The Cutaneous Microbiome: Implications for Dermatology Practice.

The human integument is inhabited by a vast array of microorganisms known collectively as the cutaneous microbiome. As a result of advances in laboratory science, our understanding of the diversity and complexity of the human microbiome is rapidly evolving. In particular, advances in the field of genomics have enabled the study of the cutaneous microbiome with a hitherto unimaginable level of detail, resulting in a maturation of our understanding of cutaneous health and disease. Herein, we review current microbiology concepts and highlight the key features of recent laboratory advances, particularly with respect to genomics. We provide a summary of new findings related to normal skin flora, interactions between host immunity and microbial communities, and microbial relationships with common skin disorders. Finally, we review the implications for dermatologists.

Atypical clinical and laboratory features of fish-tank granuloma: A case report.

We report a case of cutaneous Mycobacterium marinum infection with the unusual reported features of pruritus and paresthesia. In addition, we report a lack of in-vivo response to antibiotics based on in-vitro susceptibility testing.

Cutaneous Nontuberculous Mycobacterial Infections in Alberta, Canada: An Epidemiologic Study and Review.

BACKGROUND: Cutaneous infections caused by nontuberculous mycobacteria (NTM) occur infrequently. Nonetheless, the incidence of NTM infections is reported to be increasing. In Canada, cutaneous NTM infections have not been well described. OBJECTIVES: A database review from 2006 to 2016 was done to assess species frequency, incidence, and trends of the most common cutaneous NTMs in the province of Alberta, Canada. We also reviewed major diagnostic and epidemiologic aspects of NTM cutaneous infections with a focus on Mycobacterium marinum. RESULTS: A database search identified 244 cases of NTM infections. Mycobacterium avium-intracellulare complex had the highest incidence, causing 64% of cases. Rapid growers ( Mycobacterium abscessus, Mycobacterium chelonae, Mycobacterium fortuitum) caused 23% and M marinum 13%. Information on infection site was available for 117 cases. There was no difference noted in sex distribution; however, differences in age groups between species were noted. CONCLUSIONS: The incidence of NTM cutaneous infections in Alberta, Canada, was reported for the first time and the incidence of M marinum was found to be similar to that reported in the worldwide literature. Patients' age groups were different between species. Knowledge of the unique microbiological features of NTMs and the role of the diagnostic laboratory are important.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia.

The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.

Personalized genetic testing and norovirus susceptibility.

BACKGROUND: The availability of direct-to-consumer personalized genetic testing has enabled the public to access and interpret their own genetic information. Various genetic traits can be determined including resistance to norovirus through a nonsense mutation (G428A) in the FUT2 gene. Although this trait is believed to confer resistance to the most dominant norovirus genotype (GII.4), the spectrum of resistance to other norovirus strains is unknown. The present report describes a cluster of symptomatic norovirus GI.6 infection in a family identified to have norovirus resistance through personalized genetic testing. CASE PRESENTATION: In January 2013, four members of a family determined by a direct-to-consumer genetic test to be homozygous for the norovirus resistance trait (A/A genotype for single nucleotide polymorphism rs601338) developed symptoms consistent with acute viral gastroenteritis. Stool and vomitus samples were submitted for enteric viral pathogen testing. Samples were positive for norovirus GI.6 in three of the four cases. CONCLUSIONS: The present report is the first to describe norovirus GI.6 infection in patients with the G428A nonsense mutation in FUT2; this cluster of cases suggests that the G428A mutation in FUT2 may not confer resistance to norovirus GI.6. Direct-to-consumer genetic testing is empowering members of the public to identify novel associations with their genetic traits. Expert consultation is important for the interpretation of personalized genetic test results, and follow-up laboratory testing can confirm any potentially novel associations.

HISTORIQUE: Les tests génétiques personnalisés destinés directement aux consommateurs permettent au public d'accéder eux-mêmes à l'information génétique et à l'interpréter. Il est ainsi possible de déterminer divers traits génétiques, y compris la résistance au norovirus par une mutation nonsens (G428A) dans le gène FUT2. Même si on pense que ce trait confère une résistance au génotype du norovirus le plus dominant (GII.4), on n'en connaît pas le spectre de résistance à d'autres souches de norovirus. Le présent rapport décrit une grappe d'infection symptomatique au norovirus GI.6 au sein d'une famille dont la résistance au norovirus avait été établie au moyen de tests génétiques personnalisés. PRÉSENTATION DU CAS: En janvier 2013, quatre membres d'une famille qui, d'après un test génétique destiné directement au consommateur, étaient homozygotes au trait de résistance au norovirus (génotype A/A du polymorphisme de nucléotide simple rs601338) ont présenté des symptômes évocateurs d'une gastroentérite virale aiguë. Des coprocultures et des prélèvements de vomissures ont été soumis à un test pour déceler un virus entéropathogène. Dans trois des quatre cas, les prélèvements étaient positifs au norovirus GI.6. CONCLUSIONS: Le présent rapport est le premier à décrire l'infection à norovirus GI.6 chez des patients présentant la mutation nonsens G428A dans le gène FUT2. Ce groupe de cas laisse croire que la mutation G428A dans le gène FUT2 ne confère pas de résistance au norovirus GI.6. Les tests génétiques destinés directement aux consommateurs permettent aux membres du public d'établir de nouvelles associations avec leurs traits génétiques. Il est important de consulter un expert pour en interpréter les résultats, et des tests de laboratoire effectués en suivi peuvent confirmer ces associations potentielles.

Assessment of Giardia and Cryptosporidium spp. as a microbial source tracking tool for surface water: application in a mixed-use watershed.

Knowledge of host specificity, combined with genomic sequencing of Giardia and Cryptosporidium spp., has demonstrated a microbial source tracking (MST) utility for these common waterborne microbes. To explore the source attribution potential of these pathogens, water samples were collected in a mixed rural-urban watershed in the Township of Langley, in southwestern British Columbia (BC), Canada, over a 2-year period. Cryptosporidium was detected in 63% of surface water samples at concentrations ranging from no positive detection (NPD) to 20,600 oocysts per 100 liters. Giardia was detected in 86% of surface water samples at concentrations ranging from NPD to 3,800 cysts per 100 liters of water. Sequencing at the 18S rRNA locus revealed that 50% of Cryptosporidium samples and 98% of Giardia samples contained species/genotypes (Cryptosporidium) or assemblages (Giardia) that are capable of infecting humans, based on current knowledge of host specificity and taxonomy. Cryptosporidium genotyping data were more promising for source tracking potential, due to the greater number of host-adapted (i.e., narrow-host-range) species/genotypes compared to Giardia, since 98% of Giardia isolates were zoonotic and the potential host could not be predicted. This report highlights the benefits of parasite genomic sequencing to complement Method 1623 (U.S. Environmental Protection Agency) and shows that Cryptosporidium subtyping for MST purposes is superior to the use of Giardia subtyping, based on better detection limits for Cryptosporidium-positive samples than for Giardia-positive samples and on greater host specificity among Cryptosporidium species. These additional tools could be used for risk assessment in public health and watershed management decisions.

Foodborne botulism in Canada, 1985-2005.

During 1985-2005, a total of 91 laboratory-confirmed outbreaks of foodborne botulism occurred in Canada; these outbreaks involved 205 cases and 11 deaths. Of the outbreaks, 75 (86.2%) were caused by Clostridium botulinum type E, followed by types A (7, 8.1%) and B (5, 5.7%). Approximately 85% of the outbreaks occurred in Alaska Native communities, particularly the Inuit of Nunavik in northern Quebec and the First Nations population of the Pacific coast of British Columbia. These populations were predominantly exposed to type E botulinum toxin through the consumption of traditionally prepared marine mammal and fish products. Two botulism outbreaks were attributed to commercial ready-to-eat meat products and 3 to foods served in restaurants; several cases were attributed to non-Native home-prepared foods. Three affected pregnant women delivered healthy infants. Improvements in botulism case identification and early treatment have resulted in a reduction in the case-fatality rate in Canada.

Identifying host sources, human health risk and indicators of Cryptosporidium and Giardia in a Canadian watershed influenced by urban and rural activities.

Cryptosporidium and Giardia were characterized in a watershed in southern Ontario, Canada, over a 2½ year period. River samples were collected every two weeks, primarily near a municipal drinking water treatment plant intake. Cryptosporidium and Giardia were frequently detected with an overall occurrence rate of 88 and 97%, respectively. Giardia concentrations were higher than Cryptosporidium, with median values of 80 cysts 100 L(-1) and 12 oocysts 100 L(-1), respectively. Although pathogens rarely show a significant relationship with fecal or water quality indicators, this study determined that Cryptosporidium, but not Giardia, was significantly correlated with Escherichia coli, turbidity and river flow. There was no correlation between the two types of protozoa, and only Giardia showed a seasonal trend with higher concentrations at cold water temperatures. Cryptosporidium genotyping of all samples found that farm animals and wildlife were an important contributor of oocysts in the watershed, and that Cryptosporidium strains/genotypes of medium to high risk for human infection (C. hominis, C. parvum and C. ubiquitum) were detected in 16% of samples. This study was able to identify Cryptosporidium host sources and human health risk, and to identify differences between Cryptosporidium and Giardia occurrence in the watershed.

Use of Lean response to improve pandemic influenza surge in public health laboratories.

A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands.

Using centralized laboratory data to monitor trends in herpes simplex virus type 1 and 2 infection in British Columbia and the changing etiology of genital herpes.

OBJECTIVES: Understanding the regional epidemiology of genital Herpes Simplex Virus (HSV) infections is important for clinical and public health practice, due to the increasing availability of type-specific serologic testing in Canada and the contribution of genital HSV-2 infection to ongoing HIV transmission. We used centralized laboratory data to describe trends in viral identifications of genital HSV in BC and assess the utility of these data for ongoing population surveillance. METHODS: Records of viral identifications (1997-2005) were extracted from the Provincial Public Health Microbiology & Reference Laboratory database. Classification as genital or other site was based on documented specimen site. We conducted a descriptive analysis of trends over time, and calculated odds of HSV-1 infection among individuals with genital herpes. RESULTS: Of 48,183 viral identifications, 56.8% were genital, 10.0% were peri-oral and 9.1% cutaneous; site was unknown for 22.9%. Among genital identifications, HSV-1 infection was more likely in females, younger age groups, and later time periods. The proportion of genital herpes due to HSV-1 increased over time from 31.4% to 42.8% in BC. CONCLUSIONS: Our analysis of population-level laboratory data demonstrates that the proportion of genital herpes due to HSV-1 is increasing over time in BC, particularly among women and younger age groups; this has implications for clinical practice including the interpretation of type-specific serology. Provincial viral identification data are useful for monitoring the distribution of genital HSV-1 and HSV-2 infections over time. Improving clinical documentation of specimen site would improve the utility of these data.

Water and sewage systems, socio-demographics, and duration of residence associated with endemic intestinal infectious diseases: a cohort study.

BACKGROUND: Studies of water-related gastrointestinal infections are usually directed at outbreaks. Few have examined endemic illness or compared rates across different water supply and sewage disposal systems. We conducted a cohort study of physician visits and hospitalizations for endemic intestinal infectious diseases in a mixed rural and urban community near Vancouver, Canada, with varied and well-characterized water and sewage systems. METHODS: Cohort members and their disease events were defined via universal health insurance data from 1995 through 2003. Environmental data were derived from municipal, provincial, and federal government sources. Logistic regression was used to examine associations between disease events and water and sewage systems, socio-demographic characteristics, and temporal factors. RESULTS: The cohort included 126,499 individuals and approximately 190,000,000 person-days. Crude incidence rates were 1,353 physician visits and 33.8 hospitalizations for intestinal infectious diseases per 100,000 person-years. Water supply chlorination was associated with reduced physician visit incidence (OR: 0.92, 95% CI 0.85-1.0). Two water systems with the highest proportions of surface water had increased incidence (ORs: 1.57, 95% CI 1.39-1.78; and 1.45, 95% CI 1.28-1.64). Private well water and well depth were not associated with increased risk, likely because of residents' awareness of and attention to water quality. There was increased crude incidence with increasing precipitation in the population served by surface water supplies, but this trend did not remain with adjustment for other variables. Municipal sewer systems were associated with increased risk (OR: 1.26, 95% CI 1.14-1.38). Most socio-demographic variables had predicted associations with risk: higher rates in females, in the very young and the elderly, and in residents of low income areas. Increased duration of area residence was associated with reduced risk (OR, duration ≥ 6 years: 0.69, 95% CI 0.60-0.80 vs. < 1 year: 1.16, 95% CI 1.03-1.30). CONCLUSIONS: This large cohort study, with objective data on exposures and outcomes, demonstrated associations between endemic infectious intestinal diseases and factors related to water supply, sewage disposal, socio-demographics, and duration of residency. The results did not always follow prior expectations based on studies examining outbreaks and single systems, and underscore the importance of studying factors associated with endemic disease across water and sewage system types.

Multiplex assay detection of immunoglobulin G antibodies that recognize Giardia intestinalis and Cryptosporidium parvum antigens.

Giardiasis and cryptosporidiosis are common enteric parasitic diseases that have similar routes of transmission. In this work, we have identified epitopes within the Giardia variant-specific surface protein (VSP) sequences that are recognized by IgG antibodies from 13 of 14 (93%) sera from patients with stool-confirmed giardiasis. The conserved epitopes are shared among VSPs from both of the assemblages that commonly infect humans, and they are likely to be structural, as both sodium dodecyl sulfate treatment and dithiothreitol reduction decrease antibody recognition. In a multiplex bead assay (MBA), we used three VSP fragments from an assemblage A Giardia strain, three VSP fragments from assemblage B strains, and the α-1 giardin structural antigen to detect IgG antibodies to Giardia and used the recombinant 17- and 27-kDa antigens to simultaneously detect IgG antibodies to Cryptosporidium. The MBA differentiated between sera from Giardia and Cryptosporidium outbreaks and also identified a giardiasis outbreak that may have included cryptosporidiosis cases. Approximately 40% of cryptosporidiosis outbreak samples had high MBA responses for both the 27- and 17-kDa antigens, while <10% of nonoutbreak and giardiasis outbreak samples had high responses. At least 60% of giardiasis outbreak samples were positive for antibodies to multiple Giardia antigens, while ≤12% of nonoutbreak samples and samples from U.S. and British Columbia cryptosporidiosis outbreaks met our definition for Giardia seropositivity. A MBA using multiple parasite antigens may prove useful in the epidemiologic analysis of future waterborne or food-borne outbreaks of diarrheal disease.

The occurrence and sources of Campylobacter spp., Salmonella enterica and Escherichia coli O157:H7 in the Salmon River, British Columbia, Canada.

In this study, we wished to assess the prevalence and determine the sources of three zoonotic bacterial pathogens (Salmonella, Campylobacter, and Escherichia coli O157:H7) in the Salmon River watershed in southwestern British Columbia. Surface water, sewage, and animal faecal samples were collected from the watershed. Selective bacterial culture and PCR techniques were used to isolate these three pathogens and indicator bacteria from these samples and characterize them. Campylobacter was the most prevalent pathogen in all samples, followed by Salmonella, and E. coli O157:H7. E. coli O157:H7 and Salmonella isolation rates from water, as well as faecal coliform densities correlated positively with precipitation, while Campylobacter isolation rates correlated negatively with precipitation. Analysis of DNA extracted from water samples for the presence of Bacteroides host-species markers, and comparisons of C. jejuni flaA-RFLP types and Salmonella serovars from faecal and water samples provided evidence that human sewage and specific domestic and wild animal species were sources of these pathogens; however, in most cases the source could not be determined or more than one source was possible. The frequent isolation of these zoonotic pathogens in the Salmon River highlights the risks to human health associated with intentional and unintentional consumption of untreated surface waters.

Cyclospora spp. in herbs and water samples collected from markets and farms in Hanoi, Vietnam.

OBJECTIVE: To determine the prevalence of Cyclospora spp. oocysts in herb and water samples as well as in fecal specimens of clinical cases of diarrhoea in Hanoi, Vietnam. METHOD: From November 2004 to October 2005, water and herb samples collected from markets and farms in Hanoi were examined for the presence of Cyclospora spp. oocysts in concentrated sediments and washings using UV epifluorescence examination of a wet mount. In addition, hospital based surveillance studies were carried out using a structured questionnaire which focused on potential risk factors for cyclosporiasis. Stool specimens were collected from individuals with diarrhoea attending primary healthcare facilities and examined for Cyclospora spp. oocysts by modified acid fast smear and wet mount examination using both light and UV epifluorescence microscopy. RESULTS: Cyclospora spp. were found in 34/288 (11.8%) market water and herb samples, and in 24/287 (8.4%) farm samples. All varieties of herbs sold at the market and grown in farms were contaminated with Cyclospora spp. oocysts. A marked seasonal increase in Cyclospora spp. contamination was observed before the rainy season (39/288) from November to April compared to the rainy season (19/268) from May to October (chi(2) = 7.593, P = 0.006). However, Cyclospora spp. was not found in any stool samples collected in hospital-based surveillance studies. CONCLUSIONS: These results confirm the presence of Cyclospora spp. which varies seasonally in environmental samples (water and herbs collected from farms and markets) within the Hanoi metropolitan area.

Identification of Bacillus cereus group species associated with food poisoning outbreaks in British Columbia, Canada.

Food poisoning laboratories identify Bacillus cereus using routine methods that may not differentiate all Bacillus cereus group species. We recharacterized Bacillus food-poisoning strains from 39 outbreaks and identified B. cereus in 23 outbreaks, B. thuringiensis in 4, B. mycoides in 1, and mixed strains of Bacillus in 11 outbreaks.

Epidemiology of invasive pneumococcal disease in BC during the introduction of conjugated pneumococcal vaccine.

OBJECTIVES: Antimicrobial resistance in Streptococcus pneumoniae has increased in recent decades. We linked two surveillance programs to evaluate trends in incidence, serotype distribution, and antimicrobial resistance in invasive pneumococcal disease (IPD) since the heptavalent pneumococcal conjugate vaccine (PCV7) was introduced in BC in 2003. METHODS: IPD case reports for BC from 2002-2005 from the BC Centre for Disease Control were linked to serotype and antimicrobial susceptibility results from the National Centre for Streptococcus (NCS). RESULTS: There was a significant decrease in IPD incidence in children <5 from 54/100,000 in 2002 to 16/100,000 population in 2005 (70% decrease, p < 0.001). The most dramatic decline was in children aged 1 year, where the rate fell from 135/100,000 to 15/100,000 (89% decrease, p for trend <0.001). Overall, 728/1288 (56.5%) reported cases of IPD were referred to NCS. For all matched cases, the proportion of isolates of PCV7 preventable serotypes decreased from 68.9% to 43.8% (p for trend <0.001) between 2002 and 2005. In children <2 years, this proportion decreased from 83.0% (39/47 cases) to 16.7% (1/6 cases) (p = 0.006). The prevalence of non-susceptible isolates was highest for trimethoprim-sulfamethoxazole (15.3%, 111/725 tested), penicillin (9.1%, 66/728), and erythromycin (9.1%, 66/727). 10.3% (75/728) were non-susceptible to > or =2 classes of antimicrobials. Children <15 years of age had the highest proportion of non-susceptible isolates. DISCUSSION: The incidence of IPD in children has decreased significantly since the introduction of PCV7. Comprehensive serotype and antimicrobial susceptibility can aid in evaluating the impact of immunization programs.

Molecular methods used in clinical laboratory: prospects and pitfalls.

The role of molecular detection, identification and typing or fingerprinting of microorganisms has shifted gradually from the academic world to the routine diagnostic laboratory. Molecular methods have been used increasingly over the past decade to improve the sensitivity, specificity and turn-around time in the clinical laboratory. Molecular methods have also been used to identify new and nonculturable agents. Many high-throughput molecular tests are now available commercially, which impacts on the infrastructure in many of the diagnostic laboratories. In this paper, we take an overall look at the use of molecular methods (prospects vs. pitfalls) based on our clinical and public health experience, particularly as they related to Borrelia burgdorferi, a vector-borne pathogen, Treponema pallidum, a re-emerging sexually transmitted global pathogen, and West Nile virus, a newly recognized virus in North America.

Molecular forensic profiling of Cryptosporidium species and genotypes in raw water.

The emerging concept of host specificity of Cryptosporidium spp. was exploited to characterize sources of fecal contamination in a watershed. A method of molecular forensic profiling of Cryptosporidium oocysts on microscope slides prepared from raw water samples processed by U.S. Environmental Protection Agency Method 1623 was developed. The method was based on a repetitive nested PCR-restriction fragment length polymorphism-DNA sequencing approach that permitted the resolution of multiple species/genotypes of Cryptosporidium in a single water sample.

Enzyme immunoassay of Cryptosporidium-specific immunoglobulin G antibodies to assess longitudinal infection trends in six communities in British Columbia, Canada.

A newly developed enzyme-linked immunosorbent assay (ELISA) that detects immunoglobulin G antibodies to the 27-kDa Cryptosporidium parvum sporozoite surface antigen was used to test 4,097 sera collected from pregnant women in 6 communities in British Columbia, Canada, between January 1996, and December 1997. Waterborne outbreaks of cryptosporidiosis occurred in two of the study communities during the period of follow-up, and ELISA seropositivity was high in all six communities during the study period (77% positive to 92% positive). In the community with the largest outbreak, levels of antibody to the 27-kDa antigen increased rapidly and then decayed to background levels within 3-4 months of the peak of the epidemic curve. Trends in serologic reactivity were complex in all communities, and increased antibody levels not related temporally to known waterborne outbreaks were also observed. Serological assays may provide more accurate information regarding community levels of Cryptosporidium infection.