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We analyzed travel-associated clinical isolates of Escherichia coli O104:H4, including 1 from the 2011 German outbreak and 1 from a patient who returned from the Philippines in 2010, by genome sequencing and optical mapping. Despite extensive genomic similarity between these strains, key differences included the distribution of toxin and antimicrobial drug–resistance determinants.

Determination of emm variations may help improve vaccine design., Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections. GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein. To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002–2010. The most prevalent emm types varied little from year to year. In contrast, fine-scale geographic analysis identified inter-site variability in the most common emm types. Additionally, we observed fluctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections. We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease. These findings about the epidemiology of GAS are potentially useful for vaccine research.

Identifying geographic distribution can improve surveillance and clinical testing procedures., The water-borne pathogen Legionella pneumophila serogroup 1 (Lp1) is the most commonly reported etiologic agent of legionellosis. To examine the genetic diversity, the long-term epidemiology, and the molecular evolution of Lp1 clinical isolates, we conducted sequence-based typing on a collection of clinical isolates representing 3 decades of culture-confirmed legionellosis in Ontario, Canada. Analysis showed that the population of Lp1 in Ontario is highly diverse and combines lineages identified worldwide with local strains. Identical types were identified in sporadic and outbreak-associated strains. In the past 15 years, the incidence of some lineages distributed worldwide has tended to decrease, and local endemic clones and lineages have emerged. Comparative geographic distribution analysis suggests that some lineages are specific to eastern North America. These findings have general clinical implications for the study of Lp1 molecular evolution and for the identification of Lp1 circulating strains in North America.

Since January 2005, H3N2 influenza viruses have been isolated from pigs and turkeys throughout Canada and from a swine farmer and pigs on the same farm in Ontario. These are human/classical swine/avian reassortants similar to viruses that emerged in US pigs in 1998 but with a distinct human-lineage neuraminidase gene.

Late recognition of severe acute respiratory syndrome (SARS) was associated with no known SARS contact, hospitalization before the nosocomial outbreak was recognized, symptom onset while hospitalized, wards with SARS clusters, and postoperative status. SARS is difficult to recognize in hospitalized patients with a variety of underlying conditions in the absence of epidemiologic links.

Mycoplasma pneumoniae is a major cause of community-acquired pneumonia among children and adults (1). Macrolides are recommended for treatment of M. pneumoniae pneumonia (1). High rates of macrolide-resistant M. pneumoniae have been reported in China (>90%) and Japan (87.1%) (2,3). In Europe, reports of macrolide resistance have ranged from 3% in Germany to 9.8% in France (4,5). In the United States, 8.2% of M. pneumonia–positive specimens identified during 2007–2010 were resistant to macrolides (6). M. pneumoniae confer macrolide resistance primarily as a result of nucleotide substitutions at specific positions in the V domain of the 23S rRNA gene. Mutations at nt 2063 (A2063T/G), 2064 (A2064G), and 2617 (C2617A/G) have been shown to be associated with increased MICs to macrolides, including erythromycin, azithromycin, and clarithromycin (2,3,7,8). Use of macrolides to treat macrolide-resistant M. pneumoniae result in lower effectiveness and increased clinical severity compared with macrolide-susceptible M. pneumoniae (9). In contrast to macrolides, resistance to quinolones or tetracyclines among clinical isolates of M. pneumoniae has not been reported, although development of such resistance after use of increased concentrations of fluoroquinolones or doxycycline has been demonstrated in in vitro settings (10,11). The Public Health Ontario Laboratory, which is the reference microbiology laboratory for the province of Ontario, provides molecular testing for detection of M. pneumoniae for hospitalized and ambulatory patients. In August 2011, the positivity rate for specimens with M. pneumoniae increased to 9.3% and peaked in December 2011 to 17.5%. During the same time, increased numbers of cases of M. pneumoniae were reported throughout Europe. In response to the increased positivity rate and lack of data for Canada on macrolide resistance in M. pneumoniae, we investigated antimicrobial drug susceptibility profiles of M. pneumoniae detected during February 2010–January 2012 by using molecular methods. In addition, available M. pneumoniae isolates were characterized by sequencing the P1 gene to determine the prevalence of circulating types in Ontario, Canada (12,13).

To the Editor: Among Enterobacteriaceae, Verona integron–encoded metallo-β-lactamase 1 (VIM-1) has been found only in Klebsiella pneumoniae in North America (1). We report 4 VIM-1–producing Enterobacteriaceae isolated from 4 patients at 3 hospitals in Ontario, Canada.

Early recognition and rapid initiation of infection control precautions are currently the most important strategies for controlling severe acute respiratory syndrome (SARS). No rapid diagnostic tests currently exist that can rule out SARS among patients with febrile respiratory illnesses. Clinical features alone cannot with certainty distinguish SARS from other respiratory illnesses rapidly enough to inform early management decisions. A balanced approach to screening that allows early recognition of SARS without unnecessary isolation of patients with other respiratory illnesses will require clinicians not only to look for suggestive clinical features but also to routinely seek epidemiologic clues suggestive of SARS coronavirus exposure. Key epidemiologic risk factors include 1) exposure to settings where SARS activity is suspected or documented, or 2) in the absence of such exposure, epidemiologic linkage to other persons with pneumonia (i.e., pneumonia clusters), or 3) exposure to healthcare settings. When combined with clinical findings, these epidemiologic features provide a possible strategic framework for early recognition of SARS.

Efforts to contain severe acute respiratory syndrome (SARS) have been limited by the lack of a standardized, sensitive, and specific test for SARS-associated coronavirus (CoV). We used a standardized reverse transcription-polymerase chain reaction assay to detect SARS-CoV in lung samples obtained from well-characterized patients who died of SARS and from those who died of other reasons. SARS-CoV was detected in all 22 postmortem lung tissues (to 10(9) viral copies/g) from 11 patients with probable SARS but was not detected in any of the 23 lung control samples (sample analysis was blinded). The sensitivity and specificity (95% confidence interval) were 100% (84.6% to 100%) and 100% (85.1% to 100%), respectively. Viral loads were significantly associated with a shorter course of illness but not with the use of ribavirin or steroids. CoV was consistently identified in the lungs of all patients who died of SARS but not in control patients, supporting a primary role for CoV in deaths.

The emergence of Streptococcus pneumoniae resistance to β-lactam and macrolide antimicrobial agents has led to recommendations that fluoroquinolones with increased activity against S. pneumoniae, such as levofloxacin, moxifloxacin, and gatifloxacin, be used to treat patients at risk for infection caused by such multidrug-resistant strains (1–6). Fluoroquinolone resistance in S. pneumoniae is primarily due to mutations in the genes encoding the target topoisomerase enzymes, namely parC, which encodes the A subunit of DNA topoisomerase IV, and gyrA, which encodes the A subunit of DNA gyrase (7). Mutations in parE and gyrB have been reported, but to a lesser extent (8–10). Most pneumococcal isolates with reduced susceptibilities to fluoroquinolones have amino acid substitutions in either ParC alone or ParC and GyrA (11–14). Resistance can also be mediated by active efflux (15), although the role of efflux in contributing to resistance by the newer fluoroquinolones is unclear (16). The MIC of an antimicrobial agent is a value that has been used to determine breakpoints that predict the probability of clinical success, detect resistant populations, or both (17). Clinical breakpoints are dependent on the antimicrobial activity and pharmacology of the drug; such breakpoints are ascertained with the goals of eradicating the infection and ultimately achieving clinical success with the antimicrobial agent. In contrast, microbiologic breakpoints are established to identify isolates that may be categorized as susceptible when applying clinical breakpoints but harbor resistance mechanisms that result in their reduced susceptibility to the agent being tested. These microbiologic breakpoints are therefore useful in monitoring the emergence of resistance. The current National Committee for Clinical Laboratory Standards (NCCLS) guidelines make no distinction between these two interpretations of MIC, with clinical breakpoints used to characterize most antimicrobial agents, including the fluoroquinolones. Levofloxacin has been used as a surrogate marker to predict fluoroquinolone susceptibility in clinical laboratories and surveillance studies (18). To establish whether current levofloxacin breakpoints are also able to function as microbiologic breakpoints, we determined the percentage of S. pneumoniae isolates with first-step parC mutations that would go undetected by using the current NCCLS breakpoints for levofloxacin (19).

Diagnostic difficulties may have led to underestimation of rhinovirus infections in long-term care facilities. Using surveillance data, we found that rhinovirus caused 59% (174/297) of respiratory outbreaks in these facilities during 6 months in 2009. Disease was sometimes severe. Molecular diagnostic testing can differentiate these outbreaks from other infections such as influenza.

Recent case reports describe multidrug-resistant influenza A pandemic (H1N1) 2009 virus infection in immunocompromised patients exposed to neuraminidase inhibitors because of an I223R neuraminidase mutation. We report a case of multidrug-resistant pandemic (H1N1) 2009 bearing the I223R mutation in an ambulatory child with no previous exposure to neuraminidase inhibitors.

TOC Summary: Prevalence of colonization was 6.5%, and employment within a large-animal practice was a significant risk factor., Methicillin-resistant Staphylococcus aureus (MRSA) was isolated from nares of 27/417 (6.5%) attendees at an international veterinary conference: 23/345 (7.0%) veterinarians, 4/34 (12.0%) technicians, and 0/38 others. Colonization was more common for large-animal (15/96, 15.6%) than small-animal personnel (12/271, 4.4%) or those with no animal patient contact (0/50) (p

Infection of healthcare workers with the severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to occur primarily by either contact or large respiratory droplet transmission. However, infrequent healthcare worker infections occurred despite the use of contact and droplet precautions, particularly during certain aerosol-generating medical procedures. We investigated a possible cluster of SARS-CoV infections in healthcare workers who used contact and droplet precautions during attempted cardiopulmonary resuscitation of a SARS patient. Unlike previously reported instances of transmission during aerosol-generating procedures, the index case-patient was unresponsive, and the intubation procedure was performed quickly and without difficulty. However, before intubation, the patient was ventilated with a bag-valve-mask that may have contributed to aerosolization of SARS-CoV. On the basis of the results of this investigation and previous reports of SARS transmission during aerosol-generating procedures, a systematic approach to the problem is outlined, including the use of the following: 1) administrative controls, 2) environmental engineering controls, 3) personal protective equipment, and 4) quality control.

To the Editor: The New Delhi metallo-β-lactamase (NDM-1) was first characterized in 2009 from Klebsiella pneumoniae and Escherichia coli isolated from a patient in Sweden who had received medical care in New Delhi, India (1). Further studies have shown broad dissemination of this β-lactamase gene (blaNDM-1) in India, Pakistan, Bangladesh, and the United Kingdom (2). Additional isolates have been detected in other countries, and many of the patients with NDM-1–producing Enterobacteriaceae reported receiving medical care in the Indian subcontinent (1–7). We describe detection and characterization of an NDM-1–producing K. pneumoniae isolated in Ontario, Canada. In August 2010, a urinary tract infection was diagnosed in a 36-year-old woman in a hospital in Brampton, Ontario. An E. coli strain sensitive to multiple antibacterial drugs (including carbapenems) was isolated from a midstream urine sample; the patient was successfully treated with ciprofloxacin. One week after treatment, when the patient did not have a fever or other clinical signs, a urine culture was repeated, and a carbapenem-resistant K. pneumoniae isolate (GN529) was recovered. Travel history indicated that the patient had recently returned from India, where in mid-July she had had a miscarriage and had been hospitalized in Mumbai for 2 days. At that time, no antimicrobial drug treatment was prescribed. Susceptibility profiles of K. pneumoniae GN529 and its E. coli transconjugant were obtained by using Etest (bioMerieux, Marcy l’Etoile, France) and the agar dilution method based on the Clinical and Laboratory Standards Institute guidelines (8). Multilocus sequence typing (MLST) of isolate GN529 was performed as described (9). The Pasteur Institute online database (www.pasteur.fr/recherche/genopole/PF8/mlst/Kpneumoniae.html) was used to assign the allelic numbers and sequence type (ST). To screen for the most commonly known β-lactamase genes in enterobacteria, we performed multiplex PCRs (10). Primers were designed (NDM-F, 5′-AATGGAATTGCCCAATATTATGC-3′; NDM-R, 5′-CGAAAGTCAGGCTGTGTTG C-3′) for the specific detection of blaNDM-1 and included in 1 of the multiplex PCRs (multiplex V). Primers NDM-F and NDM-R2 (5′-TCAGCGCAGCTTGTCGGC-3′) were used to amplify and sequence the entire blaNDM-1 gene. The samples were screened for the presence of six 16S methylase genes (armA, rmtA–D, and npmA) by PCR. E. coli J53 transconjugants were selected on Luria-Bertani plates containing sodium azide and meropenem (100 µg/mL and 1 µg/mL, respectively). The plasmid harboring blaNDM-1 was identified by Southern blot analysis by using a specific digoxigenin-labeled blaNDM-1 probe (Roche Diagnostics, Indianapolis, IN, USA). K. pneumoniae GN529 was highly resistant to all β-lactams, aminoglycosides, quinolones, tetracycline, nitrofurantoin, and co-trimoxazole. MICs of 0.5 µg/mL for colistin (European Committee on Antimicrobial Susceptibility Testing colistin breakpoint for Enterobacteriaceae: susceptibility