Carriage of Neisseria meningitidis in Men Who Have Sex With Men Presenting to Public Sexual Health Clinics, New York City.

BACKGROUND: We conducted a Neisseria meningitidis (Nm) carriage study among men who have sex with men (MSM) to explore possible sexual transmission. METHODS: We paired information on patient characteristics with oropharyngeal, rectal, and urethral Nm culture results to assess associations with Nm carriage among 706 MSM at New York City sexual health clinics. The Nm isolates were characterized by whole genome sequencing. RESULTS: Twenty-three percent (163 of 706) of MSM were Nm carriers. Oropharyngeal carriage was 22.6% (159 of 703), rectal 0.9% (6 of 695), and urethral 0.4% (3 of 696). Oropharyngeal carriage was associated with the following recent (past 30 days) exposures: 3 or more men kissed (adjusted relative risk [aRR], 1.38; 95% confidence interval [CI], 1.03-1.86), performing oral sex (aRR, 1.81; 95% CI, 1.04-3.18), and antibiotic use (aRR, 0.33; 95% CI, 0.19-0.57). Sixteen clonal complexes were identified; 27% belonged to invasive lineages. CONCLUSIONS: Our findings suggest that oral sex and the number of recent kissing partners contribute to Nm carriage in MSM.

Lymphogranuloma Venereum: An Increasingly Common Anorectal Infection Among Men Who Have Sex With Men Attending New York City Sexual Health Clinics.

Using Chlamydia trachomatis anorectal specimens routinely tested for lymphogranuloma venereum (LGV) (2008-2011) and samples of archived specimens tested for LGV (2012-2015), we observed increased LGV positivity among men who have sex with men attending NYC Sexual Health Clinics. Using clinical data, we determined predictors of anorectal LGV that may guide clinical management.

Increasing Antibiotic Resistance in Shigella spp. from Infected New York City Residents, New York, USA.

Approximately 20% of Shigella isolates tested in New York City, New York, USA, during 2013-2015 displayed decreased azithromycin susceptibility. Case-patients were older and more frequently male and HIV infected than those with azithromycin-susceptible Shigella infection; 90% identified as men who have sex with men. Clinical interpretation guidelines for azithromycin resistance and outcome studies are needed.

Legionnaires' Disease Outbreak Caused by Endemic Strain of Legionella pneumophila, New York, New York, USA, 2015.

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.

Molecular characterization of methicillin-resistant Staphylococcus aureus clinical isolates obtained from the Rikers Island Jail System from 2009 to 2013.

Inmates of Rikers Island jail potentially introduce Staphylococcus aureus into New York State prisons upon transfer. In this study, methicillin-resistant Staphylococcus aureus isolates (n = 452), collected from infected inmates (2009 to 2013), were characterized. spa type t008 was the predominant clone identified, accounting for 82.3% of the isolates, with no evidence of mupirocin or chlorhexidine resistance.

Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to resolve complex clinical cases of patients with recurrent bacteremias.

Matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method of identifying microorganisms. Throughout Europe, it is already in routine use but has not yet been widely implemented in the United States, pending FDA approval. Here, we describe two medically complex patients at a large tertiary-care academic medical center with recurring bacteremias caused by distinct but related species. Bacterial identifications were initially obtained using the Vitek-2 system with the GPI card for Enterococcus and the API system for staphylococci. Initial results misled clinicians as to the source and proper management of these patients. Retrospective investigation with MALDI-TOF MS clarified the diagnosis by identifying a single microorganism as the pathogen in each case. To our knowledge, this is one of the first reports in the United States demonstrating the use of MALDI-TOF MS to facilitate the clinical diagnosis in patients with recurrent bacteremias of unclear source.

Contribution of selected gene mutations to resistance in clinical isolates of vancomycin-intermediate Staphylococcus aureus.

Infections with vancomycin-intermediate Staphylococcus aureus (VISA) have been associated with vancomycin treatment failures and poor clinical outcomes. Routine identification of clinical isolates with increased vancomycin MICs remains challenging, and no molecular marker exists to aid in diagnosis of VISA strains. We tested vancomycin susceptibilities by using microscan, Etest, and population analyses in a collection of putative VISA, methicillin-resistant S. aureus, and methicillin-sensitive S. aureus (VSSA) infectious isolates from community- or hospital-associated S. aureus infections (n = 77) and identified 22 VISA and 9 heterogeneous VISA (hVISA) isolates. Sequencing of VISA candidate loci vraS, vraR, yvqF, graR, graS, walR, walK, and rpoB revealed a high diversity of nonsynonymous single-nucleotide polymorphisms (SNPs). For vraS, vraR, yvqF, walK, and rpoB, SNPs were more frequently present in VISA and hVISA than in VSSA isolates, whereas mutations in graR, graS, and walR were exclusively detected in VISA isolates. For each of the individual loci, SNPs were only detected in about half of the VISA isolates. All but one VISA isolate had at least one SNP in any of the genes sequenced, and isolates with an MIC of 6 or 8 µg/ml harbored at least 2 SNPs. Overall, increasing vancomycin MICs were paralleled by a higher proportion of isolates with SNPs. Depending on the clonal background, SNPs appeared to preferentially accumulate in vraS and vraR for sequence type 8 (ST8) and in walK and walR for ST5 isolates. Taken together, by comparing VISA, hVISA, and VSSA controls, we observed preferential clustering of SNPs in VISA candidate genes, with an unexpectedly high diversity across these loci. Our results support a polygenetic etiology of VISA.

Epidemiologic investigation and targeted vaccination initiative in response to an outbreak of meningococcal disease among illicit drug users in Brooklyn, New York.

BACKGROUND: An outbreak of serogroup C meningococcal disease that involved illicit drug users and their contacts occurred in Brooklyn, New York, during 2005 and 2006. METHODS: The objectives of this study were to identify the population at risk for meningococcal disease, describe efforts to interrupt disease transmission, and assess the impact of a vaccine initiative. Descriptive and molecular epidemiological analysis was used to define the extent of the outbreak and the common risk factors among outbreak-related cases. A vaccine initiative that used community-based service providers was targeted to illicit drug users and their close contacts. The vaccine initiative was assessed through cessation of outbreak-related cases and the reduction in carriage rate. RESULTS: The investigation identified 23 outbreak-related cases of serogroup C meningococcal disease; 17 isolates were indistinguishable and 4 isolates were closely related according to pulsed-field gel electrophoresis. Two additional culture-negative cases had epidemiological links to laboratory-confirmed cases. The median age of patients with outbreak-related cases was 41 years, and 19 (83%) of 23 patients reported an association with illicit drug use. There were 7 outbreak-related deaths. Vaccination was administered to 2763 persons at 29 community locations, including methadone treatment centers, syringe-exchange programs, and soup kitchens. Three additional cases of meningococcal disease due to strains with the same pulsed-field gel electrophoresis pattern were identified after the vaccination initiative. CONCLUSIONS: Community-based outbreaks of meningococcal disease are difficult to control, and the decision to vaccinate is not straightforward. Current national guidelines for implementing a vaccination campaign are not strict criteria and cannot be expected to accommodate the myriad of factors that occur in community-based invasive meningococcal disease outbreaks, such as the inability to enumerate the population at risk.

Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks.

BACKGROUND: While overall rates of meningococcal disease have been declining in the United States for the past several decades, New York City (NYC) has experienced two serogroup C meningococcal disease outbreaks in 2005-2006 and in 2010-2013. The outbreaks were centered within drug use and sexual networks, were difficult to control, and required vaccine campaigns. METHODS: Whole Genome Sequencing (WGS) was used to analyze preserved meningococcal isolates collected before and during the two outbreaks. We integrated and analyzed epidemiologic, geographic, and genomic data to better understand transmission networks among patients. Betweenness centrality was used as a metric to understand the most important geographic nodes in the transmission networks. Comparative genomics was used to identify genes associated with the outbreaks. RESULTS: Neisseria meningitidis serogroup C (ST11/ET-37) was responsible for both outbreaks with each outbreak having distinct phylogenetic clusters. WGS did identify some misclassifications of isolates that were more distant from the outbreak strains, as well as those that should have been included based on high genomic similarity. Genomes for the second outbreak were more similar than the first and no polymorphism was found to either be unique or specific to either outbreak lineage. Betweenness centrality as applied to transmission networks based on phylogenetic analysis demonstrated that the outbreaks were transmitted within focal communities in NYC with few transmission events to other locations. CONCLUSIONS: Neisseria meningitidis is an ever changing pathogen and comparative genomic analyses can help elucidate how it spreads geographically to facilitate targeted interventions to interrupt transmission.

Pseudo-outbreak of Bordetella bronchiseptica infection associated with contaminated rabbit blood used as a broth culture supplement.

A cluster of clinical isolates of Bordetella bronchiseptica was identified by microbiology laboratory personnel. A clinical and molecular epidemiologic study determined that this cluster represented a pseudo-outbreak due to bacterial contamination of rabbit blood used as a broth culture supplement. This pseudo-outbreak highlights the importance of quality assurance programs in the laboratory.

A Large Community Outbreak of Legionnaires' Disease Associated With a Cooling Tower in New York City, 2015.

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.

The use of combination subtyping in the forensic evaluation of a three-year-old girl with gonorrhea.

The use of pulsed field gel electrophoresis and neisserial lipoprotein gene sequencing for subtyping Neisseria gonorrhoeae has not been reported in the evaluation of sexually abused children. We report the application and implications of combining pulsed field gel electrophoresis and lipoprotein subtyping in the evaluation of a 3-year-old girl with N. gonorrhoeae infection.

Persistence of fluoroquinolone-resistant, multidrug-resistant Streptococcus pneumoniae in a long-term-care facility: efforts to reduce intrafacility transmission.

OBJECTIVE: We describe an effort to reduce transmission of a multidrug-resistant Streptococcus pneumoniae (MDRSP) in a long-term-care facility (LTCF). DESIGN: Longitudinal cross-sectional study. SETTING: An LTCF in New York City with ongoing disease due to an MDRSP strain among residents with AIDS since a 1995 outbreak. The MDRSP outbreak strain was susceptible to vancomycin but not to other antimicrobials tested, including fluoroquinolones. PARTICIPANTS: Residents and staff members of the LTCF during 1999 through 2001. INTERVENTION: Implementing standard infection control measures, and developing and implementing "enhanced standard" infection control measures, modified respiratory droplet prevention measures to reduce inter-resident transmission. RESULTS: Before the intervention, nasopharyngeal carriage of the MDRSP outbreak strain was detected in residents with AIDS and residents with tracheostomies who were not dependent on mechanical ventilation. The prevalence of nasopharyngeal carriage of the MDRSP outbreak strain was 7.8% among residents who had AIDS and 14.6% among residents with tracheostomies. After training sessions on standard and enhanced standard infection control measures, the staff appeared to have good knowledge and practice of the infection control measures. After the intervention, new transmission among residents with tracheostomies was prevented; however, these residents were prone to persistent tracheal carriage and needed ongoing enhanced standard infection control measures. Ongoing transmission among residents with AIDS, a socially active group, was documented, although fewer cases of disease due to the outbreak strain occurred. CONCLUSIONS: Infection control contributed to less transmission of MDRSP in the LTCE Additional strategies are needed to reduce transmission and carriage among certain resident populations.

Failure to control an outbreak of multidrug-resistant Streptococcus pneumoniae in a long-term-care facility: emergence and ongoing transmission of a fluoroquinolone-resistant strain.

OBJECTIVES: To characterize risk factors associated with pneumococcal disease and asymptomatic colonization during an outbreak of multidrug-resistant Streptococcus pneumoniae (MDRSP) among AIDS patients in a long-term-care facility (LTCF), evaluate the efficacy of antimicrobial prophylaxis in eliminating MDRSP colonization, and describe the emergence of fluoroquinolone resistance in the MDRSP outbreak strain. DESIGN: Epidemiologic investigation based on chart review and characterization of SP strains by antimicrobial susceptibility testing and PFGE and prospective MDRSP surveillance. SETTING: An 80-bed AIDS-care unit in an LTCF PARTICIPANTS: Staff and residents on the unit. RESULTS: From April 1995 through January 1996, 7 cases of MDRSP occurred. A nasopharyngeal (NP) swab survey of all residents (n=65) and staff (n=70) detected asymptomatic colonization among 6 residents (9%), but no staff. Isolates were sensitive only to rifampin, ofloxacin, and vancomycin. A 7-day course of rifampin and ofloxacin was given to eliminate colonization among residents: NP swab surveys at 1, 4, and 10 weeks after prophylaxis identified 1 or more colonized residents at each follow-up with isolates showing resistance to one or both treatment drugs. Between 1996 and 1999, an additional 6 patients were diagnosed with fluoroquinolone-resistant (FQ-R) MDRSP infection, with PFGE results demonstrating that the outbreak strain had persisted 3 years after the initial outbreak was recognized. CONCLUSIONS: Chemoprophylaxis likely contributed to the development of a FQ-R outbreak strain that continued to be transmitted in the facility through 1999. Long-term control of future MDRSP outbreaks should rely primarily on vaccination and strict infection control measures.

An outbreak of Klebsiella pneumoniae and Enterobacter aerogenes bacteremia after interventional pain management procedures, New York City, 2008.

BACKGROUND AND OBJECTIVES: In October 2008, an investigation was conducted into a cluster of gram-negative bloodstream infections after invasive pain management procedures at an outpatient facility to identify additional cases and determine the source of illness. METHODS: We conducted a retrospective cohort study to determine exposures associated with illness. Eligible patients had an invasive procedure in the 4 days before or after the procedure date of the initial case-patients. Infection control assessments were made, and environmental specimens collected. RESULTS: Four laboratory-confirmed case-patients (3 with Klebsiella pneumoniae and 1 with Enterobacter aerogenes) and 5 suspect case-patients were identified. In addition to the 9 confirmed and suspect case-patients, 45 patients were interviewed. All confirmed and suspect case-patients had a sacroiliac joint steroid injection procedure; injection into the sacroiliac joint was associated with illness (9/22 versus 0/31; P < 0.0001). Multiple breaches in infection control were noted including the reuse of single-use vials for multiple patients. The 3 K. pneumoniae with positive blood cultures were indistinguishable by pulse-field gel electrophoresis, and the E. aerogenes-positive blood culture was indistinguishable by pulse-field gel electrophoresis to the culture from an open vial of 100-mL iodixanol contrast solution. CONCLUSION: Infection was associated with pain management procedures, specifically those involving injection to the sacroiliac joint. Lapses in infection control likely led to the contamination of single-use vials that were then used for multiple patients. Reuse of medication vials should be restricted, and affordable single-dose vials should be made available.

Invasive group A streptococcal infection in high school football players, New York City, 2003.

After being notified that 2 high school football teammates from New York City were hospitalized with confirmed or suspected invasive group A streptococcal infections, we conducted an investigation of possible spread among other team members. This investigation highlights a need for guidelines on management of streptococcal and other infectious disease outbreaks in team sport settings.

Profile of Salmonella enterica subsp. enterica (subspecies I) serotype 4,5,12:i:- strains causing food-borne infections in New York City.

Strains of newly emerging Salmonella enterica subsp. enterica (subspecies I) serotype 4,5,12:i:- causing food-borne infections, including a large food poisoning outbreak (n = 86) characterized by persistent diarrhea (14% bloody), abdominal pain, fever, and headache, were examined. The organisms were found in the stool samples from the patients. The biochemical profile of the organisms is consistent with that of S. enterica subsp. I serotypes, except for decreased dulcitol (13%) and increased inositol (96%) utilization. Twenty-eight percent of the strains showed resistance to streptomycin, sulfonamides, or tetracycline only; all three antimicrobial agents; or these agents either alone or in combination with ampicillin, trimethoprim, and trimethoprim-sulfamethoxazole. None of the serotype 4,5,12:i:- strains showed resistance or decreased susceptibility to chloramphenicol or ciprofloxacin. On pulsed-field gel electrophoresis (PFGE), the strains showed 11 or 12 resolvable genomic fragments with 18 banding patterns and three PFGE profile (PFP) clusters (i.e., PFP/A, PFP/B, and PFP/C). Seventy-five percent of the isolates fingerprinted were closely related (zero to three band differences; similarity [Dice] coefficient, 86 to 100%); 63% of these were indistinguishable from each other (PFP/A(1)). PFP/A(1) was common to all strains from the outbreak and 11 hospital sources. Strains from six other hospitals shared clusters PFP/B and PFP/C. PFP/C(4), of the environmental isolate, was unrelated to PFP/A and PFP/B. Nine band differences (similarity coefficient, 61%) were noted between PFP/A(1) and PFP/E of the multidrug-resistant S. enterica subsp. enterica serotype Typhimurium definitive type 104 strains. Whether these emerging Salmonella strains represent a monophasic, Dul(-) variant of serotype Typhimurium or S. enterica subsp. enterica serotype Lagos or a distinct serotype of S. enterica subsp. I is not yet known. Some of the phenotypic and genotypic properties of the serotype 4,5,12:i:- strains are described here.

Outbreak of Klebsiella pneumoniae producing a new carbapenem-hydrolyzing class A beta-lactamase, KPC-3, in a New York Medical Center.

From April 2000 to April 2001, 24 patients in intensive care units at Tisch Hospital, New York, N.Y., were infected or colonized by carbapenem-resistant Klebsiella pneumoniae. Pulsed-field gel electrophoresis identified a predominant outbreak strain, but other resistant strains were also recovered. Three representatives of the outbreak strain from separate patients were studied in detail. All were resistant or had reduced susceptibility to imipenem, meropenem, ceftazidime, piperacillin-tazobactam, and gentamicin but remained fully susceptible to tetracycline. PCR amplified a blaKPC allele encoding a novel variant, KPC-3, with a His(272)-->Tyr substitution not found in KPC-2; other carbapenemase genes were absent. In the outbreak strain, KPC-3 was encoded by a 75-kb plasmid, which was transferred in vitro by electroporation and conjugation. The isolates lacked the OmpK35 porin but expressed OmpK36, implying reduced permeability as a cofactor in resistance. This is the third KPC carbapenem-hydrolyzing beta-lactamase variant to have been reported in members of the Enterobacteriaceae, with others reported from the East Coast of the United States. Although producers of these enzymes remain rare, the progress of this enzyme group merits monitoring.

Laboratory response to anthrax bioterrorism, New York City, 2001.

In October 2001, the greater New York City Metropolitan Area was the scene of a bioterrorism attack. The scale of the public response to this attack was not foreseen and threatened to overwhelm the Bioterrorism Response Laboratory's (BTRL) ability to process and test environmental samples. In a joint effort with the Centers for Disease Control and Prevention and the cooperation of the Department of Defense, a massive effort was launched to maintain and sustain the laboratory response and return test results in a timely fashion. This effort was largely successful. The development and expansion of the facility are described, as are the special needs of a BTRL. The establishment of a Laboratory Bioterrorism Command Center and protocols for sample intake, processing, reporting, security, testing, staffing, and and quality control are also described.