Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation

Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source

The Changing Epidemiology of Coccidioidomycosis in Los Angeles (LA) County, California, 1973-2011.

Coccidioidomycosis, also known as Valley Fever, is often thought of as an endemic disease of central California exclusive of Los Angeles County. The fungus that causes Valley Fever, Coccidioides spp., grows in previously undisturbed soil of semi-arid and arid environments of certain areas of the Americas. LA County has a few large areas with such environments, particularly the Antelope Valley which has been having substantial land development. Coccidioidomycosis that is both clinically- and laboratory-confirmed is a mandated reportable disease in LA County. Population surveillance data for 1973-2011 reveals an annual rate increase from 0.87 to 3.2 cases per 100,000 population (n = 61 to 306 annual cases). In 2004, case frequency started substantially increasing with notable epidemiologic changes such as a rising 2.1 to 5.7 male-to-female case ratio stabilizing to 1.4-2.2. Additionally, new building construction in Antelope Valley greatly rose in 2003 and displayed a strong correlation (R = 0.92, Pearson p<0.0001) with overall LA County incidence rates for 1996-2007. Of the 24 LA County health districts, 19 had a 100%-1500% increase in cases when comparing 2000-2003 to 2008-2011. Case residents of endemic areas had stronger odds of local exposures, but cases from areas not known to be endemic had greater mortality (14% versus 9%) with notably more deaths during 2008-2011. Compared to the 57 other California counties during 2001-2011, LA County had the third highest average annual number of cases and Antelope Valley had a higher incidence rate than all but six counties. With the large number of reported coccidioidomycosis cases, multi-agency and community partnering is recommended to develop effective education and prevention strategies to protect residents and travelers

Health Care–Associated Infection Outbreak Investigations in Outpatient Settings, Los Angeles County, California, USA, 2000−2012

Health care services are increasingly delivered in outpatient settings. However, infection control oversight in outpatient settings to ensure patient safety has not improved and literature quantifying reported health care–associated infection outbreaks in outpatient settings is scarce. The objective of this analysis was to characterize investigations of suspected and confirmed outbreaks in outpatient settings in Los Angeles County, California, USA, reported during 2000–2012, by using internal logs; publications; records; and correspondence of outbreak investigations by characteristics of the setting, number, and type of infection control breaches found during investigations, outcomes of cases, and public health responses. Twenty-eight investigations met the inclusion criteria. Investigations occurred frequently, in diverse settings, and required substantial public health resources. Most outpatient settings investigated had >1 infection control breach. Lapses in infection control were suspected to be the outbreak source for 16 of the reviewed investigations

Annual coccidioidomycosis incidence (N = 3338) and decennial incidence rates, Los Angeles County, California, 1973–2011.

<p>Legend. Starting in 2004, substantial increases in the number of reported coccidioidomycosis cases occurred. Except for an outbreak during 1992 to 1994 involving strong winter storms and a 6.7 magnitude earthquake, annual cases numbered between 21 and 80 from 1973 to 2003. Sharp multi-year increases in cases occurred from 2003 (n = 80) to 2004 (n = 149) to 2005 (n = 225), and from 2009 (n = 173) to 2010 (n = 240) to 2011 (n = 306). Incidence rates were calculated using data from the U.S. Decennial Census. *A 1973 rate using the 1970 census count is presented because of the absence of surveillance data before 1973. These rates ranged between 0.35 and 0.87 cases per 100,000 people between 1973 and 2000, and increased 365% from 0.52 cases per 100,000 people in 2000 to 2.44 cases per 100,000 people in 2010.</p

Average annual coccidioidomycosis incidence and incidence rates (IR) by race-ethnicity (N = 2234), Los Angeles County, California, 1995–2011.

<p>Legend. *2004–2011 excludes 2006–2008 because of substantial missing race-ethnicity data during those years and the missing data coincides with substantially less white cases. **Average annual incidence rates per 100,000 people were calculated by dividing the average annual number of cases for 1995–2003 and 2004–2011 (excluding 2006–2008) by the U.S. Census population counts for 2000 and 2010, respectively. Race-ethnicity categories are mutually exclusive. Between 1995–2003 and 2004–2011, all race-ethnicity categories had large increases in average annual incidence and in average annual incidence rate. The average annual number of cases increased from 7.0 to 17.6 for Asians (151%), 10.8 to 34.4 for blacks (219%), 20.6 to 72.6 for Hispanics (252%), and 20.3 to 82.4 for whites (306%). The average annual incidence rate per 100,000 people increased from 1.16 to 4.22 (264%) for blacks, 0.69 to 3.02 (338%) for whites, 0.48 to 1.55 (223%) for Hispanics, and 0.62 to 1.33 (115%) for Asians. Whites and Hispanics had the most number of annual cases on average, but blacks and whites had the highest incidence rates.</p

Top average annual coccidioidomycosis cases and incidence rates (per 100,000 people) in California, 2001–2011 and 2008–2011.

<p>*Ranks are based on case counts and incidence rates of California counties. Antelope Valley, not a county but a large part of Los Angeles County, is included to demonstrate how high incidence rate can be within LA County. Compared to the 57 other counties in California during 2001–2011, LA County had the third highest average annual number of cases and Antelope Valley had a higher incidence rate than all but six counties.</p><p>**Counties not part of the Central California Valley are Los Angeles, San Luis Obispo, San Diego, Riverside, Ventura, Orange, San Bernardino, Monterey, Santa Clara, and Santa Barbara.</p><p>Top average annual coccidioidomycosis cases and incidence rates (per 100,000 people) in California, 2001–2011 and 2008–2011.</p

Coccidioidomycosis 4-year incidence (N = 903) comparisons by health districts not known to be endemic in Los Angeles County, California, 2000–2011.

<p>Legend. The increase in coccidioidomycosis cases has been extremely high in the health districts not known to be endemic in Los Angeles County. Year of disease onset was categorized into three 4-year time periods, 2000–2003, 2004–2007, and 2008–2011. *Only 19 of 21 health districts not known to be endemic are shown in the figure because East Los Angeles and Whittier had 14% and 18% decreases, respectively, between the first and last time periods. (For each successive time period, East LA had 7, 9, and 6 cases and Whittier had 11, 12, and 9 cases.) Case numbers rose steeply during 2004–2007 for at least eight health districts. For 18 health districts, case numbers rose steeply or continued to climb during 2008–2011. Percent increase in cases between 2000–2003 and 2008–2011 are shown and ranged between 67% and 1500%. Seventeen of the 21 health districts not known to be endemic had at least a 100% increase in the number of cases between 2000–2003 and 2008–2011.</p

Coccidioidomycosis 4-year incidence (N = 1040) comparisons by endemic health districts of Los Angeles County, California, 2000–2011.

<p>Legend. Among the 24 health districts of Los Angeles County, Antelope Valley, San Fernando, and West Valley health districts are endemic for coccidioidomycosis as they have much higher case numbers traditionally as well as environments more favorable to <i>Coccidioides</i> spp growth. Year of disease onset was categorized into three 4-year time periods, 2000–2003, 2004–2007, and 2008–2011. For all three health districts, incidence sharply rose during 2004–2007. Unlike the other two health districts, Antelope Valley continued to see even more cases during 2008–2011. Percent increase in cases between 2000–2003 and 2008–2011 were 545%, 376%, and 58% for Antelope Valley, San Fernando, and West Valley, respectively.</p