Public Health Reference Laboratories Research Articles

Evolution of COVID-19 infection in Punjab; trends during five waves of infection in the province of Punjab

BackgroundPakistan witnessed five waves of COVID-19 infections during the pandemic. Punjab, the largest province of Pakistan, remained the epicentre due to a high infection rate. Administrative data for five waves of the pandemic was analyzed to determine the rate of infections and the significance of pharmacological and non-pharmacological interventions on the severity and duration of infection.MethodologyCOVID-19 data from March 2020 to May 2023 was obtained from the Provincial Public Health Reference Laboratory (PPHRL), Punjab AIDS Control Program, Lahore. The data included samples from index cases, contacts, and recovered patients. A total of 36,252,48 cases were screened for COVID-19, and 90,923 (2.50%) were detected positive by RT-PCR, accounting for 5.69% of the cases reported positive throughout the country.ResultsAmong the positive cases, 50.86% (n = 46,244) cases were new cases (registered for the first time), 40.41% (n = 36751) were the contact cases traced from the newly identified cases and 8.62% (n = 7842) repeated cases. The positivity rates among index cases were reported to be 2.37%, 2.34%, 4.61%, 2.09%, and 1.19%, respectively, for the five respective COVID-19 pandemic waves. Distribution by gender indicated that 64% of males and 35% of females were infected during the pandemic. The age factor demonstrated the most susceptibility to infection in women aged 19-29 years, whereas most males between the ages of 29-39 had an infection. Susceptibility to COVID-19 infection was observed to be equally likely between males and females; however, clinical outcomes indicated that infections in males were more severe and often resulted in fatalities as compared to those in females. This trend was also reflected in the viral titer as measured by the Ct values, where 40% of males had Ct values < 25 (an indicator of high viral titers) compared to 30% of females with Ct values < 25.ConclusionOverall, our data indicated that infection rates remained stable throughout the pandemic except for 3rd wave, which showed a higher incidence of infection rate of 4%. Additionally, data showed a positive impact of masking, social distancing, and immunization, as indicated by the shorter window of high infection rates.

204. Clinical and Epidemiologic Review of Capnocytophaga Infections Identified at a Public Health Reference Laboratory – California, 2005 – 2021

Abstract Background Capnocytophaga spp. are bacteria commonly found in the mouths of dogs and cats, which can infect people through bites or other contact with saliva. This study describes the epidemiology and clinical features of patients from whom Capnocytophaga spp. were isolated from clinical specimens at the California State Microbial Diseases Laboratory (MDL) over a 17-year period. Methods All MDL reports of Capnocytophaga spp. isolated from human patients between 2005 and 2021, including specimen submission forms and accompanying medical records, were reviewed. Data from these records were used to identify patients in datasets of statewide hospital patient discharge (PD) and emergency department (ED) admissions when possible. Clinical and other information in the PD and ED databases were used to confirm and supplement information from laboratory records. Results Capnocytophaga spp. were isolated in 48 specimens from 47 patients. The median age of patients was 68 years (range 12 to 88 years), and 57% were male. C. canimorsus represented 83% of the Capnocytophaga spp. identified. Capnocytophaga spp. were most frequently isolated from blood (88%), followed by cerebrospinal fluid (4%) and synovial fluid (4%). The most common case presentation was sepsis (45%), followed by skin and soft tissue infection (13%). Records for 45% of patients indicated at least one comorbidity associated with immunosuppression, including current malignancy (19%), diabetes mellitus (17%), alcohol use disorder (6%), and history of splenectomy (6%). Six records (13%) reported an animal bite (five dog bites, one cat bite). Conclusion This study documented Capnocytophaga spp. infection causing rare, severe disease in older and immunocompromised persons, often without report of an animal bite. This vulnerable group should be made aware of the risk of Capnocytophaga spp. infection from contact with cats and dogs and counseled to seek prompt medical care for any signs of infection, even if no known bite occurred. Disclosures All Authors: No reported disclosures

Rapid response of a public health reference laboratory to the COVID-19 pandemic.

Introduction. Brazil was one of the most affected countries by the COVID-19 pandemic. Instituto Adolfo Lutz (IAL) is the reference laboratory for COVID-19 in São Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL-2 was created to enhance IAL's capacity for COVID-19 diagnosis.Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics.Aim. To describe the design of IAL-2 and correlate the results of RT-qPCR tests for COVID-19 with secondary data on suspected cases of SARS-CoV-2 infection in the São Paulo state.Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS-CoV-2 whose clinical samples were submitted to real-time PCR after reverse transcription (RT-qPCR) at IAL-2, between 1 April 2020 and 8 March 2022. RT-qPCR Ct results of the different kits used were also analysed.Results. IAL-2 was implemented in April 2020, just over a month after the detection of the first COVID-19 case in Brazil. The laboratory performed 304,250 RT-qPCR tests during the study period, of which 98 319 (32.3 %) were positive, 205827 (67.7 %) negative, and 104 (0.03 %) inconclusive for SARS-CoV-2. RT-qPCR Ct values≤30 for E/N genes of SARS-CoV-2 were presented by 79.7 % of all the samples included in the study.Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID-19, outlining strategies to carry out work with quality, using different RT-qPCR protocols.

Ghana’s progress towards measles elimination: Surveillance data analysis, Greater Accra Region, 2015 – 2019

IntroductionAlthough measles is targeted for global elimination by 2020, an estimated 869,770 measles cases and 207,500 deaths occurred in 2019. Ghana adopted the World Health Organization measles elimination strategies, however, evidence of a systematic, comprehensive analysis of data tracking progress towards elimination is sparse. We analyzed measles data to describe its epidemiology, surveillance, and vaccination coverage performances in the Greater Accra Region.MethodsWe reviewed and conducted a descriptive analysis of measles surveillance, laboratory, and vaccination data for 2015 to 2019 obtained from the regional health directorate and National public health reference laboratory. Case patients’ demographic and clinical variables were analyzed into frequencies, proportions, and rates. We used WHO measles elimination performance targets; at least one suspected measles case reported per 100,000 population, 80% of suspected measles cases investigated with adequate blood samples, measles incidence &amp;lt;1/1,000,000 population, 95% routine vaccination coverage and during SIAs as benchmarks.ResultsOf 930 suspected measles cases reported, 605(65.1%) were tested. Males accounted for 356(58.8%); 141(23.3%), 342(56.5%), and 122(20.2%), were children &amp;lt;1, 1–4, and ≥5 years old respectively. Of those tested, 10(1.65%) were measles IgM confirmed, of which 7(70.0%) had received at least one dose of measles vaccine. Annualized measles reporting rate ranged from 1.8 to 6.4 per 100,000 population from 2015 to 2019. District specimen collection rate was 100%, and measles incidence was between 0 – 0.6 per million population in the period 2015–2019. Measles vaccination coverage increased from 73.5% in 2016 to 102% in 2019 with 75% of districts achieving 95% coverage in 2019.ConclusionThe measles case-based surveillance system and vaccination program in the Greater Accra region showed an increasing level of performance towards Ghana’s elimination status. However, performance in laboratory testing of blood specimens was suboptimal. Authorities of Ghana’s health system should strengthen laboratory capacity for prompt diagnosis of measles.

Bacterial infections epidemiology and factors associated with multidrug resistance in the northern region of Ghana

Bacterial infections caused by multidrug resistant organisms are a major global threat. There is still a knowledge gap on this situation in the Northern Region of Ghana. This study determined the prevalence and resistance profile of bacterial infections. It also identified factors associated with multidrug resistance in the study area. This was a retrospective cross-sectional design and it analyzed data from the samples received at the Tamale Zonal Public Health Reference Laboratory from June 2018 to May 2022. The data were analyzed using the R software version 4.2.0. Univariate and multivariable binary logistic regression analyses were used to determine the factors associated with multidrug resistance. The samples included all specimen types possible. The specimens were collected for the purpose of clinical bacteriology diagnostics. Overall a total of 1222 isolates were obtained. The three (3) main bacteria responsible for infections were: Klebsiella spp. (27%), Moraxella spp. (22%), Escherichia spp. (16%). High resistance levels were found against the tested antibiotics and about 41.60% of the bacterial strains isolated were multidrug resistant. Hospitalization was associated with multidrug resistance in univariate (COR 1.96; 95% CI 1.43–2.71; P-value < 0.001) and multivariable analyses (AOR 1.78; 95% CI 1.28–2.49; P-value < 0.001). There is the need for further research on the molecular epidemiology of antibiotic resistance genes in the study area to effectively control the spread of multidrug resistant pathogens. In addition, efforts to build the capacity of health professionals on infection prevention and control as well as diagnostic and antimicrobial stewardship needs urgent attention.

Strengthening surveillance in Ghana against public health emergencies of international concern

Among western African countries, the Republic of Ghana has maintained an economic growth rate of 5% since the 1980s and is now categorized as a middle-income country. However, as with other developing countries, Ghana still has challenges in the effective implementation of surveillance for infectious diseases. Facing public health emergencies of international concern (PHEIC), it is crucial to establish a reliable sample transportation system to the referral laboratory. Previously, surveillance capacity in Ghana was limited based on Integrated Disease Surveillance and Response, and therefore the “Surveillance and Laboratory Support for Emerging Pathogens of Public Health Importance in Ghana (SLEP)” was introduced to strengthen diarrhea surveillance. The SLEP project started with a sentinel diarrhea survey supported by SATREPS/JICA in collaboration with National Public Health Reference Laboratory (NHPRL) and Noguchi Memorial Institute of Medicine (NMIMR). The base-line survey revealed the limited capacity to detect diarrhea pathogens and to transfer samples from health centers to NHPRL. The involvement of private clinic/hospital facilities into the surveillance network is also crucial to strengthen surveillance in Ghana. The strong and interactive relationship between the two top referral laboratories, NHPRL under the Ministry of Health NMIMR and under the Ministry of Education, enables Ghana Health Services and is critical for the rapid response against PHEIC. In future, we hope that the outcome of the SLEP surveillance project could contribute to building a surveillance network with more timely investigation and transfer of samples to referral labs.

Epidemiological characteristics of Lassa fever cases in Liberia: a retrospective analysis of surveillance data, 2019–2020

ObjectivesLiberia is endemic to Lassa fever (LF) and has the largest reported per capita incidence of LF patients in the West African region. Cases of the disease increased unprecedentedly in 2019 and 2020, characterized by a geographical drift in epidemiology and seasonal variation of occurrence. This study aims to describe the epidemiological and clinical characteristics of LF in Liberia from 2019 to 2020. MethodsA retrospective study was conducted on cases of LF confirmed at the National Public Health Reference Laboratory from January 2019 to December 2020. Medical records were reviewed, and epidemiological and clinical data were collected in an organized manner. Descriptive and inferential statistics were carried out using Epi Info (version 7.2.5.0). ResultsA total of 382 suspected LF cases were reported, of which 103 were laboratory-confirmed, yielding a case positivity rate of 27% (103/382). The median age of the LF cases was 20 (IQR: 9–30). Children younger than 18 years accounted for 40.8% (42/103) of the cases and healthcare workers’ cases constituted 7.7% of the cases. Bong, Nimba, and Grand Bass accounted for 87.4% of the cases with cases in new counties like Lofa, Margibi, and Grand Kru. Hemorrhage (aOR:10.2; 95% CI: 3.11–33.81), patients who did not receive ribavirin (aOR: 4.4; 95% CI: 1.12–17.57, P = 0.034), and patients aged 40 years or older (aOR: 6.2; 95% CI: 1.19–32.53, P = 0.049) were associated with LF mortality. ConclusionThe LF cases in 2019 and 2020 had a high case fatality rate and spread to new counties that had not previously reported LF. The disease occurred during most of the rainy season instead of the usual dry season. There is an urgent need to lower morbidity and mortality, improve early presentation to the hospital, and early initiation of appropriate medical care.

Feasibility of a refurbished shipping container as a transportable laboratory for rapid SARS-CoV-2 diagnostics.

BackgroundAustralia’s response to the coronavirus disease 2019 (COVID-19) pandemic relies on widespread availability of rapid, accurate testing and reporting of results to facilitate contact tracing. The extensive geographical area of Australia presents a logistical challenge, with many of the population located distant from a laboratory capable of robust severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. A strategy to address this is the deployment of a mobile facility utilizing novel diagnostic platforms. This study aimed to evaluate the feasibility of a fully contained transportable SARS-CoV-2 testing laboratory using a range of rapid point-of-care tests.MethodA 20 ft (6.1 m) shipping container was refurbished (GeneWorks, Adelaide, South Australia) with climate controls, laboratory benches, hand-wash station and a class II biosafety cabinet. Portable marquees situated adjacent to the container served as stations for registration, sample acquisition and personal protective equipment for staff. Specimens were collected and tested on-site utilizing either the Abbott ID NOW or Abbott Panbio rapid tests. SARS-CoV-2 positive results from the rapid platforms or any participants reporting symptoms consistent with COVID-19 were tested on-site by GeneXpert Xpress RT-PCR. All samples were tested in parallel with a standard-of-care RT-PCR test (Panther Fusion SARS-CoV-2 assay) performed at the public health reference laboratory. In-laboratory environmental conditions and data management-related factors were also recorded.ResultsOver a 3 week period, 415 participants were recruited for point-of-care SARS-CoV-2 testing. From time of enrolment, the median result turnaround time was 26 min for the Abbott ID NOW, 32 min for the Abbott Panbio and 75 min for the Xpert Xpress. The environmental conditions of the refurbished shipping container were found to be suitable for all platforms tested, although humidity may have produced condensation within the container. Available software enabled turnaround times to be recorded, although technical malfunction resulted in incomplete data capture.ConclusionTransportable container laboratories can enable rapid COVID-19 results at the point of care and may be useful during outbreak settings, particularly in environments that are physically distant from centralized laboratories. They may also be appropriate in resource-limited settings. The results of this pilot study confirm feasibility, although larger trials to validate individual rapid point-of-care testing platforms in this environment are required.

Assessing an Adaptation of the Universal Parasite Diagnostic Assay for Bloodborne Parasites in a US State Public Health Laboratory.

For complex clinical cases where a parasitic infection is suspected, it can be difficult for clinicians to recommend an appropriate laboratory test. These tests are usually pathogen-specific and require a certain degree of suspicion for the precise etiology. A recently described assay, the universal parasite diagnostic (UPDx) can potentially provide a diagnosis of any parasite present in a specimen. Using primers that amplify DNA from all eukaryotes, UPDx differentiates several parasitic infections in blood by amplicon-based next-generation sequencing (NGS) of the 18S rDNA locus. As the state's public health reference laboratory, the Parasitology Laboratory at the Wadsworth Center (Albany, NY) receives specimens from patients who have potentially encountered a wide variety of parasites. As such, the ability to differentiate several blood parasites using a single assay is of interest. We assessed UPDx for its ability to confirm parasitic infections for 20 specimens that were previously identified by real-time PCR (RT-PCR). This included specimens positive for Babesia microti, Trypanosoma cruzi, Leishmania tropica, various Plasmodium species, and specimens comprising mixed Plasmodium sp. infections. Results obtained using UPDx were largely concordant with the RT-PCR assays. A T. cruzi positive specimen was negative by UPDx and for two mixed Plasmodium sp. infections only one species was detected. The results obtained for other specimens were concordant. We conclude that UPDx shows promise for the detection of blood parasites in diagnostic laboratories. As NGS becomes cheaper, assays like UPDx will become increasingly amenable to use in clinical settings.

Assessment of Rapid Diagnostic Tests for Typhoid Diagnosis and Assessment of Febrile Illness Outbreaks in Fiji.

ABSTRACT.Typhoid is an endemic in Fiji with increases observed since the early 2000s and frequent outbreaks reported. We assessed the diagnostic accuracy of currently available typhoid rapid diagnostic tests (RDTs) (TUBEX, Typhidot Rapid, and Test-It assay) to establish their performance against blood culture in Fiji and to examine their suitability for rapid typhoid outbreak identification. The performance of RDTs was assessed in the public health reference laboratory in Suva, Fiji, according to the manufacturers’ instructions. A simulation was used to examine the potential use of RDTs for attribution of a febrile illness outbreak to typhoid. For the diagnostic evaluation, 179 patients were included; 49 had blood culture–confirmed typhoid, 76 had fever as a result of non-typhoid etiologies, and 54 were age-matched community controls. The median (interquartile range) age was 29 (20–46) years. Of the participants, 92 (51.4%) were male and 131 (73.2%) were indigenous Fijians. The sensitivities of the tests were 77.6% for TUBEX, 75.5% for Typhidot Rapid, and 57.1% for Test-It assay. The Test-It assay had the highest specificity of 93.4%, followed by Typhidot Rapid 85.5% and TUBEX 60.5%. Typhidot Rapid had the best performance in the simulation for attribution of a febrile illness outbreak to typhoid. Typhoid RDTs performed suboptimally for individual patient diagnosis due to low sensitivity and variable specificity. We demonstrate that RDTs could be useful in the field for rapid attribution of febrile illness outbreaks to typhoid. Typhidot Rapid had the best combination of sensitivity, specificity, positive and negative predictive values, cost, and ease of use for this purpose.

Sequencing for COVID-19 in the Pandemic Era: What Does it Mean?

Abstract Introduction/Objective SARS-CoV-2 has been developing mutations over the course of the pandemic, leading to the rise of variants. The sequencing of these variants, however, has an unclear role for the medical center providing patient treatment. Methods/Case Report Patient specimens that were positive for the presence of SARS-CoV-2 with a cycle threshold &amp;lt;30 by reverse transcriptase polymerase chain reaction (RT-PCR) were sent for sequencing at the Veterans Health Administration Public Health Reference Laboratory (PHRL). Testing for SARS-CoV-2 was by RT-PCR was initially done by either the Abbott Alinity m SARS-CoV-2 assay (Chicago IL) or the Cepheid Xpert Xpress SARS-CoV- 2/Flu/RSV assay (Sunnyvale CA). All sent patient specimens had been selected by the clinical team for concern of the presence of a SARS-CoV-2 variant. Results (if a Case Study enter NA) There were a total of 8 patients (4 males and 4 females) that were sent for sequencing. The patient ages ranged from 38 to 80 years (average 58.8). The racial proportion of the 8 patients was 2 African Americans, 2 Caucasian Americans, and 4 unanswered. All were positive for SARS-CoV-2 by RT-PCR (4 Abbott assay and 4 Cepheid assay). Six of the sequenced samples showed the NextClade 20I/501Y.V1, Pango Lineage B.1.1.7, a variant first identified in the United Kingdom; four of these six patients had documentation of vaccination prior to the infection. One sequence was a NextClade 20C Pango Lineage B.1.526.1, a variant first identified in New York. The last sequence identified was a NextClade 20G, Pango Lineage B.1, a variant predominantly seen in the United States. Conclusion At the present time, sequencing of SARS-CoV-2 does not have a clear clinical role. However, from a public health and epidemiological point of view, sequencing has a role in SARS-CoV-2 variant tracing and detection. Vaccine protection against variant SARS-CoV-2 may not be complete as some infected patients had been vaccinated.

Laboratory-based Evaluation of Wondfo HIV1/2 Rapid Test Kits in the Gambia, December 2020

Background: HIV rapid diagnosis in The Gambia is mainly done using Determine HIV-1/2 and First Response HIV 1.2.0 or SD Bioline HIV-1/2 3.0 for screening and sero-typing of HIV respectively among children and adults. Polymerase Chain Reaction (PCR) is used for the detection of the HIV viral genome among infants born to HIV positive mothers. This is the HIV testing Algorithm recommended in the HIV testing guidelines of The Gambia for both HIV Counseling and Testing (HCT), Prevention of Mother-to-Child Transmission of HIV (PMTCT) as well as other clinical requests for HIV testing. At the National Public Health Reference Laboratories (NPHRL), ELISA is the first line of testing for HIV while First Response HIV 1.2.0 or SD Bioline HIV 1/2 3.0 is used for preliminary serotyping. MP Diagnostics HIV Blot 2.2 Western Assay, which is the gold standard for HIV testing in The Gambia, is used as the tie breaker (i.e., when there are discordant results). The aim of this study was to evaluate the sensitivity and specificity of the Wondfo HIV 1/2 rapid test kit for the detection of human antibodies to HIV in serum/plasma/whole blood and dried blood spots. Methods: The sensitivity, specificity, positive and negative predictive values of Wondfo HIV 1/2 kits were evaluated in terms of HIV screening against Determine HIV1/2, GenScreen Ultra HIV Ag-Ab ELISA and First Response HIV 1.2.0 using a total of 401 samples. Of these, 351 were sera/plasma samples {100 HIV negative, 250 HIV positive and 1 indeterminate that were stored at -20°C, 26 were whole blood samples (4 negative, 22 positive), and 24 were dried blood spot (DBS) specimens (16 negative and 8 positive) were used for this evaluation. HIV positive specimens were previously sero-typed using First Response HIV-1.2.0 test cards and MP Diagnostics HIV Blot 2.2 Western Assay. Results: The evaluation shows that the sensitivity, specificity, positive and negative predictive values of Wondfo HIV 1/2 Test Kits with regards to HIV Screening when compared with the GenScreen Ultra HIV Ag-Ab ELISA and First Response 1.2.O (n=401) were 100%, 100%, 100%, and 100% respectively. Similarly, the sensitivity, specificity, positive and negative predictive values of Wondfo HIV 1/2 Test Kits with regards to HIV Screening compared to Determine HIV1/2 (n=401) were 99.64%, 100%, 100%, and 99.17% respectively. Conclusions: This study demonstrates that Wondfo HIV 1/2 test kits have a high sensitivity and specificity when used for the detection of HIV antibodies using human serum/plasma, whole blood or DBS.

The state of laboratory diagnosis, surveillance, and response to outbreaks of bacterial Meningitis, Brong Ahafo Region, Ghana, 2019

Background: One goal of WHO and Global Health Security Agenda (GHSA), is to prevent, rapidly detect, diagnose, notify and respond to infectious diseases, in order to contain them at source, and prevent spread. We assessed cerebrospinal fluid (CSF) sample management, referral, laboratory diagnostics, notification, response, and surveillance capacity in relation to bacterial meningitis in Brong Ahafo Region(BAR), Ghana. Methods and materials: We conducted a cross-sectional study in BAR in September 2019. We reviewed Meningitis case-based forms, laboratory registers, from January to August 2019, and interviewed laboratory personnel. We collected data on sample quality, type of sample container, time of collection, receipt, and outcome of culture and PCR results at the Brong Ahafo Regional Hospital Laboratory (BARHL), and the PCR Zonal Public Health Reference Laboratory (ZPHRL), in the Northern Region, respectively Results: A total of 87 CSF samples were received at BARHL, between January–August 2019, from peripheral districts in BAR. The median time for samples receipt was; 1 day;(range; 1–4). Eight, (9.2%) tested culture-positive; Streptococcus pneumoniae. Sixty-nine (79.3%) samples met the criteria for adequacy and PCR analysis at the ZPHRL. It took 21 days to receive PCR results feedback. In all, 21 (30.4%) of the 69 samples were positive by PCR; (Streptococcus pneumoniae-20, Neisseria meningitidis-1). More than half; 13(62%) of the 21 positives by PCR, had been previously declared; ‘Culture Negative’ at BARHL. Across districts, there was lack of Gram stain and rapid latex agglutination test kits. Standard sample collection tubes such as dry cryo-tubes and trans-isolate bottles (meant to sustain the viability of CSF pathogens whilst in transit) was inadequate, and often yielded contaminated results due to inappropriate handling techniques. Conclusion: Poor specimen management and weak laboratory capacity possibly accounted for the low yield of culture results at BARHL. Observation suggests a high potential of failure to rapidly diagnose, notify, respond, and contain infectious outbreaks at source. Strengthening laboratory capacity at local and district levels in Brong Ahafo Region is crucial.

Looking back to look forward: The consequences of the Zika outbreak through the eyes of a public health reference laboratory in the Netherlands

Looking back to look forward: The consequences of the Zika outbreak through the eyes of a public health reference laboratory in the Netherlands

Laboratório Central de Saúde Pública do Piauí: frequência de espécies de micobactérias e aspectos epidemiológicos, 2014-2015

Background and Objectives: Knowledge about species diversity of non-tuberculous mycobacteria (NTM) and the frequency of tuberculosis (TB) is an important issue in rural-urban regions such as Piauí (northeast of Brazil), of low incidence rate of TB , can help to improve diagnosis and prevention strategies. The aim of this study is to examine some epidemiological aspects and the frequency of Mycobacterium tuberculosis (Mtb) and NTM isolated at the central public health reference laboratory, Dr. Costa Alvarenga, Piauí (LACEN-PI). Methods: Data records of all mycobacterosis and tuberculosis cases from January 2014 to March 2015 were analyzed. Results : Of the 20% (142/706) positive growths, 70% (99) were Mtb and 10% NTM. The remainde was of inadequate clinical samples, not allowing the identification of even the suspected NTM. The most frequent clinical form was pulmonary with TB patients younger than those infected with NTM (p = 0.001), the majority living in Teresina (52%). NTMs identified were M. abscessus (36%), M. avium, M. intracellulare, Mycobacterium sp. (14% each) and M. asiaticum, M. szulgai, M. kansasii 7% (each). Mtb drug resistance (7.8%) and TB co-infection with the human immunodeficiency virus (HIV-TB) found to be high (49%, 19/39) . Conclusion: The frequencies of Mtb infection, drug resistance and HIV-TB co-infection are still underestimated and failures in the identification of NTM may decrease the actual frequency of these infections. Therefore, there is a need for improvements in TB control and in the diagnosis of NTMs in Piauí.

Detecting Cryptosporidium in Stool Samples Submitted to a Reference Laboratory

When considering methods of detecting Cryptosporidium in patient samples, clinical and public health laboratories have historically relied primarily on microscopy. However, microscopy is time intensive and requires trained personnel to accurately identify pathogens that are present. Even with skilled analysts, the parasitemia level has the potential to fall below the level of detection. In addition, public health laboratories do not always receive specimens in fixatives that are compatible with the desired microscopic method. Antigen-based and molecular methods have proven to be effective at identifying Cryptosporidium at low levels and require less training and hands-on time. Here, we have developed and validated a real-time polymerase chain reaction (RT-PCR) laboratory-developed test (LDT) that identifies Cryptosporidium hominis and Cryptosporidium parvum, and also includes detection at the genus level to identify additional species that occasionally cause disease in humans. Results of the molecular test were compared with those obtained from modified acid-fast microscopy, immunofluorescent microscopy, an antigen-based detection rapid test, and a commercial gastrointestinal panel (GI panel). Of 40 positive samples, microscopy and antigen-based methods were able to detect Cryptosporidium in only 20 and 21 samples, respectively. The GI panel detected 33 of the 40 positive samples, even though not all specimens were received in the recommended preservative. The LDT detected Cryptosporidium in all 40 positive samples. When comparing each method for the detection of Cryptosporidium, our results indicate the LDT is an accurate, reliable, and cost-effective method for a clinical public health reference laboratory.

International Public Health Laboratory Twinning: An Innovative Approach to Strengthen the National Health Laboratory System in Uganda, 2014-2017.

International initiatives to strengthen national health laboratory systems in resource-poor countries are often hampered by unfamiliarity with the country's health laboratory environment and turnover of international partners during the initiative. This study provides an overview of, and lessons learned from, the use of a laboratory long-term partnership approach (ie, "twinning") to strengthen the national public health laboratory system in an international setting. We focused on the partnering of the Uganda Ministry of Health Central Public Health Laboratory (CPHL) with the New Mexico State Public Health Laboratory to help the CPHL become Uganda's national public health reference laboratory (Uganda National Health Laboratory Services [UNHLS] Institute) and leader of its nascent Uganda National Health Laboratory Network (UNHLN). Via twinning, CPHL leadership received training on laboratory leadership and management, quality systems, facility management, and the One Health environmental strategy (ie, that the health of persons is connected to the health of animals and the environment), and drafted a National Health Laboratory Policy, UNHLS Institute business plan, and strategic and operating plans for the UNHLS Institute and UNHLN. The CPHL is now responsible for the UNHLS Institute and coordinates the UNHLN. Lessons learned include (1) twinning establishes stable long-term collaborations and (2) success requires commitment to a formal statement of activities and objectives, as well as clear and regular communication among partners.

Lessons learned from detecting and responding to recurrent measles outbreak in Liberia post Ebola-Epidemic 2016-2017.

IntroductionMeasles is an acute viral disease that remains endemic in much of sub-Sahara Africa, including Liberia. The 2014 Ebola epidemic disrupted an already fragile health system contributing to low uptake of immunization services, population immunity remained low thus facilitating recurrent outbreaks of measles in Liberia. We describe lessons learnt from detecting and responding to recurrent outbreaks of measles two years post the 2014 Ebola epidemic in Liberia.MethodsWe conducted a descriptive study using the findings from Integrated Diseases Surveillance and Response (IDSR) 15 counties, National Public Health Institute of Liberia (NPHIL), National Public Health Reference Laboratory (NPHRL) and District Health Information Software (DIHS2) data conducted from October to December, 2017. We perused the outbreaks line lists and other key documents submitted by the counties to the national level from January 2016 to December 2017.ResultsFrom January 2016 to December 2017, 2,954 suspected cases of measles were reported through IDSR. Four hundred sixty-seven (467) were laboratory confirmed (IgM-positive), 776 epidemiologically linked, 574 clinically confirmed, and 1,137 discarded (IgM-negative). Nine deaths out of 1817 cases were reported, a case fatality rate of 0.5%; 49% were children below the age of 5 years. Twenty-two percent (405/1817) of the confirmed cases were vaccinated while the vaccination status of 55% (994/1817) was unknown.ConclusionRevitalization of IDSR contributed to increased detection and reporting of suspected cases of measles thus facilitating early identification and response to outbreaks. Priority needs to be given to increasing the uptake of routine immunization services, introducing a second dose of measles vaccine in the routine immunization program and conducting a high-quality supplementary measles immunization campaign for age group 1 to 10 years to provide protection for a huge cohort of susceptible.

First occurrence of Rift Valley fever outbreak in Niger, 2016.

Rift Valley fever (RVF) is a mosquito‐borne viral zoonosis causing abortions and high mortality among animals, whereas in humans, the disease is usually mild or asymptomatic. In September 2016, the Republic of Niger declared the first RVF outbreak in the northern region of Tahoua near the Malian border. This study describes the outbreak and reports the results of serological and molecular investigations of the human and animal samples collected. Serum samples from both human and animal suspected cases have been confirmed at the Centre de Recherche Médicale et Sanitaire (CERMES) and the Laboratoire Centrale d'Elevage (LABOCEL) public health and animal reference laboratories, respectively. Techniques for biological confirmation were real time reverse transcription polymerase chain reaction (RT‐PCR) and enzyme linked immunosorbent assay (ELISA). Phylogenetic trees were established after genetic sequencing of the small and medium segments of the RVF virus (RVFV) genome. Out of the 399 human samples collected, 17 (4.3%) were confirmed positive for RVFV. Overall, 33 (8.3%) deaths occurred out of which five (29%) were among the 17 confirmed cases. Regarding animals, 45 samples were tested, three of which were RT‐PCR positive and 24 were IgG positive. The phylogenetic analyses showed that the Niger strains clustered with Senegal 2013 and Mauritania 2015 RVFV strains. This first outbreak of RVF was very challenging for public and animal health laboratories in Niger. Besides resulting in human deaths, important loss of cattle has been reported. Therefore, vigilance has to be strengthened emphasising vector control strategies and active surveillance among animals.

CLIA-compliant validation of Whole Genome Sequencing (WGS) for clinical microbiological applications: experience of one state public health reference laboratory

CLIA-compliant validation of Whole Genome Sequencing (WGS) for clinical microbiological applications: experience of one state public health reference laboratory