Tara N. Palmore

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing revealed its origin and probable modes of transmission. A Detective Story Some infections are largely a thing of the past—plague, syphilis. The unfortunate result of these antibiotic-driven successes is the emergence of drug-resistant pathogens. And, ironically enough, hospitals are at the center of the problem. An example of this occurred in 2011 at the Clinical Center of the U.S. National Institutes of Health (NIH), in which an outbreak of drug-resistant Klebsiella pneumoniae infected 18 patients, causing the death of 6 of them. Using a combination of whole-genome sequencing and patient tracking, Snitkin and his colleagues examined how the bacteria was spreading through the hospital. The results outline a complicated path of transmission within the hospital that defied standard containment methods, yielding lessons for the future. A patient known to be infected with a drug-resistant form of K. pneumoniae was admitted to the NIH Clinical Center on 13 June 2011. Enhanced isolation procedures were immediately implemented, and no spread of the bacteria was seen for the month she was in the hospital. Although all seemed well, a few weeks later on August 5th, a second infected patient was discovered, followed by a series of other patients with infection or colonization—about 1 a week to a total of 18 by the end of 2011. Six people ultimately died as a result of the bacteria. The outbreak was finally contained by rigorous control procedures. A careful survey of the bed locations of each patient did not shed much light on how the bacteria traveled on its deadly path: The first patient did not even come into contact with any of the others. So the authors performed whole-genome sequencing on all of the bacteria that were found, determining the most likely evolutionary relationships among them by comparing the variations at single nucleotides that arise as bacteria grow. Combining this evolutionary information with the physical tracking of the patients pointed to the most likely transmission scenario. The authors concluded that all of the K. pneumoniae cases likely originated with the index patient, from at least two different sites on her body, rather than by independently introduced bacteria. There were at least three different initial transmission events. Particularly disturbing was the fact that one of the infections could be linked to contamination of a ventilator that had been cleaned by thorough methods. Sophisticated deployment of whole-genome sequencing revealed the weaknesses in this medical who-done-it, informing improvements in hospital preventive measures. If applied rapidly, such analysis can even expose the causes of nosocomial infections in real time. The Gram-negative bacteria Klebsiella pneumoniae is a major cause of nosocomial infections, primarily among immunocompromised patients. The emergence of strains resistant to carbapenems has left few treatment options, making infection containment critical. In 2011, the U.S. National Institutes of Health Clinical Center experienced an outbreak of carbapenem-resistant K. pneumoniae that affected 18 patients, 11 of whom died. Whole-genome sequencing was performed on K. pneumoniae isolates to gain insight into why the outbreak progressed despite early implementation of infection control procedures. Integrated genomic and epidemiological analysis traced the outbreak to three independent transmissions from a single patient who was discharged 3 weeks before the next case became clinically apparent. Additional genomic comparisons provided evidence for unexpected transmission routes, with subsequent mining of epidemiological data pointing to possible explanations for these transmissions. Our analysis demonstrates that integration of genomic and epidemiological data can yield actionable insights and facilitate the control of nosocomial transmission.

Identification of poxvirus CD8 T cell determinants to enable rational design and characterization of smallpox vaccines

The large size of poxvirus genomes has stymied attempts to identify determinants recognized by CD8+ T cells and greatly impeded development of mouse smallpox vaccination models. Here, we use a vaccinia virus (VACV) expression library containing each of the predicted 258 open reading frames to identify five peptide determinants that account for approximately half of the VACV-specific CD8+ T cell response in C57BL/6 mice. We show that the primary immunodominance hierarchy is greatly affected by the route of VACV infection and the poxvirus strain used. Modified vaccinia virus ankara (MVA), a candidate replacement smallpox vaccine, failed to induce responses to two of the defined determinants. This could not be predicted by genomic comparison of viruses and is not due strictly to limited MVA replication in mice. Several determinants are immunogenic in cowpox and ectromelia (mousepox) virus infections, and immunization with the immunodominant determinant provided significant protection against lethal mousepox. These findings have important implications for understanding poxvirus immunity in animal models and bench-marking immune responses to poxvirus vaccines in humans.

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

Single-molecule sequencing of bacteria at the NIH Clinical Center documents diverse plasmids encoding antibiotic resistance and their transfer between microbes. How Antibiotic Resistance Spreads Among Bacteria Antibiotic-resistant microbes are spreading at an alarming rate in health care facilities throughout the world. Conlan et al. use a new DNA sequencing method to take a close look at one way in which antibiotic resistance spreads. With single-molecule sequencing, the authors completely characterized individual plasmids, the circular bits of DNA that carry the genes for antibiotic resistance in bacteria. They focused on resistance to the carbapenems, a class of antibiotics that is often used for infections that do not respond to more conventional antimicrobial agents. By using this approach in their microbial surveillance program at the NIH Clinical Center, the authors found evidence that plasmids carrying carbapenemase genes moved from one microbial species to another within the hospital environment. They also used the technique to test hypotheses about patient-to-patient transmission and to characterize a previously undescribed carbapenemase-encoding plasmid carried by diverse bacterial species that could cause dangerous clinical infections. 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.

SHEA Guideline for Management of Healthcare Workers Who Are Infected with Hepatitis B Virus, Hepatitis C Virus, and/or Human Immunodeficiency Virus •

This guideline provides the updated recommendations of the Society for Healthcare Epidemiology of America (SHEA) regarding the management of healthcare providers who are infected with hepatitis B virus (HBV), hepatitis C virus (HCV), and/or the human immunodeficiency virus (HIV). For the reasons cited in the guideline, SHEA continues to recommend that, although some aspects of the approach to and administrative management of each of these infectious syndromes in healthcare providers are similar, separate management strategies for healthcare workers who are infected with these unrelated viruses remain appropriate. As we did in both prior iterations of this document, SHEA emphasizes the use of appropriate infection control procedures to minimize exposure of patients or providers to blood, emphasizes that transfers of blood from patients to providers and from providers to patients should be avoided, and recommends that infected healthcare providers should not be totally prohibited from participating in patient-care activities solely on the basis of a bloodborne pathogen infection. The types of procedures assessed by the panel as associated with an increased risk for provider-to-patient transmission of these pathogens are discussed in detail. For each pathogen, recommendations are graduated according to the relative viral load level of the infected provider (Tables 1 and 2). However, SHEA emphasizes that, because of the complexity of these cases, each such case will be slightly different from the next, and each should be independently considered in context.

Managing Transmission of Carbapenem-Resistant Enterobacteriaceae in Healthcare Settings: A View From the Trenches

In 2011, the National Institutes of Health Clinical Center experienced a cluster of infection and colonization caused by carbapenem-resistant Klebsiella pneumoniae among profoundly immunocompromised inpatients. This manuscript describes the approach and interventions that were implemented in an attempt to curtail the cluster. Interventions employed included engagement of all stakeholders involved in care of at-risk patients; detailed and frequent communication with hospital staff about issues relating to the outbreak; aggressive microbial surveillance; use of techniques that facilitate rapid identification of resistant organisms; rapid characterization of resistance mechanisms; whole-genome sequencing of outbreak isolates to characterize the spread and to investigate mechanisms of healthcare-associated spread; implementation of enhanced contact precautions for all infected or colonized patients; geographic and personnel cohorting; daily chlorhexidine gluconate baths; dedicating equipment to be used solely for cohorted patients and aggressive decontamination of equipment that had to be reused on uncohorted patients; monitoring adherence to infection control precautions, including unwavering attention to adherence to appropriate hand hygiene procedures; and attention to the details of environmental decontamination. In addition, the manuscript discusses some of the challenges associated with managing such an event, as well as a few of the unanticipated consequences associated with the aftermath of the case cluster.

A successful mandatory influenza vaccination campaign using an innovative electronic tracking system.

BACKGROUND Although influenza vaccination of healthcare workers reduces influenza-like illness and overall mortality among patients, national rates of vaccination for healthcare providers are unacceptably low. We report the implementation of a new mandatory vaccination policy by means of a streamlined electronic enrollment and vaccination tracking system at the National Institutes of Health (NIH) Clinical Center. OBJECTIVE To evaluate the outcome of a new mandatory staff influenza vaccination program. METHODS A new hospital policy endorsed by all the component NIH institutes and the Clinical Center departments mandated that employees who have patient contact either be vaccinated annually against influenza or sign a declination specifying the reason(s) for refusal. Those who fail to comply would be required to appear before the Medical Executive Committee to explain their rationale. We collected in a database the names of all physician and nonphysician staff who had patient contact. When a staff member either was vaccinated or declined vaccination, a simple system of badge scanning and bar-coded data entry captured essential data. The database was continuously updated, and it provided a list of noncompliant employees with whom to follow up. RESULTS By February 12, 2009, all 2,754 identified patient-care employees either were vaccinated or formally declined vaccination. Among those, 2,424 (88%) were vaccinated either at the NIH or elsewhere, 36 (1.3%) reported medical contraindications, and 294 (10.7%) declined vaccination for other reasons. Among the 294 employees without medical contraindications who declined, the most frequent reason given for declination was concern about side effects. CONCLUSIONS Implementation of a novel vaccination tracking process and a hospital policy requiring influenza vaccination or declination yielded dramatic improvement in healthcare worker vaccination rates and likely will result in increased patient safety in our hospital.

Reactivation of hepatitis B with reappearance of hepatitis B surface antigen after chemotherapy and immunosuppression.

BACKGROUND & AIMS HBV infection may reactivate in the setting of immunosuppression, although the frequency and consequences of HBV reactivation are not well known. We report 6 patients who experienced loss of serologic markers of hepatitis B immunity and reappearance of HBsAg in the serum as a result of a variety of acquired immune deficiencies. METHODS Between 2000 and 2005, six patients with reactivation of hepatitis B were seen in consultation by the Liver Diseases Branch at the Clinical Center, National Institutes of Health. The course and outcome of these 6 patients were reviewed. RESULTS All 6 patients developed reappearance of HBsAg and evidence of active liver disease after stem cell transplantation (n = 4), immunosuppressive therapy (n = 1), or change in human immunodeficiency virus antiretroviral regimen (n = 1), despite having antibody to HBsAg (anti-HBs) or antibody to hepatitis B core antigen (anti-HBc) without HBsAg before. All 6 patients developed chronic hepatitis B, 2 patients transmitted hepatitis B to their spouses, and 1 patient developed cirrhosis. The diagnosis of hepatitis B reactivation was frequently missed or delayed and often required interruption of the therapy for the underlying condition. None of the patients received antiviral prophylaxis against HBV reactivation. CONCLUSIONS Serologic evidence of recovery from hepatitis B infection does not preclude its reactivation after immunosuppression. Screening for serologic evidence of hepatitis B and prophylaxis of those with positive results by using nucleoside analogue antiviral therapy should be provided to individuals in whom immunosuppressive therapy is planned.

Emergency Postexposure Vaccination With Vesicular Stomatitis Virus–Vectored Ebola Vaccine After Needlestick

IMPORTANCE Safe and effective vaccines and drugs are needed for the prevention and treatment of Ebola virus disease, including following a potentially high-risk exposure such as a needlestick. OBJECTIVE To assess response to postexposure vaccination in a health care worker who was exposed to the Ebola virus. DESIGN AND SETTING Case report of a physician who experienced a needlestick while working in an Ebola treatment unit in Sierra Leone on September 26, 2014. Medical evacuation to the United States was rapidly initiated. Given the concern about potentially lethal Ebola virus disease, the patient was offered, and provided his consent for, postexposure vaccination with an experimental vaccine available through an emergency Investigational New Drug application. He was vaccinated on September 28, 2014. INTERVENTIONS The vaccine used was VSVΔG-ZEBOV, a replicating, attenuated, recombinant vesicular stomatitis virus (serotype Indiana) whose surface glycoprotein gene was replaced by the Zaire Ebola virus glycoprotein gene. This vaccine has entered a clinical trial for the prevention of Ebola in West Africa. RESULTS The vaccine was administered 43 hours after the needlestick occurred. Fever and moderate to severe symptoms developed 12 hours after vaccination and diminished over 3 to 4 days. The real-time reverse transcription polymerase chain reaction results were transiently positive for vesicular stomatitis virus nucleoprotein gene and Ebola virus glycoprotein gene (both included in the vaccine) but consistently negative for Ebola virus nucleoprotein gene (not in the vaccine). Early postvaccination cytokine secretion and T lymphocyte and plasmablast activation were detected. Subsequently, Ebola virus glycoprotein-specific antibodies and T cells became detectable, but antibodies against Ebola viral matrix protein 40 (not in the vaccine) were not detected. CONCLUSIONS AND RELEVANCE It is unknown if VSVΔG-ZEBOV is safe or effective for postexposure vaccination in humans who have experienced a high-risk occupational exposure to the Ebola virus, such as a needlestick. In this patient, postexposure vaccination with VSVΔG-ZEBOV induced a self-limited febrile syndrome that was associated with transient detection of the recombinant vesicular stomatitis vaccine virus in blood. Strong innate and Ebola-specific adaptive immune responses were detected after vaccination. The clinical syndrome and laboratory evidence were consistent with vaccination response, and no evidence of Ebola virus infection was detected.

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

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.

Healthcare Personnel Attire in Non-Operating-Room Settings

Healthcare personnel (HCP) attire is an aspect of the medical profession steeped in culture and tradition. The role of attire in cross-transmission remains poorly established, and until more definitive information exists priority should be placed on evidence-based measures to prevent healthcare-associated infections (HAIs). This article aims to provide general guidance to the medical community regarding HCP attire outside the operating room. In addition to the initial guidance statement, the article has 3 major components: (1) a review and interpretation of the medical literature regarding (a) perceptions of HCP attire (from both HCP and patients) and (b) evidence for contamination of attire and its potential contribution to cross-transmission; (2) a review of hospital policies related to HCP attire, as submitted by members of the Society for Healthcare Epidemiology of America (SHEA) Guidelines Committee; and (3) a survey of SHEA and SHEA Research Network members that assessed both institutional HCP attire policies and perceptions of HCP attire in the cross-transmission of pathogens. Recommendations for HCP attire should attempt to balance professional appearance, comfort, and practicality with the potential role of apparel in the cross-transmission of pathogens. Although the optimal choice of HCP attire for inpatient care remains undefined, we provide recommendations on the use of white coats, neckties, footwear, the bare-below-the-elbows strategy, and laundering. Institutions considering these optional measures should introduce them with a well-organized communication and education effort directed at both HCP and patients. Appropriately designed studies are needed to better define the relationship between HCP attire and HAIs.