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Objective: To detect and characterize pertactin-negative Bordetella pertussis in Canada, especially for isolates collected in recent years. Methods: A total of 224 isolates from the years 1994–2013 were screened by Western immuno-blot for expression of pertactin. Pertactin-negative isolates were characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and genotyping of their pertactin, fimbriae 3, pertussis toxin subunit 1, and pertussis toxin gene promoter region, as well as the complete sequence of the pertactin gene. Results: Twelve isolates were pertactin-negative, giving an overall prevalence of 5.4%. However, no such isolate was found prior to 2011 and 17.8% of 62 isolates examined in 2012 were pertactin-negative. Ten pertactin-negative isolates contained a significant mutation in their pertactin (prn) genes. IS481 was found in the prn genes of eight isolates, while a single point mutation occurred either in the coding region (resulting in a premature stop codon) or in the promoter region (preventing gene transcription) in two other isolates. PFGE analysis also showed multiple profiles suggesting that several independent genetic events might have led to the emergence of these pertactin-negative strains rather than expansion of a single clone. Conclusions: As reported elsewhere, pertactin-negative B. pertussis has emerged in Canada in recent years, notably in 2012. This coincided with an increase in pertussis activity in Canada. A further systematic study with a larger geographical representative sample is required to determine how these vaccine-negative strains may contribute to the overall changing epidemiology of pertussis in Canada.

Before the introduction of the conjugate vaccine, Haemophilus influenzae serotype b (Hib) was the leading cause of bacterial meningitis in children. Although successful in reducing Hib cases, the vaccine confers no protection against other serotypes of H influenzae, such as a (Hia), or f (Hif). The emergence of invasive disease caused by non-Hib in northwestern Ontario (38 cases between 2002 and 2008) with predominance of Hia was previously reported by the authors. At that time, no cases of pediatric meningitis caused by H influenzae were recorded in the region. Continued surveillance identified 12 new cases of invasive non-Hib between January 2009 and July 2011. Among these cases, three young children developed meningitis with severe complications caused by Hia or Hif. The present article describes these cases along with the characteristics of recent H influenzae isolates from the region, (ie, their genetic background and antibiotic sensitivity). The findings point to the clonal nature of circulating Hia strains as well as to an increase in frequency and severity of pediatric invasive H influenzae infections in northwestern Ontario.

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.

While tuberculosis (TB) in Canadian cities is increasingly affecting foreign-born persons, homeless persons remain at high risk. To assess trends in TB, we studied all homeless persons in Toronto who had a diagnosis of active TB during 1998–2007. We compared Canada-born and foreign-born homeless persons and assessed changes over time. We identified 91 homeless persons with active TB; they typically had highly contagious, advanced disease, and 19% died within 12 months of diagnosis. The proportion of homeless persons who were foreign-born increased from 24% in 1998–2002 to 39% in 2003–2007. Among foreign-born homeless persons with TB, 56% of infections were caused by strains not known to circulate among homeless persons in Toronto. Only 2% of infections were resistant to first-line TB medications. The rise in foreign-born homeless persons with TB strains likely acquired overseas suggests that the risk for drug-resistant strains entering the homeless shelter system may be escalating.

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.

The Canadian Integrated Program for Antimicrobial Resistance Surveillance describes a strong correlation (r = 0.9, p

Since the widespread use of Haemophilus influenzae (Hi) type b (Hib) vaccines among children aged

BACKGROUND: Severe acute respiratory syndrome (SARS) caused the first epidemic of the 21st century and continues to threaten the global community.

We measured the prevalence and temporal trends of pulmonary nontuberculous mycobacterial disease among residents of Ontario, Canada, during 1998–2010. Five-year prevalence increased from 29.3 cases/100,000 persons in 1998–2002 to 41.3/100,000 in 2006–2010 (p

BackgroundThrough adequate screening and follow-up, cervical cancer can be prevented or detected at early-stage (stage I), which is related to excellent survival. Current guidelines recommend discontinuing screening for women ≥65 years with history of normal Pap and/or HPV tests, potentially leaving this age group vulnerable. This study examined late-stage disease in a population-based cohort.MethodsUsing California Cancer Registry data, we identified 12,442 patients ages ≥21 years with a first primary cervical cancer diagnosed during 2009-2018. Proportions of late-stage disease (stages II-IV) and early- and late-stage 5-year relative survival are presented by the age group. Among patients ages ≥65 years, multivariable logistic regression estimated associations of sociodemographic and clinical characteristics with late-stage cervical cancer.ResultsNearly one fifth of patients (n = 2,171, 17.4%) were ≥65 years. More women ages ≥65 years (71%) presented with late-stage disease than younger women (48% in patients ages

Outbreaks of invasive infections caused by group A β-hemolytic streptococcus (GAS) may occur in long-term care settings and are associated with a high case-fatality rate in debilitated adults. Targeted antibiotic treatment only to residents and staff known to be at specific risk of GAS may be an ineffective outbreak control measure. We describe two institutional outbreaks in which mass antibiotic treatment was used as a control measure. In the first instance, mass treatment was used after targeted antibiotic treatment was not successful. In the second instance, mass treatment was used to control a rapidly evolving outbreak with a high case-fatality rate. Although no further clinical cases were seen after the introduction of mass antibiotic treatment, persistence of the outbreak strain was documented in one institution >1 year after cases had ceased. Strain persistence was associated with the presence of a chronically colonized resident and poor infection control practices.

The Walkerton, Canada, waterborne outbreak of 2000 resulted from entry of Escherichia coli O157:H7 and Campylobacter spp. from neighboring farms into the town water supply. Isolates of Campylobacter jejuni and Campylobacter coli obtained from outbreak investigations were characterized by phenotypic and genotypic methods, including heat-stable and heat-labile serotyping, phage typing, biotyping, fla–restriction fragment length polymorphism (RFLP) typing, and pulsed-field gel electrophoresis. Two main outbreak strains were identified on the basis of heat-stable serotyping and fla-RFLP typing. These strains produced a limited number of types when tested by other methods. Isolates with types indistinguishable from, or similar to, the outbreak types were found only on one farm near the town of Walkerton, whereas cattle from other farms carried a variety of Campylobacter strains with different type characteristics. Results of these analyses confirmed results from epidemiologic studies and the utility of using several different typing and subtyping methods for completely characterizing bacterial populations.

The transmission and persistence of Mycobacterium tuberculosis within high risk populations is a threat to tuberculosis (TB) control. In the current study, we used whole genome sequencing (WGS) to decipher the transmission dynamics and microevolution of M. tuberculosis ON-A, an endemic strain responsible for an ongoing outbreak of TB in an urban homeless/under-housed population. Sixty-one M. tuberculosis isolates representing 57 TB cases from 1997 to 2013 were subjected to WGS. Sequencing data was integrated with available epidemiological information and analyzed to determine how the M. tuberculosis ON-A strain has evolved during almost two decades of active transmission. WGS offers higher discriminatory power than traditional genotyping techniques, dividing the M. tuberculosis ON-A strain into 6 sub-clusters, each defined by unique single nucleotide polymorphism profiles. One sub-cluster, designated ON-ANM (Natural Mutant; 26 isolates from 24 cases) was also defined by a large, 15 kb genomic deletion. WGS analysis reveals the existence of multiple transmission chains within the same population/setting. Our results help validate the utility of WGS as a powerful tool for identifying genomic changes and adaptation of M. tuberculosis.

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.

Outbreaks of respiratory infection in institutions in Ontario, Canada were studied from April 20 to June 12, 2009, during the early stages of the emergence of influenza A pandemic (H1N1) 2009. Despite widespread presence of influenza in the general population, only 2 of 83 outbreaks evaluated by molecular methods were associated with pandemic (H1N1) 2009.

Since the mid-1980s, the rate of new cases of tuberculosis (TB) diagnosed in Canada ceased to follow a downward trend, and has instead stabilized at approximately 7 cases/100,000 population. In the United States, a similar trend emerged, such that in the early 1990s there was an increase in new cases of TB. Outbreaks of drug-resistant TB also occurred with devastating clinical impact. These observations prompted laboratories to re-examine their role in halting the spread of TB. Laboratories play a critical part in the diagnosis of TB; procedures must be optimized to provide rapid and accurate results. This review discusses the role of the mycobacteriology laboratory in the diagnosis of TB, and how new technologies available today have enhanced the ability of the laboratory to provide timely, efficient and accurate results.

AIM: A population-based study was conducted over a two-year period in the Perth District (PD) and Wellington-Dufferin-Guelph (WDG) health units in Ontario to document antimicrobial resistance and antimicrobial use associated with clinical cases of laboratory-confirmed campylobacteriosis.

Streptococcus pseudopneumoniae (SPPN) is a recently described species of the viridans group streptococci (VGS). Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease. S. pseudopneumoniae can be distinguished from the closely related species, S. pneumoniae and S. mitis, by phenotypic characteristics, including optochin resistance in the presence of 5% CO2, bile insolubility, and the lack of the pneumococcal capsule. Previously, we reported the draft genome sequence of S. pseudopneumoniae IS7493, a clinical isolate obtained from an immunocompromised patient with documented pneumonia. Here, we use comparative genomics approaches to identify similarities and key differences between S. pseudopneumoniae IS7493, S. pneumoniae and S. mitis. The genome structure of S. pseudopneumoniae IS7493 is most closely related to that of S. pneumoniae R6, but several recombination events are evident. Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci. The presence of loci for competence, iron transport, pneumolysin production and antimicrobial resistance reinforce the phylogenetic position of S. pseudopneumoniae as an intermediate species between S. pneumoniae and S. mitis. Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.

Invadopodia are membrane protrusions that facilitate matrix degradation and cellular invasion. Although lipids have been implicated in several aspects of invadopodia formation, the contributions of de novo fatty acid synthesis and lipogenesis have not been defined. Inhibition of acetyl-CoA carboxylase 1 (ACC1), the committed step of fatty acid synthesis, reduced invadopodia formation in Src-transformed 3T3 (3T3-Src) cells, and also decreased the ability to degrade gelatin. Inhibition of fatty acid synthesis through AMP-activated kinase (AMPK) activation and ACC phosphorylation also decreased invadopodia incidence. The addition of exogenous 16∶0 and 18∶1 fatty acid, products of de novo fatty acid synthesis, restored invadopodia and gelatin degradation to cells with decreased ACC1 activity. Pharmacological inhibition of ACC also altered the phospholipid profile of 3T3-Src cells, with the majority of changes occurring in the phosphatidylcholine (PC) species. Exogenous supplementation with the most abundant PC species, 34∶1 PC, restored invadopodia incidence, the ability to degrade gelatin and the ability to invade through matrigel to cells deficient in ACC1 activity. On the other hand, 30∶0 PC did not restore invadopodia and 36∶2 PC only restored invadopodia incidence and gelatin degradation, but not cellular invasion through matrigel. Pharmacological inhibition of ACC also reduced the ability of MDA-MB-231 breast, Snb19 glioblastoma, and PC-3 prostate cancer cells to invade through matrigel. Invasion of PC-3 cells through matrigel was also restored by 34∶1 PC supplementation. Collectively, the data elucidate the novel metabolic regulation of invadopodia and the invasive process by de novo fatty acid synthesis and lipogenesis.

Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen.

Evidence-based priority setting is increasingly important for rationally distributing scarce health resources and for guiding future health research. We sought to quantify the contribution of a wide range of infectious diseases to the overall infectious disease burden in a high-income setting.We used health-adjusted life years (HALYs), a composite measure comprising premature mortality and reduced functioning due to disease, to estimate the burden of 51 infectious diseases and associated syndromes in Ontario using 2005-2007 data. Deaths were estimated from vital statistics data and disease incidence was estimated from reportable disease, healthcare utilization, and cancer registry data, supplemented by local modeling studies and national and international epidemiologic studies. The 51 infectious agents and associated syndromes accounted for 729 lost HALYs, 44.2 deaths, and 58,987 incident cases per 100,000 population annually. The most burdensome infectious agents were: hepatitis C virus, Streptococcus pneumoniae, Escherichia coli, human papillomavirus, hepatitis B virus, human immunodeficiency virus, Staphylococcus aureus, influenza virus, Clostridium difficile, and rhinovirus. The top five, ten, and 20 pathogens accounted for 46%, 67%, and 75% of the total infectious disease burden, respectively. Marked sex-specific differences in disease burden were observed for some pathogens. The main limitations of this study were the exclusion of certain infectious diseases due to data availability issues, not considering the impact of co-infections and co-morbidity, and the inability to assess the burden of milder infections that do not result in healthcare utilization.Infectious diseases continue to cause a substantial health burden in high-income settings such as Ontario. Most of this burden is attributable to a relatively small number of infectious agents, for which many effective interventions have been previously identified. Therefore, these findings should be used to guide public health policy, planning, and research.

BackgroundMolecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction.MethodsA candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation.Findings15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs.InterpretationThis first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes.FundingUNITAID, Wellcome, MRC, BMGF.

Adolescents and young adults (AYAs, 15-39 years) are the largest uninsured population in the Unites States, increasing the likelihood of late-stage cancer diagnosis and poor survival. We evaluated the associations between the Affordable Care Act (ACA), insurance coverage, stage at diagnosis and survival among AYAs with lymphoma. We used data from the California Cancer Registry linked to Medicaid enrollment files on AYAs diagnosed with a primary non-Hodgkin (NHL; n = 5959) or Hodgkin (n = 5378) lymphoma pre-ACA and in the early and full ACA eras. Health insurance was categorized as continuous Medicaid, discontinuous Medicaid, Medicaid enrollment at diagnosis/uninsurance, other public and private. We used multivariable regression models for statistical analyses. The proportion of AYAs uninsured/Medicaid enrolled at diagnosis decreased from 13.4% pre-ACA to 9.7% with full ACA implementation, while continuous Medicaid increased from 9.3% to 29.6% during this time (P

Nontuberculous mycobacterial (NTM) pulmonary disease (NTM-PD) is increasingly common and difficult to manage (1). Thus, understanding its epidemiology is essential but challenging because the diagnosis requires microbiological, radiological, and clinical [...]

BackgroundHodgkin lymphoma (HL) is a treatable tumor affecting children, adolescents and young adults (AYAs; 15-39 years old). Population-based studies report worse survival for non-White children and AYAs but have limited data on individual therapeutic exposures. This study examined overall and HL-specific survival in a population-based cohort of patients while adjusting for sociodemographic factors and treatment.MethodsData for 4807 patients younger than 40 years with HL (2007-2017) were obtained from the California Cancer Registry. Individual treatment information was extracted from text fields; chemotherapy regimens were defined by standard approaches for pediatric and adult HL. Multivariable Cox models examined the influence of patient and treatment factors on survival.ResultsAt a median follow-up of 4.4 years, 95% of the patients were alive. Chemotherapy differed by age, with 70% of 22- to 39-year-olds and 41% of

PurposeThrough screening and HPV vaccination, cervical cancer can mostly be prevented or detected very early, before symptoms develop. However, cervical cancer persists, and many women are diagnosed at advanced stages. Little is known about the degree to which U.S. women may begin their diagnostic workup for cervical cancer in Emergency Departments (ED). We sought to quantify the proportion of women presenting symptomatically in the ED prior to their diagnosis with cervical cancer and to describe their characteristics and outcomes.MethodsWe identified women diagnosed from 2006 to 2017 with cervical cancer in the California Cancer Registry. We linked this cohort to statewide ED discharge records to determine ED use and symptoms present at the encounter. Multivariable logistic regression models examined associations with ED use and multivariable Cox proportional hazards regression models examined associations with survival.ResultsOf the more than 16,000 women with cervical cancer in the study cohort, 28% presented symptomatically in the ED prior to diagnosis. Those presenting symptomatically were more likely to have public (odds ratio [OR] 1.16; 95% confidence interval [CI] 1.06-1.27) or no insurance (OR 4.81; CI 4.06-5.71) (vs. private), low socioeconomic status (SES) (OR 1.76; CI 1.52-2.04), late-stage disease (OR 5.29; CI 4.70-5.96), and had a 37% increased risk of death (CI 1.28-1.46).ConclusionNearly a third of women with cervical cancer presented symptomatically, outside of a primary care setting, suggesting that many women, especially those with low SES, may not be benefiting from screening or healthcare following abnormal results.

BackgroundColorectal cancer (CRC) incidence among persons older than 50 years has decreased in California and nationally, but incidence rates have increased among persons younger than 50 years. Previous studies present incidence rates among younger persons using a wide age group of 20-49 years. However, previous population-based studies did not analyze CRC incidence in subgroups defined by age, sex, race/ethnicity, and stage at diagnosis to better understand incidence trends among younger persons.Methods/approachWe identified all people diagnosed with CRC at the age of 20-49 years from the California Cancer Registry (n = 39,298; 1988-2017). We used SEER*Stat and Joinpoint software to calculate average annual percentage changes (AAPCs) in incidence rates by age at diagnosis, sex, race/ethnicity, and stage. Age was divided into 10-year intervals (20-29, 30-39, and 40-49 years), stage was categorized as early- and late-stage, and race/ethnicity as non-Hispanic White, non-Hispanic Black, Hispanic, Asian/Pacific Islander, and American Indian groups.ResultsStatistically significant increases in early-stage CRC incidence rates were observed among the 20-29, 30-39, and 40-49-year age groups in male and female non-Hispanic White populations (AAPC, 6.3%, 3.3%, and 1.9%, respectively) and Hispanic populations (AAPC, 4.9%, 3.5%, and 2.3%, respectively). Statistically significant increases in late-stage CRC incidence rates were observed among all 3 age groups of male and female non-Hispanic White people (AAPC, 2.8%, 3.1%, and 1.7%, respectively) and Hispanic females (AAPC, 4.2%, 2.3%, and 1.1%, respectively). Statistically significant increases in late-stage CRC incidence rates were also seen in the 30-39 and 40-49-year age groups among non-Hispanic White females (AAPC, 3.4% and 1.8%, respectively), Hispanic males (AAPC, 3.6% and 1.6%, respectively), and Asian/Pacific Islander females (AAPC, 1.9% and 0.7%, respectively). Statistically significant increases in late-stage CRC incidence were observed among 40-to 49-year-old Asian/Pacific Islander males (AAPC, 1.4%) and American Indian males and females (AAPC, 5.5%).ConclusionCRC is increasing among several young age groups. Because evidence suggests that younger adults present with more advanced disease, these results may be useful for educating health care providers about CRC risk and suggest that CRC screening recommendations should be developed for this population. Continued surveillance of CRC incidence rates among young adults is warranted.