Laboratory-based Surveillance Research Articles

Retrospective study of laboratory-based surveillance of rabies in wild and domestic animals in the southern United States, 2010-2021.

We performed a retrospective study of all case submissions for the rabies virus (RABV) direct fluorescent antibody test (DFAT) requested of the Tifton Veterinary Diagnostic and Investigational Laboratory (Tifton, GA, USA) between July 2010 and June 2021. Submitted were 792 samples from 23 animal species from 89 counties in Georgia, and 4 neighboring counties in Florida, 1 in South Carolina, and 1 in Alabama. In 13 (1.6%) cases, the DFAT result was inconclusive; 779 (98.4%) cases had a conclusive (positive or negative) test result. Of these 779 cases, 79 (10.1%) tested positive across 10 species. The remaining 700 (89.9%) cases were negative. The main reason for submission for RABV testing was human exposure to a potentially rabid animal in 414 (52.3%) cases. Among the 79 positive cases, 74 (93.7%) involved wildlife; raccoons (51 cases; 68.9%) were the primary host confirmed with RABV infection, followed by skunk and fox (8 cases each; 10.8%), bobcat (5 cases; 6.8%), and bats (2 cases; 2.7%). Only 5 domestic animals (6.3% of the positive cases) tested positive during our study period; one from each of the bovine, canine, caprine, equine, and feline species. Hence, the sylvatic cycle plays the predominant role in circulating RABV infection in our study area.

Laboratory-based surveillance of chronic kidney disease in people with private health coverage in Brazil

BackgroundAlthough approximately 25% of Brazilians have private health coverage (PHC), studies on the surveillance of chronic kidney disease (CKD) in this population are scarce. The objective of this study was to estimate the prevalence of CKD in individuals under two PHC regimes in Brazil, who total 8,335,724 beneficiaries.MethodsOutpatient serum creatinine and proteinuria results of individuals from all five regions of Brazil, ≥ 18 years of age, and performed between 10/01/2021 and 10/31/2022, were analyzed through the own laboratory network database. People with serum creatinine measurements were evaluated for the prevalence and staging of CKD, and those with simultaneous measurements of serum creatinine and proteinuria were evaluated for the risk category of the disease. CKD was classified according to current guidelines and was defined as a glomerular filtration rate (GFR) < 60 ml/min/1.73 m² estimated by the 2021 CKD-EPI equation.ResultsThe number of adults with serum creatinine results was 1,508,766 (age 44.0 [IQR, 33.9–56.8] years, 62.3% female). The estimated prevalence of CKD was 3.8% (2.6%, 0.8%, 0.2% and 0.2% in CKD stages 3a, 3b, 4 and 5, respectively), and it was higher in males than females (4.0% vs. 3.7%, p < 0.001, respectively) and in older age groups (0.2% among 18-29-year-olds, 0.5% among 30-44-year-olds, 2.0% among 45-59-year-olds, 9.4% among 60-74-year-olds, and 32.4% among ≥ 75-year-olds, p < 0.001) Adults with simultaneous results of creatinine and proteinuria were 64,178 (age 57.0 [IQR, 44.8–67.3] years, 58.1% female). After adjusting for age and gender, 70.1% were in the low-risk category of CKD, 20.0% were in the moderate-risk category, 5.8% were in the high-risk category, and 4.1% were in the very high-risk category.ConclusionThe estimated prevalence of CKD was 3.8%, and approximately 10% of the participants were in the categories of high or very high-risk of the disease. While almost 20% of beneficiaries with PHC had serum creatinine data, fewer than 1% underwent tests for proteinuria. This study was one of the largest ever conducted in Brazil and the first one to use the 2021 CKD-EPI equation to estimate the prevalence of CKD.

Pneumococci isolated from children in community-based practice differ from isolates identified by population and laboratory-based invasive disease surveillance.

Characterizing strains causing noninvasive and invasive pneumococcal disease (IPD) may inform the impact of new pneumococcal conjugate vaccines (PCVs). During 2011-2019, among children aged 6-36 months, pneumococcal serotype distribution and antibiotic non-susceptibility of nasopharyngeal and middle ear fluid (MEF) isolates collected at onset of acute otitis media (AOM) in Rochester, New York were compared with IPD isolates from Active Bacterial Core surveillance (ABCs) across 10 U.S. sites. From Rochester, 400 (nasopharyngeal) and 156 (MEF) pneumococcal isolates were collected from 259 children. From ABCs, 907 sterile-site isolates were collected from 896 children. Non-PCV serotypes 35B and 21 were more frequent among the Rochester AOM cases, while serotypes 3, 19A, 22F, 33F, 10A, and 12F contained in PCVs were more frequent among ABCs IPD cases. The proportion of antibiotic non-susceptible pneumococcal isolates was generally more common among IPD cases. In 2015-2019, serotype 35B emerged as the most common serotype associated with multiclass antibiotic non-susceptibility for both the Rochester AOM and ABCs IPD cases. Pneumococcal isolates from children in Rochester with AOM differ in serotype distribution and antibiotic susceptibility compared to IPD cases identified through U.S. surveillance. Non-PCV serotype 35B emerged as a common cause of AOM and IPD.

Assessment of antimicrobial resistance laboratory-based surveillance capacity of hospitals in Zambia: findings and implications for system strengthening

A well-established antimicrobial resistance (AMR) laboratory-based surveillance (LBS) is of utmost importance in a country like Zambia which bears a significant proportion of the world's communicable disease burden. This study assessed the capacity of laboratories in selected hospitals to conduct AMR surveillance in Zambia. This cross-sectional exploratory study was conducted among eight (8) purposively selected hospitals in Zambia between August 2023 and December 2023. Data were collected using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. Of the assessed facilities, none had full capacity to conduct AMR surveillance with varying capacities ranging from moderate [63% (5/8)] to low [38% (3/8)]. Some of the barriers of AMR-LBS were the lack of electronic laboratory information system (LIS) [63% (5/8)] and the lack of locally generated antibiograms [75% (6/8)]. Quality control for antimicrobial susceptibility testing (AST), pathogen identification and media preparation had the lowest overall score among all the facilities with a score of 14%, 20% and 44% respectively. The highest overall scores were in specimen processing (79%), data management (78%), specimen collection, transport, and management (71%) and safety (70%). Most facilities had standard operating procedures (SOPs) in place but lacked specimen-specific SOPs. The absence of laboratories with full capacity to conduct AMR surveillance hinders efforts to combat AMR and further complicates the treatment outcomes of infectious diseases. Establishing and strengthening LBS systems are essential in quantifying the burden of AMR and supporting the development of local antibiograms and treatment guidelines.

IJCM_219A: A “One Health” Model for Prevention and Control of Anthrax in Koraput, Odisha, India

Background: Anthrax, a neglected zoonotic disease caused by Bacillus anthracis, poses a significant threat in Odisha, India, particularly in the tribal district of Koraput, which has reported numerous human cases and deaths but lacks consistent robust surveillance. Objectives: This study aimed to pilot a “One Health” surveillance model in Koraput, involving community health workers, para-veterinarians, and block- level teams in outbreak investigations. Methodology: As part of the “One Health Approach to Anthrax Control in India (OHAI)” project Odisha University of Agriculture and Technology (OUAT), in collaboration with the Departments of Animal Husbandry and Health and Family Welfare, Government of Odisha, initiated prospective laboratory-based anthrax surveillance in three blocks of Koraput. Confirmed cases in animals were identified via microscopic, culture, or PCR testing for Bacillus anthracis. Community awareness programs and rapport-building exercises were conducted with human and veterinary officials at the block and district levels following the detection of outbreaks. Results: Between March and June 2023, five anthrax outbreaks were detected in Koraput, with four involving both cutaneous human and animal deaths and one in animals only. Livestock losses included cattle (27), goats (2), and buffalo (1). Of the 38 samples collected (blood, bone, tissue, and soil), 11 (35%) tested positive for anthrax by RT-PCR. OUAT rapidly communicated results (&lt;24 hours) to the state health department, leading to joint investigations and control measures, including livestock vaccination, safe carcass disposal, and medical outreach camps for screening and prophylaxis. In total, five district/block level meetings and two state-level consultations were held, culminating in a zoonotic roadmap draft, which included an anthrax prevention and control action plan. Conclusion: The study’s adoption of the One Health framework facilitated a rapid response to anthrax outbreaks in Koraput, effectively managing both human and animal cases. This model presents a viable approach for controlling anthrax in endemic areas of India.

A Global Perspective on Oral Vaccination of Wildlife against Rabies.

The long-term mitigation of human-domestic animal-wildlife conflicts is complex and difficult. Over the last 50 yr, the primary biomedical concepts and actualized collaborative global field applications of oral rabies vaccination to wildlife serve as one dramatic example that revolutionized the field of infectious disease management of free-ranging animals. Oral vaccination of wildlife occurred in diverse locales within Africa, Eurasia, the Middle East, and North America. Although rabies is not a candidate for eradication, over a billion doses of vaccine-laden baits distributed strategically by hand, at baiting stations, or via aircraft, resulted in widespread disease prevention, control, or local disease elimination among mesocarnivores. Pure, potent, safe, and efficacious vaccines consisted of either modified-live, highly attenuated, or recombinant viruses contained within attractive, edible baits. Since the late 1970s, major free-ranging target species have included coyotes (Canis latrans), foxes (Urocyon cinereoargenteus; Vulpes vulpes), jackals (Canis aureus; Lupulella mesomelas), raccoons (Procyon lotor), raccoon dogs (Nyctereutes procyonoides), and skunks (Mephitis mephitis). Operational progress has occurred in all but the latter species. Programmatic evaluations of oral rabies vaccination success have included: demonstration of biomarkers incorporated within vaccine-laden baits in target species as representative of bait contact; serological measurement of the induction of specific rabies virus neutralizing antibodies, indicative of an immune response to vaccine; and most importantly, the decreasing detection of rabies virus antigens in the brains of collected animals via enhanced laboratory-based surveillance, as evidence of management impact. Although often conceived mistakenly as a panacea, such cost-effective technology applied to free-ranging wildlife represents a real-world, One Health application benefiting agriculture, conservation biology, and public health. Based upon lessons learned with oral rabies vaccination of mesocarnivores, opportunities for future extension to other taxa and additional diseases will have far-reaching, transdisciplinary benefits.

Pseudomonas stutzeri bloodstream infection is a prevailing community-onset disease with important mortality rates: results from a retrospective observational study in Australia

Background The recognition of Pseudomonas stutzeri as a cause of infections in humans has been increasing. However, only case reports and small series of P. stutzeri bloodstream infections have been published. Epidemiological data on these infections are extremely scarce. Our objective was to describe the incidence, epidemiology, antimicrobial resistance rates, and outcomes of P. stutzeri bloodstream infections in a large population-based cohort in Australia. Methods Retrospective, laboratory-based surveillance study conducted in Queensland, Australia (population ≈ 5 million) during 2000–2019. Clinical information was obtained from public hospital admissions and vital statistics databases. Results In total, 228 episodes of P. stutzeri bloodstream infections were identified. Increased incidence was observed in the later years, especially in older men, and was higher during the rainy months of the year and in the warmest and more humid regions of the state. The majority of bloodstream infections were community-onset with 120 (52.6%) community-associated and 59 (25.9%) ambulatory healthcare-associated episodes. Only 49 cases (21.5%) were nosocomial. The most common foci of infection were skin and soft tissue, lower respiratory tract, and intra-abdominal. No isolate showed antimicrobial resistance. Thirty-one patients (13.6%) died. The mortality rate in patients with a respiratory infectious source was higher (21%). Conclusions P. stutzeri bloodstream infection was predominantly a community-onset condition including ambulatory healthcare related cases, with increasing incidence, especially in older males. No antimicrobial resistance was observed. Mortality was high in patients with respiratory infectious source. This new observational data have implications when considering the epidemiology of these infections and for patient management.

Increased circulation of echovirus 11 in the general population and hospital patients as elicited by the non-polio enterovirus laboratory-based sentinel surveillance in northern Italy, 2023

ObjectivesFollowing the alert of echovirus 11 (E-11) infection in neonates in EU/EEA Member States, we conducted an investigation of E-11 circulation by gathering data from community and hospital surveillance of enterovirus (EV) in northern Italy from 01 August 2021 to 30 June 2023. MethodsVirological results of EVs were obtained from the regional sentinel surveillance database for influenza-like illness (ILI) in outpatients, and from the laboratory database of ten hospitals for inpatients with either respiratory or neurological symptoms. Molecular characterization of EVs was performed by sequence analysis of the VP1 gene. ResultsIn our ILI series, the rate of EV-positive specimens showed an upward trend from the end of May 2023, culminating at the end of June, coinciding with an increase in EV-positive hospital cases. The E-11 identified belonged to the D5 genogroup and the majority (83%) were closely associated with the novel E-11 variant, first identified in severe neonatal infections in France since 2022. E-11 was identified sporadically in community cases until February 2023, when it was also found in hospitalized cases with a range of clinical manifestations. All E-11 cases were children, with 14 out of 24 cases identified through hospital surveillance. Of these cases, 60% were neonates, and 71% had severe clinical manifestations. ConclusionBaseline epidemiological data collected since 2021 through EV laboratory-based surveillance have rapidly tracked the E-11 variant since November 2022, alongside its transmission during the late spring of 2023.

Evaluation of a surveillance system for Clostridioides difficile infections for Swiss hospitals.

This study evaluated an approach to establishing a comprehensive nationwide surveillance system forClostridioides difficileinfection in Switzerland. We report the results of patient-related surveillance and calculate the incidence rate ofC. difficileinfection in Switzerland in 2022. Initiated in 2017 by the National Centre for Infection Prevention (Swissnoso), in collaboration with the Swiss Centre for Antibiotic Resistance (ANRESIS), laboratory surveillance enables the automatic import ofC. difficileinfection laboratory data and is fully operational. However, the very limited number of participating laboratories impedes the generation of representative results. To address this gap, Swissnoso introduced patient-related surveillance, with a questionnaire-based survey used across Swiss acute care hospitals. This survey revealed an incidence of 3.8 (Poisson 95% CI: 3.2-4.5)C. difficileinfection episodes per 10,000 patient-days, just above the mean rate reported by the European Centre for Disease Prevention and Control (ECDC). Additionally, we report substantial heterogeneity in laboratory tests, diagnostic criteria and infection control practices among Swiss hospitals. This study underscores the importance of a joint effort towards standardized surveillance practices in providing comprehensive insights intoC. difficileinfection epidemiology and effective prevention strategies in Swiss healthcare settings. The patient-related approach remains the gold standard forC. difficileinfection surveillance, although it demands substantial resources and provides results only annually. The proposed implementation of nationwide automated laboratory-based surveillance would be pragmatic and efficient, empowering authorities and hospitals to detect outbreaks promptly and to correlate infection rates with antibiotic consumption.

Serotype Distribution and Antimicrobial Susceptibility Pattern of Streptococcus pneumoniae in COVID-19 Pandemic Era in Brazil.

Despite the introduction of the pneumococcal vaccine, Streptococcus pneumoniae remains a cause of invasive diseases in Brazil. This study provides the distribution of serotypes and antimicrobial susceptibility patterns for pneumococcal isolates before and during the years of the COVID-19 pandemic in two age groups, <5 and ≥50 years. This is a national laboratory-based surveillance study that uses data from the Brazilian national laboratory for invasive S. pneumoniae from the pre-COVID-19 (January 2016 to January 2020) and COVID-19 (February 2020 to May 2022) periods. Antimicrobial resistance was evaluated by disk diffusion and minimum inhibitory concentration. The year 2020 was marked by a 44.6% reduction in isolates received and was followed by an upward trend from 2021 onwards, which became evident in 2022. No differences were observed in serotypes distribution between the studied periods. The COVID-19 period was marked by the high prevalence of serotypes 19A, 3, and 6C in both age groups. Serotypes 19A and 6C were related to non-antimicrobial susceptibility. We observed a reduction in S. pneumoniae, without changes in serotypes distribution and epidemiological capsular switch during the COVID-19 period. We observed elevated resistance rates, mainly to penicillin and ceftriaxone for non-meningitis cases in children under 5 years of age.

Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Sentinel laboratory compliance with best practices in Burkina Faso's antimicrobial resistance surveillance network.

Standardising procedures is the best way to harmonise and strengthen the quality of laboratory-based antimicrobial resistance surveillance. Since 2018, Burkina Faso has developed and disseminated the national manual of procedures for performing antibiotic susceptibility tests in sentinel laboratories within its national antimicrobial resistance surveillance network. Our study aimed to assess these sentinel laboratories' compliance with good practices for antibiotics susceptibility tests. Four teams evaluated the antimicrobial resistance sentinel sites laboratories throughout Burkina Faso from 19 to 28 September 2022. Eighteen out of 19 sentinel laboratories were evaluated. A four-member technical committee designed and validated the evaluation tool composed of three Microsoft Excel sheets. The evaluation emphasised quality controls for culture media, antibiotic discs and compliance with antimicrobial susceptibility testing procedures by the laboratories. Excel software was used for data recording and graphs and table design. The free R software version 4.2.0 was used for descriptive statistics. An overall score below 80% was considered noncompliance. Most (83.33%) of the sentinel laboratories conducted at least one quality control activity for culture media, and 66.67% conducted at least one quality control activity for antibiotic discs. Over three-quarters (76.47%) of the laboratories were more than 80% compliant with the modified Kirby Bauer antimicrobial susceptibility testing method. The evaluation revealed the noncompliance of sentinel laboratories with the national procedure manual, particularly in the quality control component. This study has provided baseline data on the sentinel laboratories' compliance with the national antimicrobial susceptibility testing procedures manual, particularly in areas performing quality control checks or meeting quality indicators for culture media and antibiotic discs.

On-site evaluation as external quality assessment of microbiology laboratories involved in sentinel laboratory-based antimicrobial resistance surveillance network in Burkina Faso

BackgroundThe laboratory-based surveillance of antimicrobial resistance (AMR) is a priority component of the multisectoral national action plan to combat AMR in Burkina Faso. This study aimed to assess the QMS of microbiology laboratories involved in the Sentinel laboratory-based antimicrobial resistance surveillance network in Burkina Faso.MethodsA cross-sectional study was conducted from September 1st to November 30th, 2022. The external quality assessment (EQA) method used was on-site evaluation using a checklist that was developed and validated by a technical committee of experts. Teams of two, including an antimicrobial susceptibility test (AST) specialist and a QMS specialist, were trained on this checklist to conduct the assessment. Satisfactory performance was defined as any on-site evaluation score 80% and above with the aim of developing action plans to address gaps.ResultsAll 18 laboratories were evaluated. The overall average performance score of the participating laboratories was 40%. The highest overall performance score was 58%, and the lowest overall performance score was 26%. The average overall scores were not significantly different between private and public laboratories (p value = 0.78). The only section of the checklist with the satisfactory performance concerned the “Analytical step of AST”, with 76.5% (13/17) of the sentinel laboratories having a score ≥ 80%.ConclusionThe performance of the QMS of the sentinel laboratories in Burkina Faso for AMR surveillance was unsatisfactory, and a corrective action plan was proposed to support these laboratories in improving their QMS over the next 3 years.

Molecular characterization of canine parvovirus type 2 (CPV2) reveals a high prevalence of the CPV2c genotype among dogs suffering from diarrhea

AbstractCanine parvovirus 2 (CPV-2) is a highly contagious virus in dogs that typically causes hemorrhagic enteritis and a high mortality rate in unvaccinated puppies. The genetic variability and antigenic diversity of CPV-2 hinder its effective prevention of infection by vaccination. To investigate the epidemiology and genetic characteristics of CPV-2 in China, rectal swabs from affected dogs were collected from different animal clinics in Kunshan from 2022 to 2023. Preliminary detection and capsid gene sequencing of CPV-2 were performed using previously described primers and protocols. The overall detection rate for CPV-2 was 16.5% (33/200). A significant association was found between the CPV-2-positivity and clinical signs, age, breed and vaccination status. Sequence analysis revealed the presence of CPV-2c genotypes in all positive samples, which were genetically similar to other Asian CPV-2c strains. Notably, four key mutations (A5G, F267Y, Y324I and Q370R) were detected in all isolates, and one novel mutation (I447M) was detected in three CPV-2 isolates. These mutations in the CPV-2 strains could impact vaccine efficacy and the effectiveness of the virus immune evasion. Surprisingly, no recombination events were observed between the identified CPV-2c strains and reference strains from China. Our data revealed that amino acid residues 324, 426 and 440 of VP2 may under strong selection pressure. This pattern of genetic variation in the CPV-2 lineage warrants continuous laboratory-based surveillance programs in other parts of China to better understand the pattern of seasonal distribution and association between emerging genotypes and the intensity of disease severity.

Long-term surveillance of invasive pneumococcal disease: The impact of 10-valent pneumococcal conjugate vaccine in the metropolitan region of Salvador, Brazil

BackgroundIn 2010, Brazil introduced the ten-valent pneumococcal conjugate vaccine (PCV10) in the national infant immunization program. Limited data on the long-term impact of PCV10 are available from lower-middle-income settings. We examined invasive pneumococcal disease (IPD) in Salvador, Bahia, over 11 years. MethodsProspective laboratory-based surveillance for IPD was carried out in 9 hospitals in the metropolitan region of Salvador from 2008 to 2018. IPD was defined as Streptococcus pneumoniae cultured from a normally sterile site. Serotype was determined by multiplex polymerase chain reaction and/or Quellung reaction. Incidence rates per 100,000 inhabitants were calculated for overall, vaccine-type, and non-vaccine-type IPD using census data as the denominator. Incidence rate ratios (IRRs) were calculated to compare rates during the early (2010–2012), intermediate (2013–2015), and late (2016–2018) post-PCV10 periods in comparison to the pre-PCV10 period (2008–2009). ResultsPre-PCV10, overall IPD incidence among all ages was 2.48/100,000. After PCV10 introduction, incidence initially increased (early post-PCV10 IRR 3.80, 95% CI 1.18–1.99) and then declined to 0.38/100,000 late post-PCV10 (IRR 0.15; 95% CI 0.09–0.26). The greatest reductions in the late post-PCV10 period were observed in children aged ≤2 years, with no cases (IRR not calculated) and those ≥60 years (IRR 0.11, 95% CI 0.03–0.48). Late post-PCV10, significant reductions were observed for both PCV10 serotypes (IRR 0.02; 95% CI 0.0–0.15) and non-PCV10 serotypes (IRR 0.27; 95%CI 0.14–0.53). Non-PCV10 serotypes 15B, 12F, 3, 17F, and 19A became predominant late post-PCV10 without a significant increase in serotype-specific IPD incidence compared to pre-PCV10. ConclusionSignificant declines in IPD, including among adults not eligible for vaccination, suggest direct and indirect protection up to nine years after PCV10 introduction, without evidence of significant replacement disease. Continued surveillance is needed to monitor changes in non-vaccine serotypes and inform decisions about introducing higher valent PCVs.

The barriers and facilitators of implementing a national laboratory-based AMR surveillance system in Cambodia: key informants' perspectives and assessments of microbiology laboratories.

Collecting data on antimicrobial resistance (AMR) is an essential approach for defining the scope of the AMR problem, developing evidence-based interventions and detecting new and emerging resistances. Our study aimed to identify key factors influencing the implementation of a laboratory-based AMR surveillance system in Cambodia. This will add additional insights to the development of a sustainable and effective national AMR surveillance system in Cambodia and other low- and middle-income countries. Key informants with a role in governing or contributing data to the laboratory-based surveillance system were interviewed. Emerging themes were identified using the framework analysis method. Laboratories contributing to the AMR surveillance system were assessed on their capacity to conduct quality testing and report data. The laboratory assessment tool (LAT), developed by the World Health Organisation (WHO), was adapted for assessment of a diagnostic microbiology laboratory covering quality management, financial and human resources, data management, microbiology testing performance and surveillance capacity. Key informants identified inadequate access to laboratory supplies, an unsustainable financing system, limited capacity to collect representative data and a weak workforce to be the main barriers to implementing an effective surveillance system. Consistent engagement between microbiology staff and clinicians were reported to be a key factor in generating more representative data for the surveillance system. The laboratory assessments identified issues with quality assurance and data analysis which may reduce the quality of data being sent to the surveillance system and limit the facility-level utilisation of aggregated data. A weak surveillance network and poor guidance for outbreak response were also identified, which can reduce the laboratories' opportunities in detecting critical or emerging resistance occurring in the community or outside of the hospital's geographical coverage. This study identified two primary concerns: ensuring a sustainable and quality functioning of microbiology services at public healthcare facilities and overcoming sampling bias at sentinel sites. These issues hinder Cambodia's national AMR surveillance system from generating reliable evidence to incorporate into public health measures or clinical interventions. These findings suggest that more investments need to be made into microbiology diagnostics and to reform current surveillance strategies for enhanced sampling of AMR cases at hospitals.

Ribotypes and antimicrobial susceptibility profiles of clinical Clostridioides difficile isolates: A multicenter, laboratory-based surveillance in Taiwan, 2019–2021

BackgroundThe clinical burden of Clostridioides difficile infections (CDIs) remains substantial globally. This study aimed to investigate the ribotypes (RTs) and antimicrobial susceptibility of C. difficile isolates collected in Taiwan. MethodsC. difficile isolates were prospectively collected from four medical centers in Taiwan from 2019 to 2021. In a reference laboratory, in vitro susceptibility to clindamycin, moxifloxacin, metronidazole, vancomycin, fidaxomicin, and rifaximin were tested, and ribotyping was conducted to determine their genetic diversity. ResultsA total of 568 C. difficile isolates were included. Metronidazole resistance was not observed, and the susceptibility rate of vancomycin was 99.5 %. Clindamycin showed poor activity against these isolates, with a resistance rate of 74.8 %. Fidaxomicin exhibited potent activity and 97.4 % of isolates were inhibited at 0.25 μg/mL. Rifaximin MIC90 increased from 0.015 μg/mL in 2019 to 0.03 μg/mL in 2020 and 2021. Of 40 RTs identified, two predominant RTs were RT 078/126 (78, 14 %) and 014/020 (76, 13 %). RT 017, traditional harboring truncated tcdA, accounted for 3 % (20 isolates) and there was no isolate belonging to RT 027. The proportions of RT 078 increased from 11.2 % in 2019 to 17.1 % in 2021, and the predominance of RT 078/126 was more evident in central Taiwan. ConclusionsVancomycin, fidaxomicin, and metronidazole remain in vitro effective against clinical C. difficile isolates in Taiwan. The reservoirs and genetic relatedness of two major RTs with zoonotic potentials, RT 078/126 and 014/020, warrant further investigations.

Development and application of a triplex real-time PCR assay for the detection of H3, H4, and H5 subtypes of avian influenza virus

Avian influenza virus (AIV) poses a significant threat to the poultry industry and public health. Among the diverse AIV subtypes, H3, H4, and H5 are frequently detected in waterfowl and live poultry markets (LPM). The expeditious and precise identification of these subtypes is imperative in impeding the dissemination of the disease. In this study, we have developed a triplex real-time PCR assay endowed with the capacity to simultaneously discriminate AIV subtypes H3, H4, and H5. This method showcases remarkable specificity, selectively amplifying H3, H4, and H5 AIV subtypes sans any cross-reactivity with other subtypes or common avian pathogens. Furthermore, this method exhibits high sensitivity, with a detection threshold of 2.1 × 102 copies/μL for H3, H4, and H5 AIV subtypes. Additionally, the assay demonstrates reproducibility, as evidenced by intra- and inter-assay variability, with a coefficient of variation below 1.5%. A total of 338 cloacal swabs were collected from LPM to evaluate the performance of our assay. The obtained results evinced a high level of concordance with the sequencing data. In summary, our study has developed a triplex real-time PCR method that can be employed in laboratory-based testing and surveillance of AIV. This assay holds promise in augmenting our ability to detect and monitor AIV subtypes, thereby facilitating timely interventions and safeguarding both the poultry industry and public health.

From Tick to Test: A Comprehensive Review of Tick-Borne Disease Diagnostics and Surveillance Methods in the United States.

Tick-borne diseases (TBDs) have become a significant public health concern in the United States over the past few decades. The increasing incidence and geographical spread of these diseases have prompted the implementation of robust surveillance systems to monitor their prevalence, distribution, and impact on human health. This comprehensive review describes key disease features with the geographical distribution of all known tick-borne pathogens in the United States, along with examining disease surveillance efforts, focusing on strategies, challenges, and advancements. Surveillance methods include passive and active surveillance, laboratory-based surveillance, sentinel surveillance, and a One Health approach. Key surveillance systems, such as the National Notifiable Diseases Surveillance System (NNDSS), TickNET, and the Tick-Borne Disease Laboratory Network (TBDLN), are discussed. Data collection and reporting challenges, such as underreporting and misdiagnosis, are highlighted. The review addresses challenges, including lack of standardization, surveillance in non-human hosts, and data integration. Innovations encompass molecular techniques, syndromic surveillance, and tick surveillance programs. Implications for public health cover prevention strategies, early detection, treatment, and public education. Future directions emphasize enhanced surveillance networks, integrated vector management, research priorities, and policy implications. This review enhances understanding of TBD surveillance, aiding in informed decision-making for effective disease prevention and control. By understanding the current surveillance landscape, public health officials, researchers, and policymakers can make informed decisions to mitigate the burden of (TBDs).

A One Health approach based on genomics for enhancing the Salmonella enterica surveillance in Colombia

ObjectivesThis study aimed to provide evidence of the domestic benefits of introducing an integrative genomic analysis from the One Health approach in the national surveillance of Salmonella enterica between 1997-2017 in Colombia. MethodsData on Salmonella from clinical laboratory-based surveillance between 1997-2017 and from a national cross-sectional study at chicken retail stores in Colombia were compared using a phenotypic, molecular, and genomic approaches. Additional analysis by serovar using single nucleotide polymorphism was developed to increase the resolution of the relatedness between the interfaces. ResultsLocally, the diversity and pathogenic factors of the prevalent S. enterica serovars associated with foodborne disease in Colombia were described using laboratory, pulse field gel electrophoresis, and whole genome sequencing data. For example, the resolution of pulse field gel electrophoresis allowed the description of two main foodborne clusters of Salmonella Enteritidis isolates, which were expanded to eight foodborne clades using whole genome sequencing. Likewise, virulence factors and antimicrobial resistance determinants, and mobile genetic elements that converged in the foodborne clades should be considered a public health concern in Colombia. All results by serovar were compiled in an interactive easy to share report. ConclusionWhole genome sequencing is a technology that provides a precise assessment of emerging foodborne risks such as the Salmonella foodborne clades, but it requires an integrative and continued collaboration between the stakeholders across the One Health sectors to promote appropriated actions and policies in public health.