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High-level vancomycin-resistant Staphylococcus aureus (VRSA) began to emerge in the United States in 2002 and has since then been reported worldwide. Our study reports the closed genome sequences of multiple VRSA isolates obtained in 2004 from a single patient in New York State.

Passive reporting to the Centers for Disease Control and Prevention has identified carbapenemase-producing organisms (CPOs) among solid organ transplant (SOT) recipients, potentially representing an emerging source of spread. We analyzed CPO prevalence in wards where SOT recipients receive inpatient care to inform public health action to prevent transmission.From September 2019 to June 2020, five US hospitals conducted consecutive point prevalence surveys (PPS) of all consenting patients admitted to transplant units, regardless of transplant status. We used the Cepheid Xpert Carba-R assay to identify carbapenemase genes (blaIn total, 154 patients were screened and 92 (60%) were SOT recipients. CPOs were detected among 7 (8%) SOT recipients, from two of five screened hospitals: four blaLongitudinal surveillance in transplant units, as well as PPS in areas with diverse CPO epidemiology, may inform the utility of routine screening in SOT units to prevent the spread of CPOs.

The emergence and transmission of metallo-β-lactamases are significant public health concerns that threaten the utility of antimicrobial therapy (1, 2).….

Multidrug resistant organisms are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying multidrug resistant organisms increase mortality3,4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution5, require several days before informing key clinical decisions. Rapid AST would transform the care of patients with infection while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here we describe a rapid assay for combined genotypic and phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 h faster than standard workflows, with

Aztreonam-avibactam is a drug combination pending phase 3 clinical trials and is suggested for treatment of severe infections caused by metallo-beta-lactamase (MBL)-producing Enterobacterales by combining ceftazidime-avibactam and aztreonam. Beginning in 2019, four Antibiotic Resistance Laboratory Network regional laboratories offered aztreonam-avibactam susceptibility testing by broth microdilution. For 64 clinical isolates tested, the MIC50 and MIC90 values of aztreonam-avibactam were 0.5/4 μg/ml and 8/4 μg/ml, respectively. Aztreonam-avibactam displayed potent in vitro activity against the MBL-producing Enterobacterales tested.

Detection of carbapenem-resistant Pseudomonas aeruginosa (CRPA) with carbapenemase-producing (CP) genes is critical for preventing transmission. Our objective was to assess whether certain antimicrobial susceptibility testing (AST) profiles can efficiently identify CP-CRPA. We defined CRPA as P. aeruginosa with imipenem or meropenem MICs of ≥8 μg/ml; CP-CRPA was CRPA with CP genes (blaKPC/blaIMP/blaNDM/blaOXA-48/blaVIM). We assessed the sensitivity and specificity of AST profiles to detect CP-CRPA among CRPA isolates collected by CDC’s Antibiotic Resistance Laboratory Network (AR Lab Network) and the Emerging Infections Program (EIP) during 2017 to 2019. Three percent (195/6,192) of AR Lab Network CRPA isolates were CP-CRPA. Among CRPA isolates, adding not susceptible (NS) to cefepime or ceftazidime to the definition had 91% sensitivity and 50% specificity for identifying CP-CRPA; adding NS to ceftolozane-tazobactam had 100% sensitivity and 86% specificity. Of 965 EIP CRPA isolates evaluated for CP genes, 7 were identified as CP-CRPA; 6 of the 7 were NS to cefepime and ceftazidime, and all 7 were NS to ceftolozane-tazobactam. Among 4,182 EIP isolates, clinical laboratory AST results were available for 96% of them for cefepime, 80% for ceftazidime, and 4% for ceftolozane-tazobactam. The number of CRPA isolates needed to test (NNT) to identify one CP-CRPA isolate decreased from 138 to 64 if the definition of NS to cefepime or ceftazidime was used and to 7 with NS to ceftolozane-tazobactam. Adding not susceptible to cefepime or ceftazidime to CRPA carbapenemase testing criteria would reduce the NNT by half and can be implemented in most clinical laboratories; adding not susceptible to ceftolozane-tazobactam could be even more predictive once AST for this drug is more widely available.

Since 2005, the Wadsworth Center (WC) has provided molecular testing on cerebrospinal fluid (CSF) and whole blood specimens in close collaboration with epidemiologists in New York State and New York City. In this study, we analyzed 10 years of data to demonstrate the significant value of utilizing molecular methods to assess patient specimens for etiologic agents of bacterial meningitis. A comprehensive molecular testing algorithm to detect and serotype/serogroup bacterial agents known to cause bacterial meningitis (Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus agalactiae) has evolved, and retrospective specimen testing has been essential for each improvement. Over a ten-year span from 2010 to 2019 the WC received 831 specimens from 634 patients with suspected bacterial meningitis. Real-time PCR was positive for at least one of the agents in 223 (27%) specimens from 183 patients (29%). Of the 223 positives, 146 (66%) were further characterized by real-time PCR into serogroup/serotype. Additionally, examination of 131 paired specimens of CSF and whole blood from the same patients found better detection in CSF, but whole blood is a useful alternative for diagnosis when CSF is not available. For specimens initially PCR-negative, 16S rDNA Sanger sequencing was requested by the submitter for 146 cases resulting in the identification of bacterial agents in an additional 24 (16%) specimens. In a retrospective study, Next Generation Sequencing (NGS) was evaluated for the detection of pathogens in 53 previously tested PCR-negative CSF specimens and identified bacteria in 14 (26%) specimens. This molecular testing algorithm has provided clinicians a diagnosis when culture is negative with the potential to guide therapy. It has also aided public health in determining when antibiotic prophylaxis was needed, augmented surveillance data to yield a fuller picture of community prevalence, and highlighted gaps in the spectrum of agents that cause bacterial meningitis.

Background Carbapenemase gene-positive organisms (CPOs) are associated with infections with high mortality rates and have the potential to facilitate epidemic spread of carbapenem resistance. Passive reporting to CDC identified CPOs among organ transplant recipients, potentially representing an emerging reservoir for spread. We aimed to determine the prevalence of CPOs in hospital units where solid organ transplant (SOT) recipients receive care in order to inform public health action to prevent transmission. Methods All healthcare facilities identified one medical unit where SOT recipients received inpatient care and conducted point prevalence surveys (PPS) of all consenting patients on 1-2 designated calendar days. We used the Cepheid Xpert® Carba-R assay to identify carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) from rectal swabs; carbapenemase-positive swabs were cultured for organisms. All laboratory testing was conducted at the Wadsworth Center, part of CDC’s Antibiotic Resistance Laboratory Network. Results Five participating hospitals performed nine PPS from September 2019 through June 2020. In total, 154 patients were screened and 92 (60%) were SOT recipients (Table). The most common transplanted organs were kidney (44, 48%) and liver (39, 42%). Carbapenemase genes were detected among 5 (5%) SOT recipients, all from a single healthcare facility; 4 (80%) were blaKPC and 1 (20%) was blaNDM. Of the positive specimens cultured, blaKPC was carried by Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, and Klebsiella oxytoca and blaNDM was carried by K. oxytoca; blaKPC was carried by both ECC and K. pneumoniae in a single individual. For SOT patients with CPOs, the median interval from transplantation to swab collection was 108 days (range: 12 to 323). CPOs were only detected in 1 (2%) of 62 non-transplant patients. TABLE Characteristics of Carbapenemase Gene-positive Organism (CPO) Pilot Surveillance Participants Conclusion Among participating facilities, most did not identify CPOs among patients admitted to transplant units. These findings represent a small number of patients and facilities; additional PPS in areas with varied CPO epidemiology are needed to understand whether SOT recipients should be routinely screened for CPOs. Disclosures All Authors: No reported disclosures

Background: In the United States, carbapenemases are rarely the cause of carbapenem resistance in Pseudomonas aeruginosa. Detection of carbapenemase production (CP) in carbapenem-resistant P. aeruginosa (CRPA) is critical for preventing its spread, but testing of many isolates is required to detect a single CP-CRPA. The CDC evaluates CRPA for CP through (1) the Antibiotic Resistance Laboratory Network (ARLN), in which CRPA are submitted from participating clinical laboratories to public health laboratories for carbapenemase testing and antimicrobial susceptibility testing (AST) and (2) laboratory and population-based surveillance for CRPA in 8 sites through the Emerging Infection Program (EIP). Objective: We used data from ARLN and EIP to identify AST phenotypes that can help detect CP-CRPA. Methods: We defined CRPA as P. aeruginosa resistant to meropenem, imipenem, or doripenem, and we defined CP-CRPA as CRPA with molecular identification of carbapenemase genes (blaKPC, blaIMP, blaNDM, or blaVIM). We applied CLSI break points to 2018 ARLN CRPA AST data to categorize isolates as resistant, intermediate, or susceptible, and we evaluated the sensitivity and specificity of AST phenotypes to detect CP among CRPA; isolates that were intermediate or resistant were called nonsusceptible. Using EIP data, we assessed the proportion of isolates tested for a given drug in clinical laboratories, and we applied definitions to evaluate performance and number needed to test to identify a CP-CRPA. Results: Only 203 of 6,444 of CRPA isolates (3%) tested through AR Lab Network were CP-CRPA harboring blaVIM (n = 123), blaKPC (n = 53), blaIMP (n = 16), or blaNDM (n = 13) genes. Definitions with the best performance were resistant to ≥1 carbapenem AND were (1) nonsusceptible to ceftazidime (sensitivity, 93%; specificity, 61%) (Table 1) or (2) nonsusceptible to cefepime (sensitivity, 83%; specificity, 53%). Most isolates not identified by definition 2 were sequence type 111 from a single-state blaVIM CP-CRPA outbreak. Among 4,209 CRPA isolates identified through EIP, 80% had clinical laboratory AST data for ceftazidime and 96% had clinical laboratory AST data for cefepime. Of 967 CRPA isolates that underwent molecular testing at the CDC, 7 were CP-CRPA; both definitions would have detected all 7. Based on EIP data, the number needed to test to identify 1 CP-CRPA would decrease from 135 to 42 for definition 1 and to 50 using definition 2. Conclusions: AST-based definitions using carbapenem resistance combined with ceftazidime or cefepime nonsusceptibility would rarely miss a CP-CRPA and would reduce the number needed to test to identify CP-CRPA by >60%. These definitions could be considered for use in laboratories to decrease the testing burden to detect CP-CRPA.Funding: NoneDisclosures: In the presentation we will discuss the drug combination aztreonam-avibactam and acknowledge that this drug combination is not currently FDA approved.

We describe a rare instance of donor-derived OXA-23-producing carbapenem-resistant Acinetobacter baumannii transmission during lung transplantation and the subsequent public health response. This investigation highlights how transplantation can introduce rare multidrug-resistant organisms into different healthcare facilities and regions.

A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations (“outbreaks”) that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isolates were available for each outbreak and were initially examined by pulsed-field gel electrophoresis (PFGE). Sequence-based typing alleles were extracted from WGS data yielding complete sequence types (ST) for isolates representing 8 out of the 10 outbreaks evaluated in this study. Isolates from separate outbreaks sharing the same ST also contained the fewest differences in core genome single nucleotide polymorphisms (SNPs) and the greatest proportion of identical allele sequences in a whole-genome multilocus sequence typing (wgMLST) scheme. Both core SNP and wgMLST analyses distinguished isolates from separate outbreaks, including those from two outbreaks sharing indistinguishable PFGE profiles. Isolates from a hospital-associated outbreak spanning multiple years shared indistinguishable PFGE profiles but displayed differences in their genome sequences, suggesting the presence of multiple environmental sources. Finally, the rtx gene demonstrated differences in the repeat region sequence among ST1 isolates from different outbreaks, suggesting that variation in this gene may be useful for targeted molecular subtyping approaches for L. pneumophila . This study demonstrates the utility of various genome sequence analysis approaches for L. pneumophila for environmental source attribution studies while furthering the understanding of Legionella ecology. IMPORTANCE We demonstrate that whole-genome sequencing helps to improve resolution of Legionella pneumophila isolated during laboratory investigations of legionellosis compared to traditional subtyping methods. These data can be important in confirming the environmental sources of legionellosis outbreaks. Moreover, we evaluated various methods to analyze genome sequence data to help resolve outbreak-related isolates.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB), a multidrug-resistant gram-negative bacterium, can cause difficult-to-treat infections with mortality in approximately half of CRAB cases. CRAB can spread among healthcare facilities after transfer of an infected or colonized patient. Strategies to limit CRAB spread include adherence to contact precautions, environmental cleaning with bleach, and screening to identify colonized patients. During July–September 2018, the Connecticut Department of Public Health (DPH) worked with an acute-care hospital (hospital A) to contain an outbreak of OXA-23–producing CRAB (OXA-23 is an enzyme that confers resistance to carbapenems). During November 2018–March 2019, statewide CRAB surveillance identified additional cases of related OXA-23–producing CRAB at other healthcare facilities. DPH, Connecticut State Public Health Laboratory (SPHL), and the Antibiotic Resistance Laboratory Network (ARLN) investigated to prevent additional cases. Methods: Since January 2017, CRAB isolates have been routinely sent to SPHL and ARLN for carbapenemase gene detection and whole-genome sequencing (WGS) to determine isolate relatedness. During November 2018–March 2019, DPH collected patient healthcare history for patients with CRAB isolates to identify outbreaks and provide assistance in infection control and prevention to healthcare facilities reporting CRAB cases. Beginning May 2019, DPH and ARLN offered facilities screening to identify patients colonized with OXA-23–producing CRAB. Results: Of 10 OXA-23–producing CRAB isolates reported to DPH during November 2018–March 2019, 3 were closely related to the 9 isolates from hospital A’s outbreak by WGS (single-nucleotide polymorphism difference range, 1–16). One isolate was from a patient who had been admitted to hospital A during July 2018. All 3 patients with CRAB isolates shared a history of residence at long-term–care facility A (LTCF A). Two patients received a CRAB infection diagnosis upon admission to hospital B after transfer from LTCF A. Both LTCF A and hospital B performed environmental cleaning with bleach and placed CRAB-identified patients on contact precautions. LTCF A declined screening patients for CRAB, whereas hospitals B and C, which receive frequent transfers from LTCF A, screened all patients on admission from LTCF A. During May–September 2019, among 6 patients screened, 1 was colonized with OXA-23–producing CRAB and was placed on contact precautions. Conclusions: Transfer of patients who are infected or colonized with CRAB among hospitals and LTCFs can facilitate the regional spread of CRAB. Strategies for containing the spread of carbapenemase-producing organisms include adherence to contact precautions, colonization screening, interfacility communication, and collaboration with public health.Funding: NoneDisclosures: None

We investigated the value of whole-genome sequencing (WGS) and single nucleotide polymorphism (SNP) analyses in determining the relationships among and evolutionary rates of Legionella species with long-term persistence in three healthcare facilities. We examined retrospective clinical and environmental isolates of Legionella micdadei and Legionella pneumophila serogroup 1 isolates with identical PFGE DNA fingerprints sampled over the course of up to 18 years. WGS analyses demonstrated that heterogeneous populations of Legionella were present within each facility despite displaying the same PFGE profiles. Additionally, clustering of some clinical isolates with those from a separate but related institution exposed a source of infection not previously detected, underscoring the importance of considering phylogenetic relationships when assessing epidemiological links. The data supported an average substitution rate of 0.80 SNPs per genome per year for L. micdadei but a reliable estimate for L. pneumophila serogroup 1 could not be obtained due to complicating factors such as non-chronological links among isolates and inadequate sampling depths. While the substitution rate for L. micdadei is consistent with previous estimates for L. pneumophila, the lack of a temporal signal in our sequence data for L. pneuomphila serogroup 1 isolates suggests either insufficient change to provide an estimate or variable evolutionary rates, which could reflect the presence of both actively dividing and viable but non-culturable Legionella spp. in the built environment. This study highlights the increased discriminatory power of WGS SNP analysis as compared to PFGE, emphasizes the need for extended sampling, and provides insight into the evolution of Legionella from longitudinal investigations.

We investigated an outbreak of eight Legionnaires’ disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings)

Confirmed and probable cases of invasive Neisseria meningitidis (Nm) infection are reportable in New York City. We conducted a study to identify Nm among culture-negative reports of bacterial and viral meningitis. During the study period, 262 reports of suspected meningitis were eligible. Cerebrospinal fluid (CSF) specimens from 138 patients were obtained for testing. No Nm cases were detected. Results from real-time polymerase chain reaction and 16S on CSF specimens were concordant with hospital microbiology findings in 80%; however, other pathogenic organisms were detected in 14 culture-negative specimens. New York City's surveillance system appears to be effective at capturing cases of Nm meningitis. Nucleic acid testing is useful for detecting the presence of bacterial DNA when antibiotic therapy precedes lumbar puncture or bacterial cultures are negative. It remains unanswered whether culture-negative cases of Nm bacteremia are being missed by reportable disease surveillance.

During the summer of 2015, New York, New York, USA, had one of the largest and deadliest outbreaks of Legionnaires’ disease in the history of the United States. A total of 138 cases and 16 deaths were linked to a single cooling tower in the South Bronx. Analysis of environmental samples and clinical isolates showed that sporadic cases of legionellosis before, during, and after the outbreak could be traced to a slowly evolving, single-ancestor strain. Detection of an ostensibly virulent Legionella strain endemic to the Bronx community suggests potential risk for future cases of legionellosis in the area. The genetic homogeneity of the Legionella population in this area might complicate investigations and interpretations of future outbreaks of Legionnaires’ disease.

Clinical isolates of the respiratory pathogen Bordetella pertussis in the United States have become predominantly deficient for the acellular vaccine immunogen pertactin through various independent mutations. Here, we report the complete genome sequences for four B. pertussis isolates that harbor novel deletions responsible for pertactin deficiency.

Background New York State Department of Health (NYSDOH) and Wadsworth Center (WC) participate in the Centers for Disease Control and Prevention’s Antibiotic Resistance Laboratory Network (AR Lab Network), including identification and characterization of specific bla genes in carbapenemase-producing organisms (CPO). Three investigations from November 2018–March 2019 illustrate the findings and challenges investigating CPO in a blaKPC endemic setting. Methods NYSDOH WC testing includes organism identification, drug susceptibility testing, detection of carbapenemase production, detection of carbapenemase genes, and whole-genome sequencing (WGS). NYSDOH epidemiologic (epi) investigations of novel resistance mechanisms review demographic and exposure data, conduct contact tracing with targeted rectal screening to identify colonized persons, and assess infection control (IC) and public health (PH) practices and provide recommendations. Results NYSDOH identified three nursing home residents infected with CPO with novel carbapenemase genes (Figure 1) with no travel history but multiple co-morbidities, including mechanical ventilation: blaOXA-48Klebsiella pneumoniae (KP) (Facility A), blaNDM KP (Facility B and C). Epi investigations identified CPO in 48 of 106 residents screened for rectal colonization; most isolates had genes other than the index gene. Facility A and Facility B each had no additional residents colonized with CPO with the index gene after screening; 14 and 10 residents, respectively from Facility A and B, had CPO with endemic blaKPC gene. WGS analysis identified 2 clusters of blaKPC KP within Facility A and no clusters of CPO were detected in Facility B. IC/PH recommendations were made after diagnosis at all 3 facilities; serial IC/PH assessments/recommendations and screening were needed to interrupt transmission at Facility C, where 24 residents were colonized with CPO, including 7 residents with CPO with the index gene (blaNDM), and a subset of the blaNDM isolates were related to the index case by both epi and WGS analysis. Conclusion Epi investigation and WGS were complementary to detect transmission, identify clusters within an endemic setting, and inform PH response and IC measures for these emerging CPO in NY Healthcare Facilities. Disclosures All authors: No reported disclosures.

Objectives:Infections caused by Legionella are the leading cause of waterborne disease outbreaks in the United States. We investigated a large outbreak of Legionnaires’ disease in New York City in summer 2015 to characterize patients, risk factors for mortality, and environmental exposures.Methods:We defined cases as patients with pneumonia and laboratory evidence of Legionella infection from July 2 through August 3, 2015, and with a history of residing in or visiting 1 of several South Bronx neighborhoods of New York City. We describe the epidemiologic, environmental, and laboratory investigation that identified the source of the outbreak.Results:We identified 138 patients with outbreak-related Legionnaires’ disease, 16 of whom died. The median age of patients was 55. A total of 107 patients had a chronic health condition, including 43 with diabetes, 40 with alcoholism, and 24 with HIV infection. We tested 55 cooling towers for Legionella, and 2 had a strain indistinguishable by pulsed-field gel electrophoresis from 26 patient isolates. Whole-genome sequencing and epidemiologic evidence implicated 1 cooling tower as the source of the outbreak.Conclusions:A large outbreak of Legionnaires’ disease caused by a cooling tower occurred in a medically vulnerable community. The outbreak prompted enactment of a new city law on the operation and maintenance of cooling towers. Ongoing surveillance and evaluation of cooling tower process controls will determine if the new law reduces the incidence of Legionnaires’ disease in New York City.

We have developed a single tube TaqMan(®) real-time PCR assay that differentiates the full-length and truncated erm(41) gene to predict inducible resistance to clarithromycin in Mycobacterium abscessus. A study of 87 clinical isolates found this assay to be 90.8% concordant to conventional drug susceptibility testing results for the prediction of inducible clarithromycin drug resistance.

A multiplexed, 4-target real-time polymerase chain reaction (PCR) assay for the detection and characterization of Yersinia pestis was designed and optimized for respiratory and environmental samples. The target sequences include the entF3 gene of the chromosome, pla (plasminogen activator) on the pPCP1 virulence plasmid, caf1 (F1 capsule antigen) on the pMT1 virulence plasmid, and a region located on the pCD1 plasmid. The sensitivity of this assay was determined to be less than 85 CFU per reaction for each specimen type analyzed. This assay was also determined to be 100% specific with strains of Y. pestis, 9 additional Yersinia species, and related enteric and respiratory organisms. The results show that this multiplex real-time PCR assay using TaqMan(R) (Roche Molecular Systems, Inc., Alameda, CA) chemistry is sensitive and specific, requires minimal sample input, and can yield results in approximately 4 h. This assay is the first 4-target multiplex real-time PCR assay for Y. pestis in which detection and virulence assessment of Y. pestis can occur in one reaction, from clinical and environmental samples.

Background Norovirus infections occur frequently and are widespread throughout the US population causing greater than half of all foodborne gastroenteritis cases. A rapid norovirus assay would be a useful clinical tool for identification of this common virus in gastroenteritis patient samples, thereby identifying outbreaks and facilitating rapid implementation of control measures. Objectives To determine the suitability of the RIDAQuick norovirus kit as a clinical tool by determining the specificity and sensitivity of the assay, and its cross-reactivity with other enteric viruses. Study design Archived stool specimens containing norovirus genogroup I or II or other viruses were tested using the RIDAQuick norovirus assay and results compared to those obtained with real-time RT-PCR. Results We tested 62 samples: 19 norovirus genogroup I, 25 genogroup II samples, and 18 norovirus negative samples. Compared to PCR results, RIDAQuick assay sensitivity was 61.4%, and specificity was 100%. The low sensitivity was mainly due to poor results with genogroup I specimens; only 11 of 19 were detected. Additionally, samples of four other common enteric viruses all tested negative with the RIDAQuick assay. Conclusions The RIDAQuick kit effectively detects norovirus genogroup II strains, but not genogroup I strains. We found no cross-reactivity with several common enteric viruses. As most norovirus cases are currently genogroup II strains, positive results with RIDAQuick can be used for rapid detection of norovirus in a large percentage of cases, thus also aiding in identification of outbreaks. However, final confirmation and negative results require further testing with more sensitive methods.

A great deal of information on the Legionella genus, legionellosis, the microbial ecology, as well as its pathogenicity, diagnosis and treatment has been accumulated since this pathogen caused the first known outbreak in 1976. However, the control of legionellosis relies primarily on the diagnostic testing of patients and vigilant surveillance of water systems in healthcare facilities. PCR methods offer a useful alternative for the future as they can be utilized on primary specimens, are highly sensitive and specific, and can detect all serogroups of Legionella pneumophila as well as other species of Legionella that cause disease. If approaches utilizing testing algorithms combining culture and PCR methods are utilized they will also offer advantages during outbreak investigations. Additionally, reducing exposures to Legionella and preventing disease will be improved when more is understood about the control of Legionella in water systems and vaccination strategies for Legionella are evaluated.

A Gram-staining-positive, endospore-forming rod was isolated independently from clinical specimens in New York State, USA, once in 2009 and twice in 2011. The three isolates had identical 16S rRNA gene sequences and, based on their 16S rRNA gene sequence, are most closely related to the type strains of Laceyella sediminis and L. sacchari (94.6 % similarity). The partial 23S rRNA gene sequences of the three strains were also 100 % identical. Maximum-likelihood phylogenetic analysis suggests that the new isolates belong to the family Thermoactinomycetaceae . Additional biochemical and phenotypic characteristics of the strains support the family designation and suggest that the three isolates represent a single species. In each of the strains, the predominant menaquinone is MK-7, the diagnostic diamino acid is meso-diaminopimelic acid and the major cellular fatty acids are iso-C15 : 0, anteiso-C15 : 0 and iso-C13 : 0. The polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids, four unknown aminophospholipids and an unknown lipid. It is proposed that the novel isolates represent a single novel species within a new genus, for which the name Hazenella coriacea gen. nov., sp. nov. is proposed. The type strain of Hazenella coriacea is strain 23436T ( = DSM 45707T = LMG 27204T).

Twelve independent isolates of a Gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.13 % similarity). DNA–DNA hybridization studies demonstrate that the new isolates belong to a species distinct from their nearest phylogenetic neighbours. The partial sequences of the 23S rRNA gene for the novel strains and their nearest neighbours also provide support for the novel species designation. Maximum-likelihood phylogenetic analysis of the 16S rRNA gene sequences confirmed that the new isolates are in the genus Sporosarcina. The predominant menaquinone is MK-7, the peptidoglycan has the type A4α l-Lys–Gly–d-Glu, and the polar lipids consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids are iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. In addition, biochemical and morphological analyses support designation of the twelve isolates as representatives of a single new species within the genus Sporosarcina, for which the name Sporosarcina newyorkensis sp. nov. (type strain 6062T = DSM 23544T = CCUG 59649T = LMG 26022T) is proposed.

An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species. For each species, two strains from independent sources were identified. Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri. DNA–DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours. Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation. Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis. The predominant cellular fatty acids [16 : 0, summed feature 3 (16 : 1ω7c and/or iso-15 : 0 2-OH) and 18 : 1ω7c], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov. (type strain 9715T =DSM 22247T =CIP 109934T) and Neisseria shayeganii sp. nov. (type strain 871T =DSM 22246T =CIP 109933T).

Our laboratory has developed a novel real-time polymerase chain reaction (PCR) assay for the detection of Legionella pneumophila and differentiation from other Legionella spp. in clinical and environmental samples. The 23S rRNA gene was used as a target to detect all Legionella spp., and the mip gene was targeted for the specific detection of L. pneumophila in this multiplex Taqman real-time PCR assay. The 23S rRNA gene is a novel target for Legionella testing; it detects all species and serogroups of Legionella without the contamination issues that accompany the use of the 16S rRNA gene as a target. This assay provides an analytical sensitivity of