National Surveillance Program Research Articles

Prevalence of five human pathogens in host-seeking Ixodes scapularis and Ixodes pacificus by region, state, and county in the contiguous United States generated through national tick surveillance

The majority of vector-borne disease cases reported in the United States (U.S.) are caused by pathogens spread by the blacklegged tick, Ixodes scapularis. In recent decades, the geographic ranges of the tick and its associated human pathogens have expanded, putting an increasing number of communities at risk for tick-borne infections. In 2018, the U.S. Centers for Disease Control and Prevention (CDC) initiated a national tick surveillance program to monitor changes in the distribution and abundance of ticks and the presence and prevalence of human pathogens in them. We assessed the geographical representativeness of prevalence data submitted to CDC as part of the national tick surveillance effort. We describe county, state, and regional variation in the prevalence of five human pathogens (Borrelia burgdorferi sensu stricto (s.s.), Borrelia mayonii, Borrelia miyamotoi, Anaplasma phagocytophilum, and Babesia microti) in host-seeking I. scapularis and I. pacificus nymphs and adults. Although I. scapularis and I. pacificus are widely distributed in the eastern and western U.S., respectively, pathogen prevalence was estimated predominantly in ticks collected in the Northeast, Ohio Valley, and Upper Midwest regions, where human Lyme disease cases are most commonly reported. Within these regions, we found that state and regional estimates of pathogen prevalence generally reached predictable and stable levels, but variation in prevalence estimates at the sub-state level was considerable. Borrelia burgdorferi s.s. was the most prevalent and widespread pathogen detected. Borrelia miyamotoi and A. phagocytophilum shared a similarly broad geographic range, but were consistently detected at much lower prevalence compared with B. burgdorferi s.s. Babesia microti was detected at similar prevalence to A. phagocytophilum, where both pathogens co-occurred, but was reported over a much more limited geographic range compared with A. phagocytophilum or B. burgdorferi s.s. Borrelia mayonii was identified at very low prevalence with a focal distribution within the Upper Midwest. National assessments of risk for tick-borne diseases need to be improved through collection and testing of ticks in currently under-represented regions, including the West, South, Southeast, and eastern Plains states.

Trends in Salmonella Dublin over time in Denmark from food and animal related isolates.

Salmonella enterica serovar Dublin is highly adapted to cattle and a relatively rare cause of human infections. In Denmark S. Dublin has been endemic in the cattle population for many years. A national surveillance program in the cattle population was established at herd-level to reduce the occurrence of S. Dublin. In this study, we analyzed 421S. Dublin genomes from cattle and food in order to determine the trend of S. Dublin's population size over time in Denmark and the impact of intervention in the cattle industry on the bacterial population size. A phylogenetic tree based on SNPs exhibited two major clades and one small cluster. All isolates were ST10. The temporal phylogenetic tree for the S. Dublin isolates showed that the most recent common ancestor was estimated to be in ∼1980 for the two major clades. An effective population size over time based on a Bayesian skyline plot showed that the population size of S. Dublin decreased significantly between 2014 and 2019 in both major clades. This result was concordant with the decrease of infected human cases by S. Dublin in Denmark. The strengthening of a surveillance program in Denmark could be the cause for the reduction of S. Dublin's effective population size. This study showed that whole genome sequencing combined with computer intensive phylogenetic analysis estimating the effective size of the S. Dublin's population over time is a strongly relevant measure with respect to assessing the impact of control measures aiming to reduce the bacterial population in the reservoir and the risk for human infection.

Screening for extended-spectrum beta-lactamaseEscherichia coli in recreational beach waters in Singapore.

Aims: As part of Singapore's One Health antimicrobial resistance (AMR) management, this work was designedto understand the AMR burden in recreational beach waters using extended-spectrum beta-lactamase Escherichia coli (ESBL-EC) as an indicator. Materials & methods: A total of 90 water samples were collected from six different recreational beaches over three different time periods. Only 28/90 (31.3%) water samples yielded E. coli colonies ranging from 1 to 80colony-forming units/100ml. Results & conclusion: Screening of all colonies using CHROMID® ESBL agar and Luria-Bertani broth supplemented with ceftriaxone showed that none was ESBL-EC. Further monitoring is required to understand the prevalence of ESBL-EC spatiotemporally, contributing to the national AMR surveillance program and providing timely risk assessment for exposure to ESBL-EC.

Avian Influenza Surveillance in Pigs, Dogs, Chickens and Slaughter Slabs Biosecurity in Kaduna Metropolis, Nigeria

Avian influenza is a zoonotic disease likely to be exposed to dog, pig and poultry owners & their processors who are in close contact during processing of these animals in Kaduna Metropolis, Nigeria. The study assessed the biosecurity practice of processors in pig, poultry, and dog slaughter slabs; and the prevalence of Avian Influenza (H5 subtype) antibodies in dogs, pigs, and chickens in Kaduna Metropolis. The slaughter slab biosecurity practices were evaluated using questionnaires while the H5 antibodies surveillance was determined by hemagglutination inhibition test. Serum samples from 45 dogs, 104 pigs and 75 chickens were tested for H5 subtype. H5 subtype antibodies prevalence in dogs was 2.2% with a mean titre of 9.0 ± 0 log2 while prevalence and mean titre in chicken were 6.7% and 8.5 ± 0.32 log2 respectively. All pig sera tested were negative for H5 subtype antibodies. The chicken H5 subtype prevalence in central market and railway station live bird markets were 4.3% and 13% respectively. H5 subtype antibodies were present in dogs and chickens in Kaduna metropolis. There is the need for targeted surveillance of avian influenza in dogs and pigs should be incorporated in the national avian influenza surveillance program.

Spatial distribution and ecological niche modeling of geographical spread of Anopheles gambiae complex in Nigeria using real time data

The need for evidence-based data, to inform policy decisions on malaria vector control interventions in Nigeria, necessitated the establishment of mosquito surveillance sites in a few States in Nigeria. In order to make evidence-based-decisions, predictive studies using available data becomes imperative. We therefore predict the distribution of the major members of the Anopheles gambiae s.l. in Nigeria. Immature stages of Anopheles were collected from 72 study locations which span throughout the year 2020 resulted in the identification of over 60,000 Anopheline mosquitoes. Of these, 716 breeding sites were identified with the presence of one or more vector species from the An. gambiae complex and were subsequently used for modelling the potential geographical distribution of these important malaria vectors. Maximum Entropy (MaxEnt) distribution modeling was used to predict their potentially suitable vector habitats across Nigeria. A total of 23 environmental variables (19 bioclimatic and four topographic) were used in the model resulting in maps of the potential geographical distribution of three dominant vector species under current climatic conditions. Members of the An. gambiae complex dominated the collections (98%) with Anopheles stephensi, Anopheles coustani, Anopheles funestus, Anopheles moucheti, Anopheles nilli also present. An almost equal distribution of the two efficient vectors of malaria, An. gambiae and Anopheles coluzzii, were observed across the 12 states included in the survey. Anopheles gambiae and Anopheles coluzzii had almost equal, well distributed habitat suitability patterns with the latter having a slight range expansion. However, the central part of Nigeria (Abuja) and some highly elevated areas (Jos) in the savannah appear not suitable for the proliferation of these species. The most suitable habitat for Anopheles arabiensis was mainly in the South-west and North-east. The results of this study provide a baseline allowing decision makers to monitor the distribution of these species and establish a management plan for future national mosquito surveillance and control programs in Nigeria.

Reporting England's progress towards the ambitions in the UK action plan for antimicrobial resistance: the English surveillance programme for antimicrobial utilisation and resistance (ESPAUR).

The plans for a new antimicrobial utilization and resistance national surveillance programme, alongside the development of quality measures and methods to monitor unintended outcomes of antimicrobial stewardship and both public and professional behaviour interventions were published in 2013. Since then, England has published an annual surveillance report including outlining progress against the ambitions of the UK national action plans on antimicrobial resistance (2013 to 2018 and 2019 to 2024). A decade later we provide a brief update on progress so far, with a focus on key highlights from the latest report published in November 2022. We also provide our recommendations for areas of focus as we move into the next decade. From an initial focus on antibiotic consumption and resistance, the report now includes surveillance data for antifungals, antivirals (including novel agents, such as those targeting SARS-CoV-2) and antimalarials. Evaluation of key stewardship interventions including professional and public engagement initiatives are also reported, as well as progress against NHS England's (NHSE's) improvement measures.

Risk of zoonoses involving slow-growing non-tuberculous mycobacteria: Survey of antimicrobial resistance among strains from domestic and wild animals

Non-tuberculous mycobacteria are opportunistic pathogens that cause disease mainly in immunocompromised hosts. The present study assessed the prevalence of antibiotic resistance among such mycobacteria from domestic and wild animals in Croatia sampled during several years within a national surveillance program. A total of 44 isolates belonging to nine slow-growing species were genotyped and analyzed for susceptibility to 13 antimicrobials often used to treat non-tuberculous mycobacterial infections in humans. Most prevalent resistance was to moxifloxacin (77.3%), doxycycline (76.9%), and rifampicin (76.9%), followed by ciprofloxacin (65.4%), trimethoprim-sulfamethoxazole (65.4%), and linezolid (61.4%). Few isolates were resistant to rifabutin (7.7%) or amikacin (6.8%). None of the isolates was resistant to clarithromycin. Nearly all isolates (86.4%) were resistant to multiple antibiotics. Our findings suggest substantial risk that human populations may experience zoonotic infections with non-tuberculous mycobacteria that will be difficult to treat using the current generation of antibiotics. Future work should clarify how resistance emerges in wild populations of non-tuberculous mycobacteria.

Validation of a modified Care and Comfort Score and responsiveness to hip surgery in children with cerebral palsy in Gross Motor Function Classification System levels IV and V.

The purpose of this study was to assess the reliability and responsiveness to hip surgery of a four-point modified Care and Comfort Hypertonicity Questionnaire (mCCHQ) scoring tool in children with cerebral palsy (CP) in Gross Motor Function Classification System (GMFCS) levels IV and V. This was a population-based cohort study in children with CP from a national surveillance programme. Reliability was assessed from 20 caregivers who completed the mCCHQ questionnaire on two occasions three weeks apart. Test-retest reliability of the mCCHQ was calculated, and responsiveness before and after surgery for a displaced hip was evaluated in a cohort of children. Test-retest reliability for the overall mCCHQ score was good (intraclass correlation coefficient 0.78), and no dimension demonstrated poor reliability. The surgical intervention cohort comprised ten children who had preoperative and postoperative mCCHQ scores at a minimum of six months postoperatively. The mCCHQ tool demonstrated a significant improvement in overall score from preoperative assessment to six-month postoperative follow-up assessment (p < 0.001). The mCCHQ demonstrated responsiveness to intervention and good test-retest reliability. The mCCHQ is proposed as an outcome tool for use within a national surveillance programme for children with CP.

General practitioners’ perspectives regarding early developmental surveillance for autism within the australian primary healthcare setting: a qualitative study

BackgroundSignificant challenges remain in the early identification of child developmental disabilities in the community. Implementing supports and services early in the life course has been shown to promote positive developmental outcomes for children at high likelihood of developmental disabilities, including autism. As part of a cluster randomised controlled trial, this study seeks to examine and compare the perspectives and experiences of Australian general practitioners (GPs) in relation to a digital developmental surveillance program for autism and usual care pathway, in general practice clinics.MethodsA qualitative research methodology with semi-structured interviews and thematic inductive analysis underpinned by grounded theory was utilised. All GPs from South Western Sydney (NSW) and Melbourne (Victoria) who participated in the main program (“GP Surveillance for Autism”) were invited to the interview. GPs who provided consent were interviewed either over online or in-person meeting. Interviews were audio-recorded, transcribed, and coded using NVivo12 software. Inductive interpretive approach was adopted and data were analysed thematically.ResultsTwenty-three GPs across the two sites (NSW: n = 11; Victoria: n = 12) agreed to be interviewed; data saturation had reached following this number of participants. Inductive thematic coding and analysis yielded eight major themes and highlighted common enablers such as the role of GPs in early identification and subsequent supports, enhanced communication between clinicians/professionals, relationship-building with patients, and having standardised screening tools. Specific facilitators to the feasibility and acceptability of a digital screening program for the early identification of developmental disabilities, including the early signs of autism, and encouraging research and education for GPs. However, several practical and socioeconomic barriers were identified, in addition to limited knowledge and uptake of child developmental screening tools as well as COVID-19 lockdown impacts. Common and specific recommendations involve supporting GPs in developmental/paediatrics training, streamlined screening process, and funding and resources in the primary healthcare services.ConclusionsThe study highlighted the need for practice and policy changes, including further training of GPs alongside sufficient time to complete developmental checks and appropriate financial remuneration through a Medicare billing item. Further research is needed on implementation and scale up of a national surveillance program for early identification of developmental disabilities, including autism.

Vaccine use in Canadian cow-calf herds and opportunities for improvement.

Vaccinations are one of the most impactful tools available to cow-calf producers to control within herd disease and later, in feedlots. While vaccine use has been studied across Canada, inconsistent and variable regional data makes analysis and interpretation difficult. The objective of this study was to describe vaccination protocols and factors associated with vaccine use in Canadian cow-calf herds and define associations between vaccine use and productivity outcomes. Surveys describing vaccine use in 2020 were collected from 131 cow-calf herds (40 eastern, 91 western), recruited through a national beef cattle surveillance program. Ninety-two percent of cows and replacement heifers, and 72% of bulls were vaccinated with Infectious Bovine Rhinotracheitis (IBR), Bovine Viral Diarrhea Virus (BVDV), Parainfluenza3 Virus (PI3), and Bovine Respiratory Syncytial Virus (BRSV). At least half of cows and bulls were vaccinated for clostridial pathogens and cows and heifers for viral calf scours. Clostridial vaccines were significantly more likely to be used in western Canada compared to eastern Canada. While 92% of producers vaccinated suckling calves against IBR/BRSV/PI3, only 47% provided a second vaccine prior to weaning; 78% of calves were also vaccinated at least once for BVDV before weaning. Producers who vaccinated calves against IBR/BRSV/PI3 before 3 months of age provided a second dose prior to weaning more often than producers who administer the first IBR/BRSV/PI3 vaccine later. Vaccine use has increased across Canada, particularly in calves, prior to weaning. Relative to label recommendations for annual vaccination, clostridial vaccines were generally underutilized in cows and bulls, and by producers in eastern Canada as compared to western Canada. Opportunities also exist to improve adherence to label recommendations for the booster dose of scours vaccine when used in bred replacement heifers. Protocols including product choices, the timing and boosting of respiratory vaccines in nursing calves vary widely across herds. Use of intranasal vaccines in neonatal calves less than 2 weeks old has increased in western Canada compared to previous reports. There is a need to better understand how timing of vaccination in nursing calves contributes to effectiveness, for respiratory disease in nursing and weaned calves.

Comorbidities directly extracted from the hospital database for adjusting SSI risk in the new national semiautomated surveillance system in France: The SPICMI network.

To evaluate the performance of a comorbidity-based risk-adjustment model for surgical-site infection (SSI) reporting and benchmarking using a panel of variables extracted from the hospital discharge database (HDD), including comorbidities, compared to other models that use variables from different data sources. The French national surveillance program for SSI (SPICMI) has collected data from voluntary hospitals in the first 6 months of 2020 and 2021, for 16 selected surgery procedures, using a semiautomated algorithm for detection. Four risk-adjustment models were selected with logistic regression analysis, combining the different patterns of variables: National Nosocomial Infections Surveillance System (NNIS) risk-index components, individual operative data, and 6 individual comorbidities according to International Classification of Disease, Tenth Revision (ICD-10) diagnosis: obesity, diabetes, malnutrition, hypertension, cancer, or immunosuppression. Areas under the curve (AUCs) were calculated and compared. Overall, 294 SSI were detected among 11,975 procedures included. All 6 comorbidities were related to SSI in the univariate analysis. The AUC of the selected model including comorbidities (0.675; 95% confidence interval [CI], 0.642-0.707), was significantly higher than the AUC of the model without comorbidities (0.641; 95% CI, 0.609-0.672; P = .016) or the AUC using the NNIS-index components (0.598; 95% CI, 0.564-0.630; P < .001). The HDD-based model AUC (0.659; 95% CI, 0.625-0.692) did not differ significantly from the selected model without comorbidities (P = .23). Including HDD-based comorbidities as patient case-mix variables instead of NNIS risk index factors could be an effective approach for risk-adjustment of automated SSI surveillance more widely accessible to hospitals.

First Report of the Root-Knot Nematode Meloidogyne luci on Tomato in Serbia.

Root-knot nematode (RKN) Meloidogyne luci Carneiro, Correa, Almeida, Gomes, Deimi, Castagnone-Sereno, and Karssen, 2014 was described from Brazil, Chile and Iran, parasitizing in various crops (Carneiro et al. 2014). It was later also described from Slovenia, Italy, Greece, Portugal, Turkey and Guatemala (review in Gerič Stare et al. 2017). It is considered an extremely damaging pest as it has a wide host range and infects numerous higher plants, including monocotyledons and dicotyledons as well as herbaceous and woody plants. This species was included in the European Plant Protection Organisation Alert List of harmful organisms. In Europe, M. luci has been detected in both greenhouse and field agricultural production (review in Gerič Stare et al. 2017). Furthermore, M. luci has been shown to survive winter in the field under continental and sub-Mediterranean climatic conditions (Strajnar et al. 2011). In August 2021, an official survey for quarantine RKN in Serbia (Province Vojvodina) revealed in a greenhouse in the village of Lugovo (43043'32,562; 19008'55,168), near Sombor, yellowing, stunning and extensive root galls on tomato (Solanum lycopersicum L.) cultivar Diva F1 caused by an unknown Meloidogyne sp. (Fig. 1). As correct identification is essential for effective pest management program, the next step was to identify the nematode species. Morphological characterization performed on freshly isolated females revealed perineal patterns similar to M. incognita (Kofoid and White, 1919) Chitwood, 1949. The shape was oval to squarish with the dorsal arch rounded to moderately high and without shoulders. The dorsal striae were wavy and continuous. The ventral striae were smooth and the lateral lines were weakly demarcated. The perivulval region was without striae (Fig. 2). The female stylet was robust with well-developed knobs and the stylet cone slightly curved dorsally. Although morphological characters was very variable, the nematode was suspected as M. luci based on comparison with originally described M. luci and M. luci populations from Slovenia, Greece and Turkey. Identification was achieved with subsequent species-specific PCR and sequence analysis. The nematode was determined to belong to the tropical RKN group and the M. ethiopica group using two PCR reactions as described by Gerič Stare et al. (2019) (Figs. 3 and 4). Identification was confirmed by species-specific PCR of M. luci as described by Maleita et al. (2021), and a band of approximately 770 bp was obtained (Fig. 5). In addition, the identification was confirmed by sequence analyses. The region of mtDNA was amplified with primers C2F3 and 1108 (Powers and Harris 1993), cloned, sequenced (acc. no. OQ211107), and compared to other Meloidogyne spp. sequences from the Genbank. The determined sequence is 100% identical to an unidentified Meloidogyne sp. from Serbia, while the next highest scores are sequences of M. luci from Slovenia, Greece and Iran, all of which have 99.94% sequence identity. In phylogenetic tree, all M. luci sequences including the sequence from Serbia belong to a single clade. Egg masses isolated from infected tomato roots were used to establish a nematode culture in greenhouse and they caused typical root galls on cultivar Maraton of tomato. The galling index assessed 110 days-post-inoculation was in the range 4-5 according to the scoring scheme (1-10) for field evaluation of RKN infestations (Zeck 1971). To our knowledge, this is the first report of M. luci in Serbia. The authors hypothesize that climate change and higher temperatures could lead to much greater spread and damage to various agricultural crops in the field by M. luci in the future. National surveillance program for RKN in Serbia continued in 2022 and 2023. A management program to control the spread and damage from M. luci will be implemented in Serbia in 2023. Acknowledgments: This work was financially supported by the Serbian Plant Protection Directorate of MAFWM in the frame of Program of Measures in Plant Health in 2021, the Slovenian Research Agency in the frame of Research Programme Agrobiodiversity (P4-0072) and the Ministry of Agriculture, Forestry and Food of the Republic of Slovenia in the frame of Expert work in the field of plant protection (C2337).

Progress of schistosomiasis control in People's Republic of China in 2022

This report presented the endemic status of schistosomiasis and analyzed the data collected from the national schistosomiasis prevention and control system and national schistosomiasis surveillance program in the People's Republic of China in 2022. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis, Shanghai Municipality, Zhejiang Province, Fujian Province, Guangdong Province and Guangxi Zhuang Autonomous Region continued to maintain the achievements of schistosomiasis elimination, and Sichuan and Jiangsu provinces maintained the criteria of transmission interruption, while Yunnan, Hubei, Anhui, Jiangxi and Hunan provinces maintained the criteria of transmission control by the end of 2022. A total of 452 counties (cites, districts) were found to be endemic for schistosomiasis in China in 2022, with 27 434 endemic villages covering 73 424 400 people at risk of infections. Among the 452 endemic counties (cities, districts), 75.89% (343/452), 23.45% (106/452) and 0.66% (3/452) achieved the criteria of elimination, transmission interruption and transmission control of schistosomiasis, respectively. In 2022, 4 317 356 individuals received serological tests for schistosomiasis, and 62 228 were sero-positive. A total of 208 646 individuals received stool examinations for schistosomiasis, with one positive and another two cases positive for urine microscopy, and these three 3 cases were imported schistosomiasis patients from Africa. There were 28 565 cases with advanced schistosomiasis documented in China by the end of 2022. Oncomelania hupensis snail survey was performed in 18 891 endemic villages in China in 2022 and O. hupensis snails were found in 6 917 villages (36.62% of all surveyed villages), with 8 villages identified with emerging snail habitats. Snail survey was performed at an area of 655 703.01 hm2 and 183 888.60 hm2 snail habitats were found, including 110.58 hm2 emerging snail habitats and 844.35 hm2 re-emerging snail habitats. There were 477 200 bovines raised in the schistosomiasis endemic areas of China in 2022, and 113 946 bovines received serological examinations for schistosomiasis, with 204 sero-positives detected. Among the 131 715 bovines received stool examinations, no positives were identified. In 2022, there were 19 726 schistosomiasis patients receiving praziquantel chemotherapy, and expanded chemotherapy was performed in 714 465 person-time for humans and 234 737 herd-time for bovines in China. In 2022, snail control with chemical treatment was performed at an area of 119 134.07 hm2, and the actual area of chemical treatment was 65 825.27 hm2, while environmental improvements were performed at an area of 1 163.96 hm2. Data from the national schistosomiasis surveillance program of China showed that the mean prevalence of Schistosoma japonicum infections was both zero in humans and bovines in 2022, and no S. japonicum infection was detected in O. hupensis snails. These data demonstrated that the endemic status of schistosomiasis continued to decline in China in 2022, with 3 confirmed schistosomiasis patients that had a foreign nationality and all imported from Africa, and the areas of snail habitats remained high. Further improvements in the construction of the schistosomaisis surveillance and forecast system, and reinforcement of O. hupensis survey and control are required to prevent the re-emerging schistosomiasis.

Analysis of dust and noise exposure levels in the mining industry from the national surveillance program in 2019

Objective: To understand the exposure level of dust and noise in the mining industry and provide data support for revising policy for the prevention and control of occupational diseases. Methods: In May 2022, Data was collected through the National Surveillance Program for Occupational Hazards in the Workplace. Descriptive analysis was conducted for dust and noise levels by industry type and enterprise size from 7, 679 enterprises in the mining industry among 29 provincial regions nationwide. Results: The enterprises in the mining industry included in the National Surveillance Program for Occupational Hazards in the Workplace are mainly small and micro, accounting for 47.97% (3684/7679) and 30.00% (230/7679) respectively. The industry is mainly compred of employers in the non-metallic ming and beneficiation industry, accounting for 50.25% (3859/7679). Among the enterprises with silica dust, coal dust, and noise hazards, the proportion of enterprises where total dust concentration and noise intensity exceed the standard is higher than 50%. 30% of the posts are with an exposure level of silica dust, coal dust, and noise that exceeds the standard. The exceedance rate and the median of the time-weighted average concentration of total coal dust among large and medium-sized enterprises are higher than those among small and micro-sized enterprises (P<0.05) . Conclusion: The dust and noise hazards in the mining industry are lower than in the past in China, but more than 25% of workers are still at a high risk of occupational pneumoconiosis and noise deafness. Therefore, intervention and surveillance strategies should be strengthened in the future.

A critical view on the current use of daptomycin in Spain: The daptomise study

BackgroundThe Study on the Clinical Use of DAPTOMycin in Spain (DAPTOMISE Study) is a national surveillance program of daptomycin use. The objectives of this study are to evaluate the current variability in daptomycin consumption across the different hospitals and the adequacy of therapy, specially focused on underdosing. MethodsAll adult and pediatric patients who received, at least, one dose of daptomycin in a single week in 98 institutions in Spain were included. The adequacy of daptomycin use was evaluated with respect to the indication, dosage, adjustments after microbiology results, switching to an oral agent and length of treatment. ResultsA total of 615 patients received daptomycin during the study week. The prevalence use was 2.3 patients / 100,000 inhabitants per week, 12.4 patients / 1000 admissions and 9.2 Days of Therapy (DOT) / 1000 hospital stays. These rates varied between hospitals: from 0 to 13.9 patients / 100,000 inhabitants, from 0 to 76.1 patients / 1000 admissions and from 0 to 49.4 DOT / 1000 hospital stays. The most frequent infections were bacteremia (31.6 %) and skin and soft tissue infections (17.9 %). Microbiological results were available in only 65.4 % of infections. The most frequent microorganisms were Staphylococcus aureus (192 isolates, of which 87 were resistant to methicillin) and coagulase-negative staphylococci (124 isolates). A total of 136 prescriptions (22.1 %) were underdosed. Dosages < 8 mg/kg were used for 35.6 % of endovascular infections and for 26.2 % of osteoarticular infections. Overall, 57.2 % of prescriptions were not optimal in, at least, one item. Clinical cure rate was 76.1% and mortality attributable to the infection 8.1%. ConclusionThis is the first registry that identifies the prevalence of use of daptomycin in Spain and shows a high variability in the consumption between the different hospitals. Daptomycin underdosing was present in more than 20 % of cases.

A SARS-CoV-2 variant of C-36 lineage with L452R mutation infects a family in Sri Lanka, but has limited spread – A Case Series

We report a family cluster of six members who tested positive for SARS-CoV-2 infection in April 2021 at University Hospital, Kotelawala Defence University, Sri Lanka. Samples from three members were subjected to Next Generation Sequencing (NGS) and all were identified as SARS-CoV-2 variant of pangolin lineage C.36, containing the L452R mutation which is associated with high infectivity. All patients recovered with mild symptoms and no complications. This is the first report identifying a new variant of the C.36 lineage containing the L452R mutation from Sri Lanka followed by detection of the same lineage from Northern Sri Lanka in June 2021 and no reported cases hereafter. At that time, it was relatively rare for a whole family to get infected, and the concern was that this strain would spread rapidly. Due to unknown circumstances it never spread to be detected by the national surveillance programme. Other variants, B.1.411 and B.1.1.7, more dominant and infectious, were already in circulation and presumably outcompeted this strain.

Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018.

Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized. We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE. The phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling. Recombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.

Epidemiology of measles in Angola: Results from routine surveillance from 2015 to 2021

Measles, an acute infectious disease of extremely contagious viral aetiology, has been eliminated in some parts of the world. To the best of the authors' knowledge, this is the first study on the epidemiological pattern of the measles virus in Angola, and it was carried out through a review of 7 years of observational retrospective data from the national measles laboratory surveillance programme. A retrospective study using national databases on the laboratory surveillance of measles was performed. Patients of all ages with suspected measles from all provinces of Angola were included. Serum samples were used to detect IgM-type measles-virus-specific antibodies by enzyme-linked immunosorbent assay. In total, 3690 suspected measles samples were sent to the Instituto Nacional de Investigação em Saúde. There were 962 (26.1%) laboratory-confirmed cases, and the most affected age group was children aged 1-4 years. The highest incidence rate per 100,000 population was found in Benguela (17.9%), followed by Huambo (16.7%) and Cuanza Sul (13.6%). Of the study years, the incidence rate per 1,000,000 population was highest in 2020 (11.9%). The most common complication was diarrhoea (n=406, 42.2%). Of the confirmed cases, 209 (21.7%) were vaccinated, 633 (65.8%) were unvaccinated, and 120 (12.5%) had unknown vaccination status. For all study years, vaccination coverage was <70%. Measles continues to be a serious problem in Angola, and more efforts are needed to increase measles surveillance and achieve a high percentage of vaccination coverage.

Whole-genome sequencing of Shigella for surveillance purposes shows (inter)national relatedness and multidrug resistance in isolates from men who have sex with men.

In the Netherlands, more than half of domestic shigellosis cases are among men who have sex with men (MSM), particularly in the Amsterdam region. However, there is limited insight into which Shigella strains circulate in the Netherlands. Our objective was to assess the added value of whole-genome sequencing (WGS)-based surveillance for Shigella. To this end, we determined the relatedness among Shigella spp. isolates from patients in the Amsterdam region, as well as in an international context, including antimicrobial resistance markers, using WGS. The following criteria were used: it should provide insight into (1) clustering of shigellosis cases and the affected population, (2) the extent of admixture of MSM-associated isolates with those from the broader population and (3) the presence of antimicrobial resistance. It should then lead to more opportunities for targeted control measures. For this study, Shigella isolates from three laboratories in the Amsterdam region obtained between February 2019 and October 2021 were subjected to Illumina WGS at the National Institute for Public Health and the Environment (RIVM). Raw data were quality-checked and assembled, the Shigella serotype was determined with ShigaTyper, and antimicrobial resistance markers were detected using ResFinder and PointFinder. For Shigella sonnei, subclades were determined using Mykrobe. Relatedness of isolates, including 21 international reference genomes, was assessed with core genome multilocus sequence typing. In total, 109 isolates were included, of which 27 were from females (25 %) and 66 were from males (61 %), with which the majority (n=48, 73 %) being from MSM. No information on sex was available for the remaining 16 cases. The WGS data for all isolates, comprising 55 S. sonnei, 52 Shigella flexneri, 1 Shigella boydii and 1 Shigella dysenteriae, met the quality criteria. In total, 14 clusters containing 51 isolates (49 %) were identified, with a median cluster size of 2.5 cases (range: 2-15). Nine out of 14 clusters were MSM-associated, and 8 clusters (57 %) were travel-related. Six of the MSM clusters were related to international reference genomes. The prevalence of antimicrobial resistance markers was higher among isolates from MSM than non-MSM patients, particularly for ciprofloxacin (89 vs 33 %) and azithromycin (58 vs 17 %). In conclusion, about half of Shigella spp. patients were part of a cluster, of which a substantial part were related to international reference genomes, particularly among MSM, and a high prevalence of antimicrobial resistance markers was found. These findings indicate widespread international circulation of Shigella spp., particularly among MSM, with multidrug resistance that hampers treatment of patients. Moreover, the results of this study led to the implementation of a national WGS-based laboratory surveillance programme for Shigella spp. that started in April 2022.

Whole-Genome Sequencing-Based Characterization of Clinical Listeria monocytogenes Isolates in China, 2013-2019.

Invasive listeriosis is a rare but serious foodborne disease that causes maternal-neonatal, central nervous system, and bloodstream infections. The aim of this study was to assess the whole-genome sequencing (WGS)-based genetic diversity of clinical Listeria monocytogenes isolates over a 7-year period and prove the effect of WGS application in food vehicle investigation. A total of 360 isolates were recovered during 2013 and 2019 through the national listeriosis special surveillance program. Two hundred twenty-six isolates (62.8%) were associated with pregnancy. All isolates belonged to lineage I (214 isolates) or lineage II (146 isolates), with 4 serogroups (46.9% IIb, 39.7% IIa, 12.5% IVb, and 0.8% IIc). All isolates were in 25 clonal complexes (CCs) and 3 singletons, with CC87, CC8, and CC5 being the most common causes of human listeriosis. All clinical isolates were positive for Listeria pathogenicity island 1 (LIPI-1), LIPI-3 was present in 21.4% of isolates and LIPI-4 was detected in 29.2% of isolates. LIPI-4-positive isolates, including CC87, sequence type (ST)619, ST382, CC4, and CC2, have been shown to confer hypervirulence. Fifteen isolates harbored at least one antimicrobial encoding gene, including tet (M), mef (A), msr (D), and dfr (G). The sublineage designations were consistent with CC designations, and 215 distinct cgMLST types (CTs) were classified, the most abundant being CT58 and CT750. In summary, there is a high level of genetic diversity among the clinical isolates. WGS has strengthened listeriosis surveillance and will be implemented for other foodborne bacteria in the National Molecular Tracing Network for Foodborne Disease.