Methicillin-resistant Staphylococcus aureus (MRSA) clusters in neonatal intensive care units (NICUs) and other neonatal units in New York State (NYS), 2001 to 2017.

BACKGROUND: New York State (NYS) mandates reporting of all hospital-associated communicable disease outbreaks. We describe trends in NYS surveillance for neonatal unit methicillin-resistant Staphylococcus aureus (MRSA) outbreaks, the evolution of national MRSA infection prevention and control (IPC) recommendations, and IPC measures taken by NYS neonatal units. METHODS: We evaluated trends of reported neonatal unit MRSA outbreaks by etiology from 2001 to 2017. We reviewed all reports and the use of IPC recommendations over time. RESULTS: From 2001 to 2017, 124 MRSA outbreaks were reported in 47 hospital neonatal units, with a total of 1,055 laboratory-confirmed infant cases, 18 infant deaths, and 52 laboratory-confirmed staff cases. The number of outbreaks increased with the level of care. During the study period, a higher proportion of hospitals reported implementing IPC measures, including reinforcing hand hygiene compliance (increased from 79.2% to 95.1%) and enhancing environmental cleaning and disinfection (increased from 4.2% to 78.0%) as well as performing active surveillance testing (AST) on exposed neonates (increased from 4.2% to 51.2%) and molecular testing on MRSA-positive isolates (increased from 5.3% to 18.9%). CONCLUSIONS: From 2001 to 2017, IPC measures in neonatal units increased in parallel with expanded national IPC recommendations. However, MRSA outbreaks in neonatal units continued to be frequent occurrences in NYS.

Candida auris admission screening pilot in select units of New York City health care facilities, 2017-2019.

BACKGROUND: This pilot project implemented admission screening for Candida auris (C. auris) using real-time polymerase chain reaction (rt-PCR) in select high-risk units within health care facilities in New York City. METHODS: An admission screening encounter consisted of collecting 2 swabs, to be tested by rt-PCR, and a data collection form for individuals admitted to ventilator units at 2 nursing homes (NHA and NHB), and the ventilator/pulmonary unit, intensive care unit, and cardiac care unit at a hospital (Hospital C) located in New York City from November 2017 to November 2019. RESULTS: C. auris colonization was identified in 6.9% (n = 188/2,726) of admissions to participating units. Rates were higher among admissions to NHA and NHB (20.7% and 22.0%, respectively) than Hospital C (3.6%). Within Hospital C, the ventilator/pulmonary unit had a higher rate (5.7%) than the intensive care unit (3.8%) or cardiac care unit (2.5%). DISCUSSION: Consistent with prior research, we found that individuals admitted to ventilator units were at higher risk of C. auris colonization. CONCLUSIONS: This project demonstrates the utility of admission screening using rt-PCR testing to rapidly identify C. auris colonization among admissions to health care facilities so that appropriate transmission-based precautions and control measures can be implemented rapidly to help decrease transmission.

Comparative analysis of multiplexed PCR and short- and long-read whole genome sequencing to investigate a large Klebsiella pneumoniae outbreak in New York State.

In 2017, the New York State Department of Health investigated a large Klebsiella pneumoniae outbreak in a health care facility. A retrospective analysis was conducted to compare the use of multiple molecular typing methods for characterizing the outbreak. Forty-four isolates were characterized using the rapid real-time PCR OpGen Acuitas® AMR Gene Panel. Additionally, short-read whole genome sequencing (WGS) analysis was used to identify antimicrobial resistance (AMR) genes and assess isolate relatedness. Long-read Oxford Nanopore MinION WGS was used to characterize the plasmid content of a subset of isolates. All methods showed overall concordance, identifying four clusters, with a few discrepancies in the clustering of individual isolates. Though short- and long-read WGS results provided a more nuanced understanding of the molecular epidemiology of this outbreak, this study highlights the utility of the Acuitas® PCR-based approach, which can more easily be performed by health care facilities, for rapid clustering of patient isolates.

Antifungal Resistance Trends of Candida auris Clinical Isolates in New York and New Jersey from 2016 to 2020.

About 55% of U.S. Candida auris clinical cases were reported from New York and New Jersey from 2016 through 2020. Nearly all New York-New Jersey clinical isolates (99.8%) were fluconazole resistant, and 50% were amphotericin B resistant. Echinocandin resistance increased from 0% to 4% and pan-resistance increased from 0 to <1% for New York C. auris clinical isolates but not for New Jersey, highlighting the regional differences.

Real-time virtual infection prevention and control assessments in skilled nursing homes, New York, March 2020-A pilot project.

OBJECTIVE: To describe a pilot project infection prevention and control (IPC) assessment conducted in skilled nursing facilities (SNFs) in New York State (NYS) during a pivotal 2-week period when the region became the nation's epicenter for coronavirus disease 2019 (COVID-19). DESIGN: A telephone and video assessment of IPC measures in SNFs at high risk or experiencing COVID-19 activity. PARTICIPANTS: SNFs in 14 New York counties, including New York City. INTERVENTION: A 3-component remote IPC assessment: (1) screening tool; (2) telephone IPC checklist; and (3) COVID-19 video IPC assessment (ie, "COVIDeo"). RESULTS: In total, 92 SNFs completed the IPC screening tool and checklist: 52 (57%) were conducted as part COVID-19 investigations, and 40 (43%) were proactive prevention-based assessments. Among the 40 proactive assessments, 14 (35%) identified suspected or confirmed COVID-19 cases. COVIDeo was performed in 26 (28%) of 92 assessments and provided observations that other tools would have missed: personal protective equipment (PPE) that was not easily accessible, redundant, or improperly donned, doffed, or stored and specific challenges implementing IPC in specialty populations. The IPC assessments took ∼1 hour each and reached an estimated 4 times as many SNFs as on-site visits in a similar time frame. CONCLUSIONS: Remote IPC assessments by telephone and video were timely and feasible methods of assessing the extent to which IPC interventions had been implemented in a vulnerable setting and to disseminate real-time recommendations. Remote assessments are now being implemented across New York State and in various healthcare facility types. Similar methods have been adapted nationally by the Centers for Disease Control and Prevention.

A description of the first Candida auris-colonized individuals in New York State, 2016-2017.

Candida auris (C. auris) is a globally emerging multidrug-resistant yeast. New York State (NYS) first detected C. auris in July 2016 and is the state most affected. This brief report describes characteristics of the first 114 individuals colonized with C. auris identified through active surveillance/screening by NYS Department of Health. "Colonized/screened" individuals were old (median age, 74 year), had extensive health care exposures and underlying conditions (multiple health care facility admissions in the 90 days prior with more than 80% requiring mechanical ventilation), and had 30- and 90-day mortality rates of 17.5% and 37.7%, respectively (with approximately 60% expired in the 2-year follow-up period). This description is helpful to inform additional prevention measures and add to the collective understanding of C. auris in the United States.

Congenital Measles in a Premature 25-week Gestation Infant.

We describe a premature infant with congenital measles. Laboratory testing confirmed measles in the mother (polymerase chain reaction- and IgM-positive) and congenital measles in the infant (polymerase chain reaction-positive, culture-positive and IgM-positive). The infant never developed a rash, pneumonia, or neurologic complications. This case supports using compatible laboratory findings to diagnose congenital measles in infants without clinical manifestations of measles.

Investigation of Presumptive HIV Transmission Associated with Hospitalization Using Nucleotide Sequence Analysis - New York, 2017.

Since implementation of Standard Precautions* for the prevention of bloodborne pathogen transmission in 1985, health care-associated transmission of human immunodeficiency virus (HIV) in the United States has been rare (1). In October 2017, the New York City Department of Health and Mental Hygiene (NYCDOHMH) and the New York State Department of Health (NYSDOH) were notified by a clinician of a diagnosis of acute HIV infection in a young adult male (patient A) without recognized risk factors (i.e., he was monogamous, had an HIV-negative partner, and had no injection drug use) who had recently been hospitalized for a chronic medical condition. The low risk coupled with the recent hospitalization and medical procedures prompted NYSDOH, NYCDOHMH, and CDC to investigate this case as possible health care-associated transmission of HIV. Among persons with known HIV infection who had hospitalization dates overlapping those of patient A, one person (patient B) had an HIV strain highly similar to patient A's strain by nucleotide sequence analysis. The sequence relatedness, combined with other investigation findings, indicated a likely health care-associated transmission. Nucleotide sequence analysis, which is increasingly used for detecting HIV clusters (i.e., persons with closely related HIV strains) and to inform public health response (2,3), might also be used to identify possible health care-associated transmission of HIV to someone with health care exposure and no known HIV risk factors (4).

Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned.

Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in New York (NY) from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/nonselective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of the internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal gene for C. auris genotyping. Results included (a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates as well as identification of 277 clinical cases and 350 colonized cases from 151 health care facilities, including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, (b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, (c) demonstration of relatively heavier colonization of C. auris in nares than in the axilla/groin, and (d) predominance of the South Asia clade I with intrinsic resistance to fluconazole and elevated MIC to voriconazole (81%), amphotericin B (61%), flucytosine (5FC) (3%), and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

Multiple introductions and subsequent transmission of multidrug-resistant Candida auris in the USA: a molecular epidemiological survey.

BACKGROUND: Transmission of multidrug-resistant Candida auris infection has been reported in the USA. To better understand its emergence and transmission dynamics and to guide clinical and public health responses, we did a molecular epidemiological investigation of C auris cases in the USA. METHODS: In this molecular epidemiological survey, we used whole-genome sequencing to assess the genetic similarity between isolates collected from patients in ten US states (California, Connecticut, Florida, Illinois, Indiana, Maryland, Massachusetts, New Jersey, New York, and Oklahoma) and those identified in several other countries (Colombia, India, Japan, Pakistan, South Africa, South Korea, and Venezuela). We worked with state health departments, who provided us with isolates for sequencing. These isolates of C auris were collected during the normal course of clinical care (clinical cases) or as part of contact investigations or point prevalence surveys (screening cases). We integrated data from standardised case report forms and contact investigations, including travel history and epidemiological links (ie, patients that had shared a room or ward with a patient with C auris). Genetic diversity of C auris within a patient, a facility, and a state were evaluated by pairwise differences in single-nucleotide polymorphisms (SNPs). FINDINGS: From May 11, 2013, to Aug 31, 2017, isolates that corresponded to 133 cases (73 clinical cases and 60 screening cases) were collected. Of 73 clinical cases, 66 (90%) cases involved isolates related to south Asian isolates, five (7%) cases were related to South American isolates, one (1%) case to African isolates, and one (1%) case to east Asian isolates. Most (60 [82%]) clinical cases were identified in New York and New Jersey; these isolates, although related to south Asian isolates, were genetically distinct. Genomic data corroborated five (7%) clinical cases in which patients probably acquired C auris through health-care exposures abroad. Among clinical and screening cases, the genetic diversity of C auris isolates within a person was similar to that within a facility during an outbreak (median SNP difference three SNPs, range 0-12). INTERPRETATION: Isolates of C auris in the USA were genetically related to those from four global regions, suggesting that C auris was introduced into the USA several times. The five travel-related cases are examples of how introductions can occur. Genetic diversity among isolates from the same patients, health-care facilities, and states indicates that there is local and ongoing transmission. FUNDING: US Centers for Disease Control and Prevention.

Candida auris in Healthcare Facilities, New York, USA, 2013-2017.

Candida auris is an emerging yeast that causes healthcare-associated infections. It can be misidentified by laboratories and often is resistant to antifungal medications. We describe an outbreak of C. auris infections in healthcare facilities in New York City, New York, USA. The investigation included laboratory surveillance, record reviews, site visits, contact tracing with cultures, and environmental sampling. We identified 51 clinical case-patients and 61 screening case-patients. Epidemiologic links indicated a large, interconnected web of affected healthcare facilities throughout New York City. Of the 51 clinical case-patients, 23 (45%) died within 90 days and isolates were resistant to fluconazole for 50 (98%). Of screening cultures performed for 572 persons (1,136 total cultures), results were C. auris positive for 61 (11%) persons. Environmental cultures were positive for samples from 15 of 20 facilities. Colonization was frequently identified during contact investigations; environmental contamination was also common.

Two Imported Cases of Congenital Rubella Syndrome and Infection-Control Challenges in New York State, 2013-2015.

Rubella was declared eliminated in the United States in 2004. During 2013-2015, 2 infants with congenital rubella syndrome (CRS) were born in New York State. Both mothers were foreign born and traveled to Yemen during their pregnancy. Delayed consideration of CRS led to preventable exposures and a substantial public health response.

Investigation of the First Seven Reported Cases of Candida auris, a Globally Emerging Invasive, Multidrug-Resistant Fungus - United States, May 2013-August 2016.

Candida auris, an emerging fungus that can cause invasive infections, is associated with high mortality and is often resistant to multiple antifungal drugs. C. auris was first described in 2009 after being isolated from external ear canal discharge of a patient in Japan (1). Since then, reports of C. auris infections, including bloodstream infections, have been published from several countries, including Colombia, India, Israel, Kenya, Kuwait, Pakistan, South Africa, South Korea, Venezuela, and the United Kingdom (2-7). To determine whether C. auris is present in the United States and to prepare for the possibility of transmission, CDC issued a clinical alert in June 2016 informing clinicians, laboratorians, infection control practitioners, and public health authorities about C. auris and requesting that C. auris cases be reported to state and local health departments and CDC (8). This report describes the first seven U.S. cases of C. auris infection reported to CDC as of August 31, 2016. Data from these cases suggest that transmission of C. auris might have occurred in U.S. health care facilities and demonstrate the need for attention to infection control measures to control the spread of this pathogen.

Epidemiology of human metapneumovirus in a pediatric long-term care facility.

BACKGROUND: Viral respiratory pathogens cause outbreaks in pediatric long-term care facilities (LTCFs), but few studies have used viral diagnostic testing to identify the causative pathogens. We describe the use of such testing during a prolonged period of respiratory illness and elucidate the epidemiology of human metapneumovirus (hMPV) at our LTCF. DESIGN: Retrospective study of influenza-like illness (ILI). SETTING: A 136-bed pediatric LTCF from January 1 through April 30, 2010. METHODS: The ILI case definition included fever, cough, change in oropharyngeal secretions, increase in oxygen requirement, and/or wheezing. RESULTS: During the study period, 69 episodes of ILI occurred in 61 (41%) of 150 residents. A viral pathogen was detected in 27 (39%) of the episodes, including respiratory syncytial virus (RSV) (n = 3), influenza A virus (not typed; n = 2), parainfluenza virus (n =2), adenovirus (n = 1), and hMPV (n = 19). Twenty-seven of the residents with ILI (44%) required transfer to acute care hospitals (mean length of hospitalization, 12 days; range, 3-47 days). Residents with tracheostomies were more likely to have ILI (adjusted odds ratio [OR], 3.99 [95% confidence interval {CI}, 1.87-8.53]; P = .0004). The mortality rate for residents with ILI was 1.6%. Residents with hMPV were younger (P = .03), more likely to be transferred to an acute care facility (OR, 3.73 [95% CI, 1.17-11.95]; P = .02), and less likely to have a tracheostomy (adjusted OR, 0.19 [95% CI, 0.047-0.757]; P = .02 ). DISCUSSION: Diverse pathogens, most notably hMPV, caused ILI in our pediatric LTCF during a prolonged period of time. Viral testing was helpful in characterizing the epidemiology of ILI in this population.

Transmission of hepatitis B virus associated with assisted monitoring of blood glucose at an assisted living facility in New York State.

BACKGROUND: Hepatitis B virus (HBV) transmission has been reported after patient-to-patient blood exposure during assisted monitoring of blood glucose (AMBG). Three assisted-living facility (ALF) residents who underwent AMBG developed acute HBV infection (HBVI) within 10 days. We investigated HBV transmission and implemented preventive measures. METHODS: A retrospective cohort study was conducted. Infection control practices were assessed. HBVI screening was conducted for all staff and epidemiologically linked residents. Viral DNA sequences were compared for a subset of isolates. RESULTS: Lancing devices and glucometers were shared among residents without proper sanitization. Serologic testing of all 34 residents with diabetes and 12 epidemiologically linked residents present during the exposure period detected 6 residents with diabetes with current HBVI and 4 residents with diabetes and 1 epidemiologically linked resident with previous HBVI. A cohort study of 32 individuals with diabetes identified AMBG as a significant risk factor for HBVI (relative risk, 6.7; 95% confidence interval, 1.7-26.3). Viral DNA sequences for 5 AMBG-exposed residents' isolates were identical, suggesting a common source. CONCLUSIONS: AMBG was significantly associated with HBVI in ALF residents with diabetes. Despite clear preventive recommendations, bloodborne pathogen transmission continues to occur in the setting of AMBG. Strengthening direct care provider, infection preventionist, and health department partnerships with ALFs is crucial to ensure safe AMBG practices and prevent HBV transmission.

Investigation of an electronic emergency department information system as a data source for respiratory syndrome surveillance.

Emergency department syndromic surveillance may provide early warning of disease outbreaks due to bioterrorism or natural phenomena. The purpose of this investigation was to explore how an electronic emergency department information system could be used as a data source for respiratory syndrome surveillance. The process of data collection, entry, and transmission is described, and then a subset of data elements with potential epidemiological value is selected. The quality of the data contained in the system was evaluated by conducting a retrospective analysis of emergency department visits recorded in the system during 2001 and by reviewing clinical charts of cases with respiratory diagnoses. Diagnosis codes, discharge disposition, and demographic data were relatively complete; additional clinical data were not. Diagnosis codes were rapidly and reliably recorded. Data available in the system allows a description of emergency department visits for respiratory syndrome in terms of age, gender, location, severity of illness, and distribution in time. Encrypted data were transmitted every four hours to the health department without added work for emergency department personnel. Although significant obstacles remain, electronic emergency department information systems such as this may provide rapid, reliable data for syndromic surveillance.

Electronic reporting of pelvic inflammatory disease from an emergency department.

BACKGROUND AND OBJECTIVES: Pelvic inflammatory disease (PID) is a clinically diagnosed condition that is preventable and underreported. We developed an electronic emergency department (ED) PID reporting system by using an automatic and secure system to send computerized clinician PID diagnoses to the state health department. GOAL: The goal of this study was to assess if electronic transmission of ED PID data could enhance the completeness and timeliness of PID surveillance. STUDY DESIGN: We conducted a retrospective chart review. METHODS: To validate electronic ED diagnoses, we reviewed charts of 157 women with 7 clinicians' diagnoses compatible with PID. We determined which women met the Centers for Disease Control and Prevention (CDC) PID surveillance case definition and determined the positive predictive values of electronic ED diagnoses of PID. We compared completeness of electronic PID reporting with state sexually transmitted disease surveillance. RESULTS: Three diagnoses were appropriate for electronic PID surveillance. Information on women with these diagnoses is sent daily to the health department with no extra effort needed from ED clinicians. Less than 10% of women who met the CDC PID case definition were reported within 6 months through conventional methods. CONCLUSIONS: Electronic ED surveillance will improve completeness and timeliness of PID reporting.

Congenital syphilis in Russia: the value of counting epidemiologic cases and clinical cases.

BACKGROUND: Congenital syphilis (CS) reports in Russia increased 26-fold from 1991 to 1999. Case reports included only infants who were clinical cases, had persistent serologic changes, or confirmed syphilitic stillbirth. Although not reported, policies stipulate that infants of inadequately treated or untreated mothers receive preventive penicillin treatment. GOAL: We examined whether risk factors and consequences for epidemiologic cases of CS (infants of inadequately treated mothers) resembled those of clinical cases and differed from those of noncases (infants of adequately treated mothers). STUDY DESIGN: A retrospective record review from Maternity Houses in 5 sites identified 715 syphilis-infected women who gave birth. RESULTS: Among women with maternal syphilis, 11% (n = 81) of infants were clinical cases, 56% (n = 402) were epidemiologic cases, and 33% (n = 232) were noncases of CS. Compared with noncases, maternal risk factors for epidemiologic cases included nonresidence (P <0.01), late syphilis (P <0.01), unemployment (P <0.01), no prenatal care (P <0.01), and syphilis testing at >/=28 weeks (P <0.01). Each of these was also significant for being a clinical case. Associated consequences of CS for the epidemiologic cases included increases in stillbirth (P <0.01), preterm birth (P <0.01), low birth weight (P <0.01), transfer to a pediatric hospital (P <0.01), and abandonment (P <0.05). Each of these except stillbirth was significantly elevated among clinical cases. Nearly half of the epidemiologic cases had no record of any penicillin treatment for the infant. Epidemiologic cases were significantly more likely than noncases to have no clinical or laboratory follow up. CONCLUSION: In Russia, maternal risk factors and perinatal consequences for epidemiologic cases of CS resembled those of clinical cases. Expanding national reporting to include epidemiologic cases would strengthen CS prevention and monitoring.

Agreement between self-reported information and medical claims data on diagnosed diabetes in Oregon's Medicaid population.

Recent trends in Oregon indicated that diabetes is on the rise. Medicaid self-reported data estimated about 11 percent are affected by diabetes, which is twice the prevalence of the general population in Oregon. Little is known about the agreement between self-reported information and medical claims data in the Medicaid population. This study provides an opportunity to compare prevalence of diabetes when the estimates are computed from the two different data sources. A sample of 2,154 Medicaid adults in Oregon (18 to 64 years old) were identified in both the Medicaid claims and self-report survey. The result reported a strong agreement of diabetes definition between the Medicaid claim data and the self-reported survey.

Outbreak of tuberculosis among homeless persons coinfected with human immunodeficiency virus.

We investigated a cluster of patients with tuberculosis (TB) in North Carolina and determined the extent of transmission of 1 strain of Mycobacterium tuberculosis. A retrospective cohort study was conducted. Homeless shelter attendance and medical records for 1999 and 2000 were reviewed. The period of exposure to M. tuberculosis was determined, and shelter residents were offered TB screening. DNA fingerprinting was performed on 72 M. tuberculosis isolates. In addition to the initial index cluster of 9 patients, another 16 patients were identified. Isolates of M. tuberculosis from all 25 patients shared a matching DNA fingerprint pattern. All but 1 patient was male, 22 (88%) were African American, and 14 (56%) were human immunodeficiency virus-infected. An epidemiological link to a single shelter was identified for all but 1 patient. Earlier recognition of this shelter as a site of M. tuberculosis transmission could have been facilitated through innovative approaches to contact investigation and through genetic typing of isolates.