectious diarrhea in hospitals worldwide, owing its preeminence to the emergence of hyperendemic strains, such as ribotype 027 (RT027). A major CDI risk factor is antibiotic exposure, which alters gut microbiota, resulting in the loss of colonization resistance. Current murine models of CDI also depend on pretreatment of animals with antibiotics to establish disease. The outbreak that we report here is unique in that the CDI occurred in mice with no antibiotic exposure and is associated with a pre- and perinatal methyl supplementation donor diet intervention study. Our investigation subsequently reveals that the outbreak strain that we term 16N203 is an RT027 strain, and this isolated strain is also pathogenic in an established murine model of CDI (with antibiotics). Our report of this spontaneous outbreak offers additional insight into the importance of environmental factors, such as diet, and CDI susceptibility.
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http://dx.doi.org/10.1128/mSphereDirect.00138-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429045PMC
March 2019

Contamination of Hospital Plumbing: A Source or a Sink for Antibiotic-Resistant Organisms?

Authors:
Evan S Snitkin

JAMA Netw Open 2019 02 1;2(2):e187660. Epub 2019 Feb 1.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor.

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http://dx.doi.org/10.1001/jamanetworkopen.2018.7660DOI Listing
February 2019

A retrospective cohort study of antibiotic exposure and vancomycin-resistant Enterococcus recolonization.

Infect Control Hosp Epidemiol 2019 04 7;40(4):414-419. Epub 2019 Feb 7.

National Institutes of Health,Bethesda,Maryland.

Objective: In the National Institutes of Health (NIH) Clinical Center, patients colonized or infected with vancomycin-resistant Enterococcus (VRE) are placed in contact isolation until they are deemed "decolonized," defined as having 3 consecutive perirectal swabs negative for VRE. Some decolonized patients later develop recurrent growth of VRE from surveillance or clinical cultures (ie, "recolonized"), although that finding may represent recrudescence or new acquisition of VRE. We describe the dynamics of VRE colonization and infection and their relationship to receipt of antibiotics.

Methods: In this retrospective cohort study of patients at the National Institutes of Health Clinical Center, baseline characteristics were collected via chart review. Antibiotic exposure and hospital days were calculated as proportions of VRE decolonized days. Using survival analysis, we assessed the relationship between antibiotic exposure and time to VRE recolonization in a subcohort analysis of 72 decolonized patients.

Results: In total, 350 patients were either colonized or infected with VRE. Among polymerase chain reaction (PCR)-positive, culture (Cx)-negative (PCR+/Cx-) patients, PCR had a 39% positive predictive value for colonization. Colonization with VRE was significantly associated with VRE infection. Among 72 patients who met decolonization criteria, 21 (29%) subsequently became recolonized. VRE recolonization was 4.3 (P = .001) and 2.0 (P = .22) times higher in patients with proportions of antibiotic days and antianaerobic antibiotic days above the median, respectively.

Conclusion: Colonization is associated with clinical VRE infection and increased mortality. Despite negative perirectal cultures, re-exposure to antibiotics increases the risk of VRE recolonization.
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http://dx.doi.org/10.1017/ice.2019.15DOI Listing
April 2019

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota.

Elife 2018 10 8;7. Epub 2018 Oct 8.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, United States.

As part of the Reproducibility Project: Cancer Biology we published a Registered Report (Eaton et al., 2015) that described how we intended to replicate selected experiments from the paper "Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota" (Arthur et al., 2012). Here we report the results. We observed no impact on bacterial growth or colonization capacity when the polyketide synthase () genotoxic island was deleted from NC101, similar to the original study (Supplementary Figure 7; Arthur et al., 2012). However, for the experiment that compared inflammation, invasion, and neoplasia in azoxymethane (AOM)-treated interleukin-10-deficient mice mono-associated with NC101 or NC101[Formula: see text] the experimental timing of the replication attempt was longer than that of the original study. This difference was because in the original study the methodology was not clearly stated and likely led to the increased mortality and severity of inflammation observed in this replication attempt. Additionally, early death occurred during AOM treatment with higher mortality observed in NC101[Formula: see text] mono-associated mice compared to NC101, which was in the same direction, but more severe than the original study (Suppleme1ntal Figure 10; Arthur et al., 2012). A meta-analysis suggests that mice mono-associated with NC101[Formula: see text] have higher mortality compared to NC101. While these data were unable to address whether, under the conditions of the original study, NC101 and NC101[Formula: see text] differ in inflammation, invasion, and neoplasia this replication attempt demonstrates that clear description of experimental methods is essential to ensure accurate reproduction of experimental studies.
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http://dx.doi.org/10.7554/eLife.34364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175580PMC
October 2018

Genomic epidemiology of multidrug-resistant Gram-negative organisms.

Ann N Y Acad Sci 2019 01 31;1435(1):39-56. Epub 2018 Mar 31.

Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA.

The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.
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http://dx.doi.org/10.1111/nyas.13672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167210PMC
January 2019

Rapid Growth of Uropathogenic during Human Urinary Tract Infection.

mBio 2018 03 6;9(2). Epub 2018 Mar 6.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA

Uropathogenic (UPEC) strains cause most uncomplicated urinary tract infections (UTIs). These strains are a subgroup of extraintestinal pathogenic (ExPEC) strains that infect extraintestinal sites, including urinary tract, meninges, bloodstream, lungs, and surgical sites. Here, we hypothesize that UPEC isolates adapt to and grow more rapidly within the urinary tract than other isolates and survive in that niche. To date, there has not been a reliable method available to measure their growth rate Here we used two methods: segregation of nonreplicating plasmid pGTR902, and peak-to-trough ratio (PTR), a sequencing-based method that enumerates bacterial chromosomal replication forks present during cell division. In the murine model of UTI, UPEC strain growth was robust , matching or exceeding growth rates and only slowing after reaching high CFU counts at 24 and 30 h postinoculation (hpi). In contrast, asymptomatic bacteriuria (ABU) strains tended to maintain high growth rates at 6, 24, and 30 hpi, and population densities did not increase, suggesting that host responses or elimination limited population growth. Fecal strains displayed moderate growth rates at 6 hpi but did not survive to later times. By PTR, in urine of human patients with UTIs displayed extraordinarily rapid growth during active infection, with a mean doubling time of 22.4 min. Thus, in addition to traditional virulence determinants, including adhesins, toxins, iron acquisition, and motility, very high growth rates and resistance to the innate immune response appear to be critical phenotypes of UPEC strains. Uropathogenic (UPEC) strains cause most urinary tract infections in otherwise healthy women. While we understand numerous virulence factors are utilized by to colonize and persist within the urinary tract, these properties are inconsequential unless bacteria can divide rapidly and survive the host immune response. To determine the contribution of growth rate to successful colonization and persistence, we employed two methods: one involving the segregation of a nonreplicating plasmid in bacteria as they divide and the peak-to-trough ratio, a sequencing-based method that enumerates chromosomal replication forks present during cell division. We found that UPEC strains divide extraordinarily rapidly during human UTIs. These techniques will be broadly applicable to measure growth rates of other bacterial pathogens during host colonization.
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http://dx.doi.org/10.1128/mBio.00186-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844997PMC
March 2018

Genomic Investigation of a Putative Endoscope-Associated Carbapenem-Resistant Enterobacter cloacae Outbreak Reveals a Wide Diversity of Circulating Strains and Resistance Mutations.

Clin Infect Dis 2018 01;66(3):460-463

Department of Microbiology and Immunology, University of Michigan Medical School.

A genomic epidemiologic investigation of a putative carbapenem-resistant Enterobacter cloacae outbreak revealed few plausible instances of nosocomial transmission, highlighting instead the frequent importation of E. cloacae into our hospital. Searching for genetic determinants of carbapenem resistance demonstrated that most resistance is due to convergent mutations in phylogenetically diverse E. cloacae.
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http://dx.doi.org/10.1093/cid/cix934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850560PMC
January 2018

Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant in a regional outbreak.

Sci Transl Med 2017 Nov;9(417)

Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.

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 by performing an integrated analysis of genomic and interfacility patient-transfer data. Genomic analysis yielded a high-resolution transmission network that assigned directionality to regional transmission events and discriminated between intra- and interfacility transmission when epidemiologic data were ambiguous or misleading. Examining the genomic transmission network in the context of interfacility patient transfers (patient-sharing networks) supported the role of patient transfers in driving the outbreak, with genomic analysis revealing that a small subset of patient-transfer events was sufficient to explain regional spread. Further integration of the genomic and patient-sharing networks identified one nursing home as an important bridge facility early in the outbreak-a role that was not apparent from analysis of genomic or patient-transfer data alone. Last, we found that when simulating a real-time regional outbreak, our methodology was able to accurately infer the facility at which patients acquired their infections. This approach has the potential to identify facilities with high rates of intra- or interfacility transmission, data that will be useful for triggering targeted interventions to prevent further spread of multidrug-resistant organisms.
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http://dx.doi.org/10.1126/scitranslmed.aan0093DOI Listing
November 2017

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms.

Proc Natl Acad Sci U S A 2017 09 12;114(39):10467-10472. Epub 2017 Sep 12.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109-5680;

The emergence and spread of multidrug-resistant organisms (MDROs) across global healthcare networks poses a serious threat to hospitalized individuals. Strategies to limit the emergence and spread of MDROs include oversight to decrease selective pressure for MDROs by promoting appropriate antibiotic use via antibiotic stewardship programs. However, restricting the use of one antibiotic often requires a compensatory increase in the use of other antibiotics, which in turn selects for the emergence of different MDRO species. Further, the downstream effects of antibiotic treatment decisions may also be influenced by functional interactions among different MDRO species, with the potential clinical implications of such interactions remaining largely unexplored. Here, we attempt to decipher the influence network between antibiotic treatment, MDRO colonization, and infection by leveraging active surveillance and antibiotic treatment data for 234 nursing home residents. Our analysis revealed a complex network of interactions: antibiotic use was a risk factor for primary MDRO colonization, which in turn increased the likelihood of colonization and infection by other MDROs. When we focused on the risk of catheter-associated urinary tract infections (CAUTI) caused by , and we observed that cocolonization with specific pairs of MDROs increased the risk of CAUTI, signifying the involvement of microbial interactions in CAUTI pathogenesis. In summary, our work demonstrates the existence of an underappreciated healthcare-associated ecosystem and strongly suggests that effective control of overall MDRO burden will require stewardship interventions that take into account both primary and secondary impacts of antibiotic treatments.
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http://dx.doi.org/10.1073/pnas.1710235114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625923PMC
September 2017

Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections.

J Infect Dis 2017 06;215(11):1640-1647

Division of Infectious Diseases, Rush University Medical Center/Stroger Hospital of Cook County, Chicago, Illinois.

Background: We examined whether disparities existed in hospital-onset (HO) Staphylococcus aureus bloodstream infections (BSIs) and used whole-genome sequencing (WGS) to identify factors associated with USA300 transmission networks.

Methods: We evaluated HO methicillin-susceptible S. aureus (MSSA) and HO methicillin-resistant S. aureus (MRSA) BSIs for 2009-2013 at 2 hospitals and used an adjusted incidence for modeling. WGS and phylogenetic analyses were performed on a sample of USA300 BSI isolates. Epidemiologic data were analyzed in the context of phylogenetic reconstructions.

Results: On multivariate analysis, male sex, African-American race, and non-Hispanic white race/ethnicity were significantly associated with HO-MRSA BSIs whereas Hispanic ethnicity was negatively associated (rate ratio, 0.41; P = .002). Intermixing of community-onset and HO-USA300 strains on the phylogenetic tree indicates that these strains derive from a common pool. African-American race was the only factor associated with genomic clustering of isolates.

Conclusions: In a multicenter assessment of HO-S. aureus BSIs, African-American race was significantly associated with HO-MRSA but not MSSA BSIs. There appears to be a nexus of USA300 community and hospital transmission networks, with a community factor being the primary driver. Our data suggest that HO-USA300 BSIs likely are due to colonizing strains acquired in the community before hospitalization. Therefore, prevention efforts may need to extend to the community for maximal benefit.
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http://dx.doi.org/10.1093/infdis/jiw647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5853804PMC
June 2017

Whole Genome Sequencing-Implications for Infection Prevention and Outbreak Investigations.

Curr Infect Dis Rep 2017 Apr;19(4):15

Department of Microbiology and Immunology, Department of Medicine, Division of Infectious Diseases, Center for Microbial Systems, University of Michigan, 1520D MSRB I, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5680, USA.

Purpose Of Review: Whole genome sequencing (WGS) is a laboratory method that has emerged as a promising tool for epidemiologic investigations.

Recent Findings: Genomic epidemiology approaches have been utilized in outbreak settings, community settings, within acute care hospitals, and across healthcare facilities to better understand transmission and spread of potential pathogens. These studies have highlighted how essential robust epidemiologic data is in these analyses as well as how results can be translated into clinical practice and infection control and prevention. Existing studies have highlighted both the promise and challenges of using WGS as an epidemiologic tool in a community and healthcare setting and across a region. Costs for performing and interpreting WGS analyses are decreasing, and availability of and experience with WGS analyses in healthcare epidemiology are increasing. With these favorable trends, this laboratory method soon could emerge as the gold standard for epidemiologic evaluations.
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http://dx.doi.org/10.1007/s11908-017-0570-0DOI Listing
April 2017

Pseudomonas aeruginosa adaptation to human hosts.

Nat Genet 2015 Jan;47(1):2-3

National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA.

Bacterial whole-genome sequencing of longitudinally collected isolates enables the investigation of evolutionary trajectories, which may inform both the prevention and treatment of human-associated pathogen infections. A new study explores the adaptation of multiple lineages of Pseudomonas aeruginosa to the lungs of young patients with cystic fibrosis and finds evidence of convergent molecular evolution and historical contingencies.
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http://dx.doi.org/10.1038/ng.3172DOI Listing
January 2015

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.

Sci Transl Med 2014 Sep;6(254):254ra126

National Human Genome Research Institute, Bethesda, MD 20892, USA.

Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae species may spread resistance to carbapenems, an antibiotic class of last resort, thereby rendering common health care-associated infections nearly impossible to treat. To determine the diversity of carbapenemase-encoding plasmids and assess their mobility among bacterial species, we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae isolated simultaneously from a single patient harbored two different carbapenemase-encoding plasmids, indicating that plasmid transfer between organisms was unlikely within this patient. We did, however, find evidence of horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E. cloacae, and C. freundii in the hospital environment. Our data, including full plasmid identification, challenge assumptions about horizontal gene transfer events within patients and identify possible connections between patients and the hospital environment. In addition, we identified a new carbapenemase-encoding plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E. cloacae, and Pantoea species, in unrelated patients and in the hospital environment.
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http://dx.doi.org/10.1126/scitranslmed.3009845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203314PMC
September 2014

Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment.

Genome Res 2013 Jul 5;23(7):1155-62. Epub 2013 Apr 5.

Epithelial Biology Section, GMBB, NHGRI, Bethesda, Maryland 20892, USA.

Bacterial whole-genome sequencing (WGS) of human pathogens has provided unprecedented insights into the evolution of antibiotic resistance. Most studies have focused on identification of resistance mutations, leaving one to speculate on the fate of these mutants once the antibiotic selective pressure is removed. We performed WGS on longitudinal isolates of Acinetobacter baumannii from patients undergoing colistin treatment, and upon subsequent drug withdrawal. In each of the four patients, colistin resistance evolved via mutations at the pmr locus. Upon colistin withdrawal, an ancestral susceptible strain outcompeted resistant isolates in three of the four cases. In the final case, resistance was also lost, but by a compensatory inactivating mutation in the transcriptional regulator of the pmr locus. Notably, this inactivating mutation reduced the probability of reacquiring colistin resistance when subsequently challenged in vitro. On face value, these results supported an in vivo fitness cost preventing the evolution of stable colistin resistance. However, more careful analysis of WGS data identified genomic evidence for stable colistin resistance undetected by clinical microbiological assays. Transcriptional studies validated this genomic hypothesis, showing increased pmr expression of the initial isolate. Moreover, altering the environmental growth conditions of the clinical assay recapitulated the classification as colistin resistant. Additional targeted sequencing revealed that this isolate evolved undetected in a patient undergoing colistin treatment, and was then transmitted to other hospitalized patients, further demonstrating its stability in the absence of colistin. This study provides a unique window into mutational pathways taken in response to antibiotic pressure in vivo, and demonstrates the potential for genome sequence data to predict resistance phenotypes.
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http://dx.doi.org/10.1101/gr.154328.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698508PMC
July 2013