Last data update: Jan 27, 2025. (Total: 48650 publications since 2009)
Records 1-28 (of 28 Records) |
Query Trace: Fields BS[original query] |
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Dynamic incidence of typhoid fever over a 10-year period (2010-2019) in Kibera, an urban informal settlement in Nairobi, Kenya
Ng'eno E , Lind M , Audi A , Ouma A , Oduor C , Munywoki PK , Agogo GO , Odongo G , Kiplangat S , Wamola N , Osita MP , Mugoh R , Ochieng C , Omballa V , Mogeni OD , Mikoleit M , Fields BS , Montgomery JM , Gauld J , Breiman RF , Juma B , Hunsperger E , Widdowson MA , Bigogo G , Mintz ED , Verani JR . Am J Trop Med Hyg 2023 109 (1) 22-31 Typhoid fever burden can vary over time. Long-term data can inform prevention strategies; however, such data are lacking in many African settings. We reexamined typhoid fever incidence and antimicrobial resistance (AMR) over a 10-year period in Kibera, a densely populated urban informal settlement where a high burden has been previously described. We used data from the Population Based Infectious Diseases Surveillance platform to estimate crude and adjusted incidence rates and prevalence of AMR in nearly 26,000 individuals of all ages. Demographic and healthcare-seeking information was collected through household visits. Blood cultures were processed for patients with acute fever or lower respiratory infection. Between 2010 and 2019, 16,437 participants were eligible for blood culture and 11,848 (72.1%) had a culture performed. Among 11,417 noncontaminated cultures (96.4%), 237 grew Salmonella enterica serovar Typhi (2.1%). Overall crude and adjusted incidences were 95 and 188 cases per 100,000 person-years of observation (pyo), respectively. Annual crude incidence varied from 144 to 233 between 2010 and 2012 and from 9 to 55 between 2013 and 2018 and reached 130 per 100,000 pyo in 2019. Children 5-9 years old had the highest overall incidence (crude, 208; adjusted, 359 per 100,000 pyo). Among isolates tested, 156 of 217 were multidrug resistant (resistant to chloramphenicol, ampicillin, and trimethoprim/sulfamethoxazole [71.9%]) and 6 of 223 were resistant to ciprofloxacin (2.7%). Typhoid fever incidence resurged in 2019 after a prolonged period of low rates, with the highest incidence among children. Typhoid fever control measures, including vaccines, could reduce morbidity in this setting. |
Building laboratory capacity to detect and characterize pathogens of public and global health security concern in Kenya
Hunsperger E , Juma B , Onyango C , Ochieng JB , Omballa V , Fields BS , Njenga MK , Mwangi J , Bigogo G , Omore R , Otieno N , Chaves SS , Munyua P , Njau DM , Verani J , Lowther S , Breiman RF , Montgomery JM , De Cock KM , Widdowson MA . BMC Public Health 2019 19 477 Since 1979, multiple CDC Kenya programs have supported the development of diagnostic expertise and laboratory capacity in Kenya. In 2004, CDC's Global Disease Detection (GDD) program within the Division of Global Health Protection in Kenya (DGHP-Kenya) initiated close collaboration with Kenya Medical Research Institute (KEMRI) and developed a laboratory partnership called the Diagnostic and Laboratory Systems Program (DLSP). DLSP built onto previous efforts by malaria, human immunodeficiency virus (HIV) and tuberculosis (TB) programs and supported the expansion of the diagnostic expertise and capacity in KEMRI and the Ministry of Health. First, DLSP developed laboratory capacity for surveillance of diarrheal, respiratory, zoonotic and febrile illnesses to understand the etiology burden of these common illnesses and support evidenced-based decisions on vaccine introductions and recommendations in Kenya. Second, we have evaluated and implemented new diagnostic technologies such as TaqMan Array Cards (TAC) to detect emerging or reemerging pathogens and have recently added a next generation sequencer (NGS). Third, DLSP provided rapid laboratory diagnostic support for outbreak investigation to Kenya and regional countries. Fourth, DLSP has been assisting the Kenya National Public Health laboratory-National Influenza Center and microbiology reference laboratory to obtain World Health Organization (WHO) certification and ISO15189 accreditation respectively. Fifth, we have supported biosafety and biosecurity curriculum development to help Kenyan laboratories safely and appropriately manage infectious pathogens. These achievements, highlight how in collaboration with existing CDC programs working on HIV, tuberculosis and malaria, the Global Health Security Agenda can have significantly improve public health in Kenya and the region. Moreover, Kenya provides an example as to how laboratory science can help countries detect and control of infectious disease outbreaks and other public health threats more rapidly, thus enhancing global health security. |
The prevalence of hepatitis C virus antibody in HIV-negative persons in Kenya, 2007
Ly KN , Kim AA , Drobenuic J , Kodani M , Montgomery JM , Fields BS , Teshale EH . Am J Trop Med Hyg 2018 98 (6) 1876-1879 The prevalence of hepatitis C virus (HCV) infection in the Kenyan population has not been previously determined. We estimated the Kenyan HCV prevalence in HIV-negative persons aged 15-64 years. This is a retrospective cross-sectional study using data from the 2007 Kenya AIDS Indicator Survey-a nationally representative sample of 15,853 persons aged 15-64 years who completed a health interview and provided a blood specimen. Of the 1,091 randomly selected participants, 50 tested positive for HCV antibody using the automated chemiluminescence immunoassay, corresponding to a weighted HCV antibody positivity rate of 4.4% (95% confidence interval: 3.3-5.9%) or 848,000 (range: 634,000-1,100,000) persons. Hepatitis C virus RNA, a marker for current infection, was not detected in any of the tested antibody-positive specimens. The high HCV antibody prevalence together with no current infection suggests that some HCV antibody serologic testing in Kenya may result in false positives whereas others may be because of spontaneous viral clearance. |
A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania
Hercik C , Cosmas L , Mogeni OD , Wamola N , Kohi W , Omballa V , Ochieng M , Lidechi S , Bonventure J , Ochieng C , Onyango C , Fields BS , Mfinanga S , Montgomery JM . PLoS One 2017 12 (12) e0189712 INTRODUCTION: In low-resource settings, empiric case management of febrile illness is routine as a result of limited access to laboratory diagnostics. The use of comprehensive fever syndromic surveillance, with enhanced clinical microbiology, advanced diagnostics and more robust epidemiologic investigation, could enable healthcare providers to offer a differential diagnosis of fever syndrome and more appropriate care and treatment. METHODS: We conducted a year-long exploratory study of fever syndrome among patients >/= 1 year if age, presenting to clinical settings with an axillary temperature of >/=37.5 degrees C and symptomatic onset of </=5 days. Blood and naso-pharyngeal/oral-pharyngeal (NP/OP) specimens were collected and analyzed, respectively, using AFI and respiratory TaqMan Array Cards (TAC) for multi-pathogen detection of 57 potential causative agents. Furthermore, we examined numerous epidemiologic correlates of febrile illness, and conducted demographic, clinical, and behavioral domain-specific multivariate regression to statistically establish associations with agent detection. RESULTS: From 15 September 2014-13 September 2015, 1007 febrile patients were enrolled, and 997 contributed an epidemiologic survey, including: 14% (n = 139) 1<5yrs, 19% (n = 186) 5-14yrs, and 67% (n = 672) >/=15yrs. AFI TAC and respiratory TAC were performed on 842 whole blood specimens and 385 NP/OP specimens, respectively. Of the 57 agents surveyed, Plasmodium was the most common agent detected. AFI TAC detected nucleic acid for one or more of seven microbial agents in 49% of AFI blood samples, including: Plasmodium (47%), Leptospira (3%), Bartonella (1%), Salmonella enterica (1%), Coxiella burnetii (1%), Rickettsia (1%), and West Nile virus (1%). Respiratory TAC detected nucleic acid for 24 different microbial agents, including 12 viruses and 12 bacteria. The most common agents detected among our surveyed population were: Haemophilus influenzae (67%), Streptococcus pneumoniae (55%), Moraxella catarrhalis (39%), Staphylococcus aureus (37%), Pseudomonas aeruginosa (36%), Human Rhinovirus (25%), influenza A (24%), Klebsiella pneumoniae (14%), Enterovirus (15%) and group A Streptococcus (12%). Our epidemiologic investigation demonstrated both age and symptomatic presentation to be associated with a number of detected agents, including, but not limited to, influenza A and Plasmodium. Linear regression of fully-adjusted mean cycle threshold (Ct) values for Plasmodium also identified statistically significant lower mean Ct values for older children (20.8), patients presenting with severe fever (21.1) and headache (21.5), as well as patients admitted for in-patient care and treatment (22.4). CONCLUSIONS: This study is the first to employ two syndromic TaqMan Array Cards for the simultaneous survey of 57 different organisms to better characterize the type and prevalence of detected agents among febrile patients. Additionally, we provide an analysis of the association between adjusted mean Ct values for Plasmodium and key clinical and demographic variables, which may further inform clinical decision-making based upon intensity of infection, as observed across endemic settings of sub-Saharan Africa. |
Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study
Marks F , von Kalckreuth V , Aaby P , Adu-Sarkodie Y , El Tayeb MA , Ali M , Aseffa A , Baker S , Biggs HM , Bjerregaard-Andersen M , Breiman RF , Campbell JI , Cosmas L , Crump JA , Espinoza LM , Deerin JF , Dekker DM , Fields BS , Gasmelseed N , Hertz JT , Van Minh Hoang N , Im J , Jaeger A , Jeon HJ , Kabore LP , Keddy KH , Konings F , Krumkamp R , Ley B , Lofberg SV , May J , Meyer CG , Mintz ED , Montgomery JM , Niang AA , Nichols C , Olack B , Pak GD , Panzner U , Park JK , Park SE , Rabezanahary H , Rakotozandrindrainy R , Raminosoa TM , Razafindrabe TJL , Sampo E , Schütt-Gerowitt H , Sow AG , Sarpong N , Seo HJ , Sooka A , Soura AB , Tall A , Teferi M , Thriemer K , Warren MR , Yeshitela B , Clemens JD , Wierzba TF . Lancet Glob Health 2017 5 (3) e310-e323 BACKGROUND: Available incidence data for invasive salmonella disease in sub-Saharan Africa are scarce. Standardised, multicountry data are required to better understand the nature and burden of disease in Africa. We aimed to measure the adjusted incidence estimates of typhoid fever and invasive non-typhoidal salmonella (iNTS) disease in sub-Saharan Africa, and the antimicrobial susceptibility profiles of the causative agents. METHODS: We established a systematic, standardised surveillance of blood culture-based febrile illness in 13 African sentinel sites with previous reports of typhoid fever: Burkina Faso (two sites), Ethiopia, Ghana, Guinea-Bissau, Kenya, Madagascar (two sites), Senegal, South Africa, Sudan, and Tanzania (two sites). We used census data and health-care records to define study catchment areas and populations. Eligible participants were either inpatients or outpatients who resided within the catchment area and presented with tympanic (≥38.0 degrees C) or axillary temperature (≥37.5 degrees C). Inpatients with a reported history of fever for 72 h or longer were excluded. We also implemented a health-care utilisation survey in a sample of households randomly selected from each study area to investigate health-seeking behaviour in cases of self-reported fever lasting less than 3 days. Typhoid fever and iNTS disease incidences were corrected for health-care-seeking behaviour and recruitment. FINDINGS: Between March 1, 2010, and Jan 31, 2014, 135 Salmonella enterica serotype Typhi (S Typhi) and 94 iNTS isolates were cultured from the blood of 13 431 febrile patients. Salmonella spp accounted for 33% or more of all bacterial pathogens at nine sites. The adjusted incidence rate (AIR) of S Typhi per 100 000 person-years of observation ranged from 0 (95% CI 0-0) in Sudan to 383 (274-535) at one site in Burkina Faso; the AIR of iNTS ranged from 0 in Sudan, Ethiopia, Madagascar (Isotry site), and South Africa to 237 (178-316) at the second site in Burkina Faso. The AIR of iNTS and typhoid fever in individuals younger than 15 years old was typically higher than in those aged 15 years or older. Multidrug-resistant S Typhi was isolated in Ghana, Kenya, and Tanzania (both sites combined), and multidrug-resistant iNTS was isolated in Burkina Faso (both sites combined), Ghana, Kenya, and Guinea-Bissau. INTERPRETATION: Typhoid fever and iNTS disease are major causes of invasive bacterial febrile illness in the sampled locations, most commonly affecting children in both low and high population density settings. The development of iNTS vaccines and the introduction of S Typhi conjugate vaccines should be considered for high-incidence settings, such as those identified in this study. FUNDING: Bill & Melinda Gates Foundation. |
Prevalence of hepatitis B virus infection in Kenya, 2007
Ly KN , Kim AA , Umuro M , Drobenuic J , Williamson J , Montgomery JM , Fields BS , Teshale EH . Am J Trop Med Hyg 2016 95 (2) 348-53 Current estimates put the prevalence of hepatitis B virus (HBV) infection in Kenya at 5-8%. We determined the HBV infection prevalence in the human immunodeficiency virus (HIV)-negative Kenyan adult and adolescent population based on samples collected from a national survey. We analyzed data from HIV-negative participants in the 2007 Kenya AIDS Indicator Survey to estimate the HBV infection prevalence. We defined past or present HBV infection as presence of total hepatitis B core antibody (HBcAb), and chronic HBV infection (CHBI) as presence of both total HBcAb and hepatitis B surface antigen (HBsAg). We calculated crude and adjusted odds of HBV infection by demographic characteristics and risk factors using logistic regression analyses. Of 1,091 participants aged 15-64 years, approximately 31.5% (95% confidence interval [CI] = 28.0-35.3%) had exposure to HBV, corresponding to approximately 6.1 million (CI = 5.4-6.8 million) with past or present HBV infection. The estimated prevalence of CHBI was 2.1% (95% CI = 1.4-3.1%), corresponding to approximately 398,000 (CI = 261,000-602,000) with CHBI. CHBI is a major public health problem in Kenya, affecting approximately 400,000 persons. Knowing the HBV infection prevalence at baseline is important for planning and public health policy decision making and for monitoring the impact of viral hepatitis prevention programs. |
Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007-2013
Waiboci LW , Mott JA , Kikwai G , Arunga G , Xu X , Mayieka L , Emukule GO , Muthoka P , Njenga MK , Fields BS , Katz MA . Vaccine 2016 34 (23) 2593-601 INTRODUCTION: Every year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains. METHODS: We collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule. RESULTS: During the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing. CONCLUSION: In six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined. |
Serologic evidence for hepatitis E virus infection among patients with undifferentiated acute febrile illness in Kibera, Kenya
Furukawa NW , Teshale EH , Cosmas L , Ochieng M , Gikunju S , Fields BS , Montgomery JM . J Clin Virol 2016 77 106-108 BACKGROUND: Hepatitis E (HEV) is an emerging cause of viral hepatitis mainly transmitted through the fecal-oral route. Residents of the Kibera slum of Nairobi, Kenya are at risk for fecal-orally transmitted infections. OBJECTIVE: To quantify the incidence and prevalence of HEV infection among acute febrile illness (AFI) cases using a population-based infectious disease surveillance network. STUDY DESIGN: Cross-sectional serum samples from AFI case-patients between 2009 and 2012 were matched to the age and gender distribution of the Kibera population and tested by IgM and IgG enzyme immunoassays (EIA) and nucleic acid testing (NAT). Serum from healthy residents was also tested by EIA. RESULTS: Of the 482 AFI serum samples tested, 124 (25.7%) and 182 (37.8%) were IgM and IgG reactive, respectively. On multivariate analysis, IgM reactivity was associated with HIV (RR 1.66, 95%CI 1.07, 2.60; p=0.024) while IgG reactivity was associated with increasing age (p<0.001) and HIV (RR 1.93, 95%CI 1.52, 2.46; p<0.001). AFI case-patients were more likely to be IgM (p=0.002) and IgG (p<0.001) reactive compared to healthy residents. The seroincidence by HEV-specific IgM was 84.0 per 1000 person years, however, all 482 samples were negative by NAT. CONCLUSIONS: Serologic evidence for HEV in Kibera suggests a high burden of infection, but NAT did not confirm HEV viremia. Additional testing is needed to determine whether EIAs are susceptible to false positivity in undifferentiated AFI populations before their widespread use. |
Serologic evidence of the geographic distribution of bacterial zoonotic agents in Kenya, 2007
Omballa VO , Musyoka RN , Vittor AY , Wamburu KB , Wachira CM , Waiboci LW , Abudo MU , Juma BW , Kim AA , Montgomery JM , Breiman RF , Fields BS . Am J Trop Med Hyg 2015 94 (1) 43-51 Diseases of zoonotic origin contribute to the burden of febrile illnesses in developing countries. We evaluated serologic evidence of exposure to Bacillus anthracis, Brucella spp., spotted fever group rickettsioses (SFGR), and typhus group rickettsioses (TGR) from samples of persons aged 15-64 years collected during a nationwide human immunodeficiency virus (HIV) serosurvey conducted in 2007 in Kenya. The seropositivity observed for pathogens was B. anthracis 11.3% (141/1,091), Brucella spp. 3.0% (27/968), SFGR 23.3% (191/770), and TGR 0.6% (12/770). On univariate analysis, seropositivity for each pathogen was significantly associated with the following risk factors: B. anthracis with province of residence; Brucella spp. with sex, education level, and wealth; SFGR with age, education level, wealth, and province of residence; and TGR with province of residence. On multivariate analysis, seropositivity remained significantly associated with wealth and province for B. anthracis; with sex and age for Brucella spp; and with sex, education level, and province of residence for SFGR whereas TGR had no significance. High IgG seropositivity to these zoonotic pathogens (especially, B. anthracis and SFGR) suggests substantial exposure. These pathogens should be considered in the differential diagnosis of febrile illness in Kenya. |
Burden of invasive nontyphoidal Salmonella disease in a rural and urban site in Kenya, 2009-2014
Verani JR , Toroitich S , Auko J , Kiplang'at S , Cosmas L , Audi A , Mogeni OD , Aol G , Oketch D , Odiembo H , Katieno J , Wamola N , Onyango CO , Juma BW , Fields BS , Bigogo G , Montgomery JM . Clin Infect Dis 2015 61 Suppl 4 S302-9 BACKGROUND: Invasive infections with nontyphoidal Salmonella (NTS) lead to bacteremia in children and adults and are an important cause of illness in Africa; however, few data on the burden of NTS bacteremia are available. We sought to determine the burden of invasive NTS disease in a rural and urban setting in Kenya. METHODS: We conducted the study in a population-based surveillance platform in a rural setting in western Kenya (Lwak), and an informal urban settlement in Nairobi (Kibera) from 2009 to 2014. We obtained blood culture specimens from participants presenting with acute lower respiratory tract illness or acute febrile illness to a designated outpatient facility in each site, or any hospital admission for a potentially infectious cause (rural site only). Incidence was calculated using a defined catchment population and adjusting for specimen collection and healthcare-seeking practices. RESULTS: A total of 12 683 and 9524 blood cultures were analyzed from Lwak and Kibera, respectively. Of these, 428 (3.4%) and 533 (5.6%) grew a pathogen; among those, 208 (48.6%) and 70 (13.1%) were positive for NTS in Lwak and Kibera, respectively. Overall, the adjusted incidence of invasive NTS disease was higher in Lwak (839.4 per 100 000 person-years of observation [PYO]) than in Kibera (202.5 per 100 000 PYO). The highest adjusted incidences were observed in children <5 years of age (Lwak 3914.3 per 100 000 PYO and Kibera 997.9 per 100 000 PYO). The highest adjusted annual incidence was 1927.3 per 100 000 PYO (in 2010) in Lwak and 220.5 per 100 000 PYO (in 2011) in Kibera; the lowest incidences were 303.3 and 62.5 per 100 000 PYO, respectively (in 2012). In both sites, invasive NTS disease incidence generally declined over the study period. CONCLUSIONS: We observed an extremely high burden of invasive NTS disease in a rural area of Kenya and a lesser, but still substantial, burden in an urban slum. Although the incidences in both sites declined during the study period, invasive NTS infections remain an important cause of morbidity in these settings, particularly among children <5 years old. |
Severe acute respiratory infection in children in a densely populated urban slum in Kenya, 2007-2011
Breiman RF , Cosmas L , Njenga MK , Williamson J , Mott JA , Katz MA , Erdman DD , Schneider E , Oberste MS , Neatherlin JC , Njuguna H , Ondari DM , Odero K , Okoth GO , Olack B , Wamola N , Montgomery JM , Fields BS , Feikin DR . BMC Infect Dis 2015 15 (95) 95 BACKGROUND: Reducing acute respiratory infection burden in children in Africa remains a major priority and challenge. We analyzed data from population-based infectious disease surveillance for severe acute respiratory illness (SARI) among children <5 years of age in Kibera, a densely populated urban slum in Nairobi, Kenya. METHODS: Surveillance was conducted among a monthly mean of 5,874 (range=5,778-6,411) children <5 years old in two contiguous villages in Kibera. Participants had free access to the study clinic and their health events and utilization were noted during biweekly home visits. Patients meeting criteria for SARI (WHO-defined severe or very severe pneumonia, or oxygen saturation <90%) from March 1, 2007-February 28, 2011 had blood cultures processed for bacteria, and naso- and oro-pharyngeal swabs collected for quantitative real-time reverse transcription polymerase chain reaction testing for influenza viruses, parainfluenza viruses (PIV), respiratory syncytial virus (RSV), adenovirus, and human metapneumovirus (hMPV). Swabs collected during January 1, 2009-February 28, 2010 were also tested for rhinoviruses, enterovirus, parechovirus, Mycoplasma pneumoniae, and Legionella species. Swabs were collected for simultaneous testing from a selected group of control-children visiting the clinic without recent respiratory or diarrheal illnesses. RESULTS: SARI overall incidence was 12.4 cases/100 person-years of observation (PYO) and 30.4 cases/100 PYO in infants. When comparing detection frequency in swabs from 815 SARI cases and 115 healthy controls, only RSV and influenza A virus were significantly more frequently detected in cases, although similar trends neared statistical significance for PIV, adenovirus and hMPV. The incidence for RSV was 2.8 cases/100 PYO and for influenza A was 1.0 cases/100 PYO. When considering all PIV, the rate was 1.1 case/100 PYO and the rate per 100 PYO for SARI-associated disease was 1.5 for adenovirus and 0.9 for hMPV. RSV and influenza A and B viruses were estimated to account for 16.2% and 6.7% of SARI cases, respectively; when taken together, PIV, adenovirus, and hMPV may account for >20% additional cases. CONCLUSIONS: Influenza viruses and RSV (and possibly PIV, hMPV and adenoviruses) are important pathogens to consider when developing technologies and formulating strategies to treat and prevent SARI in children. |
Evaluation of fast-track diagnostics and TaqMan array card real-time PCR assays for the detection of respiratory pathogens.
Driscoll AJ , Karron RA , Bhat N , Thumar B , Kodani M , Fields BS , Whitney CG , Levine OS , O'Brien KL , Murdoch DR . J Microbiol Methods 2014 107c 222-226 ![]() Several commercial assays are now available to detect the nucleic acid of multiple respiratory pathogens from a single specimen. Head-to-head comparisons of such assays using a single set of standard specimens provide additional information about key assay parameters such as sensitivity, specificity and lower limits of detection, and help to inform the decision regarding which method to use. We evaluated two real-time PCR platforms: the Fast-track Diagnostics(R) (FTD) multiplex respiratory panel and a TaqMan array card (TAC) for simultaneous uniplex detection of multiple respiratory pathogens. Two sets of samples were used to evaluate the assays. One set was created by spiking pooled nasal wash or phosphate buffered saline with specified volumes of known concentrations of virus and/or bacteria. Clinical nasal wash specimens from children with lower respiratory tract illness comprised the other set. Thirteen pathogen targets were compared between the two platforms. Testing with a validation panel of spiked samples revealed a sensitivity of 96.1% and 92.9% for the FTD and TAC assays, respectively. Specificity could not be reliably calculated due to a suspected contamination of the sample substrate. Inter-assay agreement was high (>95%) for most targets. Previously untested clinical specimens tested by both assays revealed a high percent agreement (>95%) for all except rhinovirus, enterovirus and Streptococcus pneumoniae. Limitations of this evaluation included extraction of the validation samples by two different methods and the evaluation of the assays in different laboratories. However, neither of these factors significantly impacted inter-assay agreement for these sets of samples, and it was demonstrated that both assays could reliably detect clinically relevant concentrations of bacterial and viral pathogens. |
Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya
Agoti CN , Mayieka LM , Otieno JR , Ahmed JA , Fields BS , Waiboci LW , Nyoka R , Eidex RB , Marano N , Burton W , Montgomery JM , Breiman RF , Nokes DJ . BMC Infect Dis 2014 14 (1) 178 BACKGROUND: A recent longitudinal study in the Dadaab refugee camp near the Kenya-Somalia border identified unusual biannual respiratory syncytial virus (RSV) epidemics. We characterized the genetic variability of the associated RSV strains to determine if viral diversity contributed to this unusual epidemic pattern. METHODS: For 336 RSV positive specimens identified from 2007 through 2011 through facility-based surveillance of respiratory illnesses in the camp, 324 (96.4%) were sub-typed by PCR methods, into 201 (62.0%) group A, 118 (36.4%) group B and 5 (1.5%) group A-B co-infections. Partial sequencing of the G gene (coding for the attachment protein) was completed for 290 (89.5%) specimens. These specimens were phylogenetically analyzed together with 1154 contemporaneous strains from 22 countries. RESULTS: Of the 6 epidemic peaks recorded in the camp over the period, the first and last were predominantly made up of group B strains, while the 4 in between were largely composed of group A strains in a consecutive series of minor followed by major epidemics. The Dadaab group A strains belonged to either genotype GA2 (180, 98.9%) or GA5 (2, < 1%) while all group B strains (108, 100%) belonged to BA genotype. In sequential epidemics, strains within these genotypes appeared to be of two types: those continuing from the preceding epidemics and those newly introduced. Genotype diversity was similar in minor and major epidemics. CONCLUSION: RSV strain diversity in Dadaab was similar to contemporaneous diversity worldwide, suggested both between-epidemic persistence and new introductions, and was unrelated to the unusual epidemic pattern. |
Recreational vehicle water tanks as a possible source for Legionella infections
Litwin CM , Asebiomo B , Wilson K , Hafez M , Stevens V , Fliermans CB , Fields BS , Fisher JF . Case Rep Infect Dis 2013 2013 286347 We investigated recreational vehicle (RV) water reservoirs in response to a case of pneumonia in which Legionella pneumophila was cultured both from the patient and a RV reservoir in which he travelled. Water samples processed and cultured at the CDC according to standard protocol were positive for Legionella spp. in 4/17 (24%) faucets, 1/11 (9%) water tanks from 4/20 (20%) RVs from three different campsites. Legionella spp. that were isolated included L. pneumophila (serogroups 1 and 6), L. anisa, L. feeleii, and L. quateriensis. Environmental controls from the potable water of the three campsites were culture-negative. A survey of maintenance practices by the RV users at the campsites revealed that chlorine disinfection of the water tanks was rarely performed. To prevent the possibility of Legionella infections, RV owners should implement regular chlorine disinfection of their water tanks and follow the recommended maintenance guidelines according to their owner's manuals. |
Epidemiology of respiratory syncytial virus infection in rural and urban Kenya
Bigogo GM , Breiman RF , Feikin DR , Audi AO , Aura B , Cosmas L , Njenga MK , Fields BS , Omballa V , Njuguna H , Ochieng PM , Mogeni DO , Aol GO , Olack B , Katz MA , Montgomery JM , Burton DC . J Infect Dis 2013 208 Suppl 3 S207-16 ![]() BACKGROUND: Information on the epidemiology of respiratory syncytial virus (RSV) infection in Africa is limited for crowded urban areas and for rural areas where the prevalence of malaria is high. METHODS: At referral facilities in rural western Kenya and a Nairobi slum, we collected nasopharyngeal/oropharyngeal (NP/OP) swab specimens from patients with influenza-like illness (ILI) or severe acute respiratory illness (SARI) and from asymptomatic controls. Polymerase chain reaction assays were used for detection of viral pathogens. We calculated age-specific ratios of the odds of RSV detection among patients versus the odds among controls. Incidence was expressed as the number of episodes per 1000 person-years of observation. RESULTS: Between March 2007 and February 2011, RSV was detected in 501 of 4012 NP/OP swab specimens (12.5%) from children and adults in the rural site and in 321 of 2744 NP/OP swab specimens (11.7%) from those in the urban site. Among children aged <5 years, RSV was detected more commonly among rural children with SARI (odds ratio [OR], 2.0; 95% confidence interval [CI], 1.2-3.3), urban children with SARI (OR, 8.5; 95% CI, 3.1-23.6), and urban children with ILI (OR, 3.4; 95% CI, 1.2-9.6), compared with controls. The incidence of RSV disease was highest among infants with SARI aged <1 year (86.9 and 62.8 episodes per 1000 person-years of observation in rural and urban sites, respectively). CONCLUSIONS: An effective RSV vaccine would likely substantially reduce the burden of respiratory illness among children in rural and urban areas in Africa. |
Role of global disease detection laboratories in investigations of acute respiratory illness
Fields BS , House BL , Klena J , Waboci LW , Whistler T , Farnon EC . J Infect Dis 2013 208 Suppl 3 S173-6 Since 2001, the Centers for Disease Control and Prevention (CDC) has established 10 GDD Regional Centers, serving primarily resource-constrained locations in Thailand, Kenya, Guatemala, Egypt, China, Bangladesh, Kazakhstan, India, South Africa, and Georgia [1]. GDD laboratories support the following GDD Center programs that require diagnostic testing for emerging infectious diseases: the International Emerging Infections Program (IEIP), the One Health Program, the Field Epidemiology Training Program, the Influenza Program, and the Refugee Health Program (unique to the GDD Regional Center in Kenya). The laboratory leaders at each GDD Center also serve as the center's advisor for the Strengthening Laboratory Capacity Program, through which they advise the host country on means of improving laboratory capacity to support the International Health Regulations [2]. In the 6 GDD Centers whose IEIP programs conduct population-based surveillance for acute respiratory illness and other syndromes, laboratory support is provided through GDD laboratories (in Thailand, Kenya, and Guatemala), through laboratories run by the GDD partner institution (in China and Bangladesh), or a combination of both (in Egypt). |
Legionnaires' disease case-finding algorithm, attack rates, and risk factors during a residential outbreak among older adults: an environmental and cohort study
Silk BJ , Foltz JL , Ngamsnga K , Brown E , Munoz MG , Hampton L , Jacobs-Slifka K , Kozak NA , Underwood JM , Krick J , Travis T , Farrow O , Fields BS , Blythe D , Hicks LA . BMC Infect Dis 2013 13 (1) 291 BACKGROUND: During a Legionnaires' disease (LD) outbreak, combined epidemiological and environmental investigations were conducted to identify prevention recommendations for facilities where elderly residents live independently but have an increased risk of legionellosis. METHODS: Survey responses (n = 143) were used to calculate attack rates and describe transmission routes by estimating relative risk (RR) and 95% confidence intervals (95% CI). Potable water collected from five apartments of LD patients and three randomly-selected apartments of residents without LD (n = 103 samples) was cultured for Legionella. RESULTS: Eight confirmed LD cases occurred among 171 residents (attack rate = 4.7%); two visitors also developed LD. One case was fatal. The average age of patients was 70 years (range: 62--77). LD risk was lower among residents who reported tub bathing instead of showering (RR = 0.13, 95% CI: 0.02--1.09, P = 0.03). Two respiratory cultures were characterized as L. pneumophila serogroup 1, monoclonal antibody type Knoxville (1,2,3), sequence type 222. An indistinguishable strain was detected in 31 (74%) of 42 potable water samples. CONCLUSIONS: Managers of elderly-housing facilities and local public health officials should consider developing a Legionella prevention plan. When Legionella colonization of potable water is detected in these facilities, remediation is indicated to protect residents at higher risk. If LD occurs among residents, exposure reduction, heightened awareness, and clinical surveillance activities should be coordinated among stakeholders. For prompt diagnosis and effective treatment, clinicians should recognize the increased risk and atypical presentation of LD in older adults. |
Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries
Lindsay B , Ochieng JB , Ikumapayi UN , Toure A , Ahmed D , Li S , Panchalingam S , Levine MM , Kotloff K , Rasko DA , Morris CR , Juma J , Fields BS , Dione M , Malle D , Becker SM , Houpt ER , Nataro JP , Sommerfelt H , Pop M , Oundo J , Antonio M , Hossain A , Tamboura B , Stine OC . J Clin Microbiol 2013 51 (6) 1740-6 ![]() Estimates of the prevalence of Shigella spp. are limited by the suboptimal sensitivity of current diagnostic and surveillance methods. We used a quantitative PCR (qPCR) assay to detect Shigella in the stool samples of 3,533 children aged <59 months from the Gambia, Mali, Kenya, and Bangladesh, with or without moderate-to-severe diarrhea (MSD). We compared the results from conventional culture to those from qPCR for the Shigella ipaH gene. Using MSD as the reference standard, we determined the optimal cutpoint to be 2.9 x 10(4) ipaH copies per 100 ng of stool DNA for set 1 (n = 877). One hundred fifty-eight (18%) specimens yielded >2.9 x 10(4) ipaH copies. Ninety (10%) specimens were positive by traditional culture for Shigella. Individuals with ≥ 2.9 x 10(4) ipaH copies have 5.6-times-higher odds of having diarrhea than those with <2.9 x 10(4) ipaH copies (95% confidence interval, 3.7 to 8.5; P < 0.0001). Nearly identical results were found using an independent set of samples. qPCR detected 155 additional MSD cases with high copy numbers of ipaH, a 90% increase from the 172 cases detected by culture in both samples. Among a subset (n = 2,874) comprising MSD cases and their age-, gender-, and location-matched controls, the fraction of MSD cases that were attributable to Shigella infection increased from 9.6% (n = 129) for culture to 17.6% (n = 262) for qPCR when employing our cutpoint. We suggest that qPCR with a cutpoint of approximately 1.4 x 10(4) ipaH copies be the new reference standard for the detection and diagnosis of shigellosis in children in low-income countries. The acceptance of this new standard would substantially increase the fraction of MSD cases that are attributable to Shigella. |
Survey of Legionella species found in Thai soil
Travis TC , Brown EW , Peruski LF , Siludjai D , Jorakate P , Salika P , Yang G , Kozak NA , Kodani M , Warner AK , Lucas CE , Thurman KA , Winchell JM , Thamthitiwat S , Fields BS . Int J Microbiol 2012 2012 218791 Members of the Gram-negative genus Legionella are typically found in freshwater environments, with the exception of L. longbeachae, which is present in composts and potting mixes. When contaminated aerosols are inhaled, legionellosis may result, typically as either the more serious pneumonia Legionnaires' disease or the less severe flu-like illness Pontiac fever. It is presumed that all species of the genus Legionella are capable of causing disease in humans. As a followup to a prior clinical study of legionellosis in rural Thailand, indigenous soil samples were collected proximal to cases' homes and workplaces and tested for the presence of legionellae by culture. We obtained 115 isolates from 22/39 soil samples and used sequence-based methods to identify 12 known species of Legionella represented by 87 isolates. |
Eight years of Legionnaires' disease transmission in travellers to a condominium complex in Las Vegas, Nevada
Silk BJ , Moore MR , Bergtholdt M , Gorwitz RJ , Kozak NA , Tha MM , Brown EW , Winchester JL , Labus BJ , Rowley P , Middaugh JP , Fields BS , Hicks LA . Epidemiol Infect 2012 140 (11) 1-10 SUMMARY: Travel is a risk factor for Legionnaires' disease. In 2008, two cases were reported in condominium guests where we investigated a 2001 outbreak. We reinvestigated to identify additional cases and determine whether ongoing transmission resulted from persistent colonization of potable water. Exposures were assessed by matched case-control analyses (2001) and case-series interviews (2008). We sampled potable water and other water sources. Isolates were compared using sequence-based typing. From 2001 to 2008, 35 cases were identified. Confirmed cases reported after the cluster in 2001-2002 were initially considered sporadic, but retrospective case-finding identified five additional cases. Cases were more likely than controls to stay in tower 2 of the condominium [matched odds ratio (mOR) 6.1, 95% confidence interval (CI) 1.6-22.9]; transmission was associated with showering duration (mOR 23.0, 95% CI 1.4-384). We characterized a clinical isolate as sequence type 35 (ST35) and detected ST35 in samples of tower 2's potable water in 2001, 2002, and 2008. This prolonged outbreak illustrates the importance of striving for permanent Legionella eradication from potable water. |
Accuracy and precision of Legionella isolation by US laboratories in the ELITE program pilot study
Lucas CE , Taylor TH Jr , Fields BS . Water Res 2011 45 (15) 4428-36 A pilot study for the Environmental Legionella Isolation Techniques Evaluation (ELITE) Program, a proficiency testing scheme for US laboratories that culture Legionella from environmental samples, was conducted September 1, 2008 through March 31, 2009. Participants (n=20) processed panels consisting of six sample types: pure and mixed positive, pure and mixed negative, pure and mixed variable. The majority (93%) of all samples (n=286) were correctly characterized, with 88.5% of samples positive for Legionella and 100% of negative samples identified correctly. Variable samples were incorrectly identified as negative in 36.9% of reports. For all samples reported positive (n=128), participants underestimated the cfu/ml by a mean of 1.25 logs with standard deviation of 0.78 logs, standard error of 0.07 logs, and a range of 3.57 logs compared to the CDC re-test value. Centering results around the interlaboratory mean yielded a standard deviation of 0.65 logs, standard error of 0.06 logs, and a range of 3.22 logs. Sampling protocol, treatment regimen, culture procedure, and laboratory experience did not significantly affect the accuracy or precision of reported concentrations. Qualitative and quantitative results from the ELITE pilot study were similar to reports from a corresponding proficiency testing scheme available in the European Union, indicating these results are probably valid for most environmental laboratories worldwide. The large enumeration error observed suggests that the need for remediation of a water system should not be determined solely by the concentration of Legionella observed in a sample since that value is likely to underestimate the true level of contamination. |
Application of TaqMan low-density arrays for simultaneous detection of multiple respiratory pathogens.
Kodani M , Yang G , Conklin LM , Travis TC , Whitney CG , Anderson LJ , Schrag SJ , Taylor TH Jr , Beall BW , Breiman RF , Feikin DR , Njenga MK , Mayer LW , Oberste MS , Tondella ML , Winchell J , Lindstrom S , Erdman DD , Fields BS . J Clin Microbiol 2011 49 (6) 2175-82 ![]() The large and growing number of viral and bacterial pathogens responsible for respiratory infections poses a challenge for laboratories to provide rapid and comprehensive pathogen identification. We evaluated a novel application of the TaqMan(R) Low Density Array (TLDA) cards for real-time PCR detection of 21 respiratory pathogen targets. TLDA performance was compared to individual real-time PCR (IRTP) assays with the same primers and probes using 1) nucleic acids extracted from the 21 pathogen strains and 66 closely-related viruses and bacteria and 2) 292 clinical respiratory specimens. Using spiked samples, TLDA cards were about ten-fold less sensitive than the IRTP assays. Using 292 clinical specimens to generate 2238 paired individual assays, TLDA exhibited 89% sensitivity (95% confidence interval [CI] 86-92; 47-100 range per target) and 98% specificity (95% CI 97-99; 85-100 range per target) overall compared to IRTP real-time assays as the gold standard with a Ct cut-off of 43. The TLDA card approach offers promise for rapid and simultaneous identification of multiple respiratory pathogens for outbreak investigations and disease surveillance. |
Legionella nagasakiensis sp. nov., isolated from water samples in Japan and Australia and from a patient with pneumonia in the United States
Yang PG , Benson RF , Ratcliff R , Brown EW , Steigerwalt AG , Thacker LW , Daneshvar M , Morey RE , Saito A , Fields BS . Int J Syst Evol Microbiol 2011 62 284-288 ![]() A novel Legionella species was identified based on 16S rRNA and mip (macrophage infectivity potentiator) gene sequencing analysis, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens, and quantitative DNA-DNA hybridization. The strain CDC-1796-JAP-E(T) was isolated from well water at the Nagassaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. The strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires' disease in the U.S. The cells from these four strains were gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, beta-lactamase, and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described Legionellaceae. DNA hybridization studies indicated DNAs from the four strains were highly related (78-84%) but showed 29% relatedness to L. oakridgensis (ATCC 33761(T)) and less than 10% to other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov is proposed, for the type strain CDC-1796-JAP-E(T) (=ATCC BAA-1557(T)=JCM 15315(T)). |
Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens.
Yang G , Erdman DE , Kodani M , Kools J , Bowen MD , Fields BS . J Virol Methods 2011 171 (1) 195-9 ![]() This study compared six automated nucleic acid extraction systems and one manual kit for their ability to recover nucleic acids from human nasal wash specimens spiked with five respiratory pathogens, representing Gram-positive bacteria (Streptococcus pyogenes), Gram-negative bacteria (Legionella pneumophila), DNA viruses (adenovirus), segmented RNA viruses (human influenza virus A), and non-segmented RNA viruses (respiratory syncytial virus). The robots and kit evaluated represent major commercially available methods that are capable of simultaneous extraction of DNA and RNA from respiratory specimens, and included platforms based on magnetic-bead technology (KingFisher mL, Biorobot EZ1, easyMAG, KingFisher Flex, and MagNA Pure Compact) or glass fiber filter technology (Biorobot MDX and the manual kit Allprep). All methods yielded extracts free of cross-contamination and RT-PCR inhibition. All automated systems recovered L. pneumophila and adenovirus DNA equivalently. However, the MagNA Pure protocol demonstrated more than 4-fold higher DNA recovery from the S. pyogenes than other methods. The KingFisher mL and easyMAG protocols provided 1- to 3-log wider linearity and extracted 3- to 4-fold more RNA from the human influenza virus and respiratory syncytial virus. These findings suggest that systems differed in nucleic acid recovery, reproducibility, and linearity in a pathogen specific manner. |
Prevalence of Acanthamoeba spp. and other free-living amoebae in household water, Ohio, USA-1990-1992
Stockman LJ , Wright CJ , Visvesvara GS , Fields BS , Beach MJ . Parasitol Res 2010 108 (3) 621-7 Knowledge of the prevalence of free-living amoebae (FLA) in US household water can provide a focus for prevention of amoeba-associated illnesses. Household water samples from two Ohio counties, collected and examined for amoebae during 1990-1992, were used to describe the prevalence of Acanthamoeba and other FLA in a household setting. Amoebae were isolated and identified by morphologic features. A total of 2,454 samples from 467 households were examined. Amoebae were found in water samples of 371 (79%) households. Sites most likely to contain amoeba were shower heads (52%) and kitchen sprayers (50%). Species of Hartmannella, Acanthamoeba, or Vahlkampfia were most common. Detection was higher in biofilm swab samples than in water samples. Detection of FLA and Acanthamoeba, at 79% and 51%, respectively, exceed estimates that have been published in previous surveys of household sources. We believe FLA are commonplace inhabitants of household water in this sample as they are in the environment. |
Virulence factors encoded by Legionella longbeachae identified on the basis of the genome sequence analysis of clinical isolate D-4968
Kozak NA , Buss M , Lucas CE , Frace M , Govil D , Travis T , Olsen-Rasmussen M , Benson RF , Fields BS . J Bacteriol 2009 192 (4) 1030-44 ![]() Legionella longbeachae causes most cases of legionellosis in Australia and may be under-reported worldwide due to the lack of L. longbeachae-specific diagnostic tests. L. longbeachae displays distinctive differences in intracellular trafficking, caspase-1 activation, and infection of mouse models compared to L. pneumophila, yet both species have an indistinguishable clinical presentation in humans. Unlike other legionellae, which inhabit fresh water systems, L. longbeachae is found predominantly in moist soil. In this study, we sequenced and annotated the genome of a L. longbeachae clinical isolate, D-4968, from Oregon, US, and compared it to the published genomes of L. pneumophila. The study revealed that the D-4968 genome is larger with a gene order that is different from L. pneumophila. Genes encoding structural components of type II, type IV Lvh, and type IV Icm/Dot secretion systems are conserved. In contrast, only 42/140 homologs of L. pneumophila Icm/Dot substrates have been found in the D-4968 genome. L. longbeachae encodes numerous proteins with eukaryotic motifs and eukaryotic-like proteins unique to this species, including 16 ankyrin repeat-containing proteins and a novel U-box protein. We predict that these proteins are secreted by the L. longbeachae Icm/Dot secretion system. In contrast to L. pneumophila, the L. longbeachae D-4968 genome does not carry flagellar biosynthesis genes, yet contains a chemotaxis operon. The lack of a flagellum explains the failure of L. longbeachae to activate caspase-1 and trigger pyroptosis in murine macrophages. These unique features of the L. longbeachae genome may reflect adaptation of this species to life in soil. |
Distribution of lag-1 alleles and sequence-based types among Legionella pneumophila serogroup 1 clinical and environmental isolates in the United States
Kozak NA , Benson RF , Brown E , Alexander NT , Taylor TH Jr , Shelton BG , Fields BS . J Clin Microbiol 2009 47 (8) 2525-35 ![]() Approximately 84% of legionellosis cases are due to Legionella pneumophila serogroup 1. Moreover, a majority of L. pneumophila serogroup 1 clinical isolates react positively with monoclonal antibody 2 (MAb2) of the international standard panel. Over 94% of the legionellosis outbreaks investigated by the Centers for Disease Control and Prevention are due to this subset of L. pneumophila serogroup 1. To date, there is no complete explanation for the enhanced ability of these strains to cause disease. To better characterize these organisms, we subtyped 100 clinical L. pneumophila serogroup 1 isolates and 50 environmental L. pneumophila serogroup 1 isolates from the United States by (i) reactivity with MAb2, (ii) presence of a lag-1 gene required for the MAb2 epitope, and (iii) sequence-based typing analysis. Our results showed that the MAb2 epitope and lag-1 gene are overrepresented in clinical L. pneumophila serogroup 1 isolates. MAb2 recognized 75% of clinical isolates but only 6% of environmental isolates. Similarly, 75% of clinical isolates but only 8% of environmental isolates harbored lag-1. We identified three distinct lag-1 alleles, referred to as Philadelphia, Arizona, and Lens alleles, among 79 isolates carrying this gene. The Arizona allele is described for the first time in this study. We identified 59 different sequence types (STs), and 34 STs (58%) were unique to the United States. Our results support the hypothesis that a select group of STs may have an enhanced ability to cause legionellosis. Combining sequence typing and lag-1 analysis shows that STs tend to associate with a single lag-1 allele type, suggesting a hierarchy of virulence genotypes. Further analysis of ST and lag-1 profiles may identify genotypes of L. pneumophila serogroup 1 that warrant immediate intervention. |
Evaluation of tetramethylrhodamine and black hole quencher 1 labeled probes and five commercial amplification mixes in TaqMan real-time RT-PCR assays for respiratory pathogens
Yang GP , Erdman DD , Tondella ML , Fields BS . J Virol Methods 2009 162 288-90 ![]() Tetramethylrhodamine (TAMRA) and black hole quencher 1 (BHQ1) quenched probes and five one-step RT-PCR kits were evaluated in TaqMan real-time RT-PCR assays for detection of respiratory pathogens. The intra-assay variability of the BHQ1 probes were 1.2-2.8-fold lower than those of the TAMRA probes. All kits amplified the specific targets, but differed in their sensitivity by up to 3 orders of magnitude. The AgPath-ID kit provided the best overall performance for all assay targets. |
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