National Laboratory-based Surveillance Research Articles

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.

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.

An assessment of the public health surveillance strategy based on molecular testing during three major pandemic waves of COVID-19 in Brazil.

A national laboratory-based surveillance system was adapted to monitor the situation of SARS-CoV-2 in Brazil. The objective of the study was to compare the challenges in implementing COVID-19 surveillance strategies based on the Ministry of Health's (MoH) distribution of RT-PCR tests to different types of laboratories. This retrospective study analyzed the MoH's testing policies and distribution of RT-PCR tests to laboratories during the first, second, and third waves. Recipient laboratories were divided into groups: public health laboratories that belonged to the national network of public health laboratories (Group 1); public laboratories granted authorization during the pandemic (Group 2); and High-Capacity Testing Centers (Group 3). We analyzed the timing and duration of COVID-19 testing policies and the allocation of tests to laboratories by group and wave. Using t-tests, we analyzed the difference in the weekly average of tests distributed to labs by group and using Pearson's correlation coefficient, analyzed the test distribution according to infection and death rates. Between epiweek 9, 2020, and epiweek 22, 2022, the MoH distributed an average of 263,004 RT-PCR tests per week. The weekly average of tests distributed was highest in the second wave (310,327 tests), followed by the first (218,005 tests) and third waves (201,226 tests). There was a significant increase in the mean weekly tests distributed in the second wave compared to the first and third waves (p = 0.047; IC 8.29-1110.71). We found a significant difference between the weekly average of tests distributed in the first and second wave (p < 0.001; IC -209.83-76.20) to Group 2. Group 3 received the second-highest number of tests from the MoH overall, with a reduction during the third wave to first-wave levels. The distribution of RT-PCR tests was not correlated with the case and death incidence.

Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi.

The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi (Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one (n=11 isolates), cluster two (n=13 isolates), and cluster three (n=14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B, catA1, sul1, sul2, dfrA7). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.

Increase in Acute Respiratory Illnesses Among Children and Adolescents Associated with Rhinoviruses and Enteroviruses, Including Enterovirus D68 - United States, July-September 2022.

Increases in severe respiratory illness and acute flaccid myelitis (AFM) among children and adolescents resulting from enterovirus D68 (EV-D68) infections occurred biennially in the United States during 2014, 2016, and 2018, primarily in late summer and fall. Although EV-D68 annual trends are not fully understood, EV-D68 levels were lower than expected in 2020, potentially because of implementation of COVID-19 mitigation measures (e.g., wearing face masks, enhanced hand hygiene, and physical distancing) (1). In August 2022, clinicians in several geographic areas notified CDC of an increase in hospitalizations of pediatric patients with severe respiratory illness and positive rhinovirus/enterovirus (RV/EV) test results.* Surveillance data were analyzed from multiple national data sources to characterize reported trends in acute respiratory illness (ARI), asthma/reactive airway disease (RAD) exacerbations, and the percentage of positive RV/EV and EV-D68 test results during 2022 compared with previous years. These data demonstrated an increase in emergency department (ED) visits by children and adolescents with ARI and asthma/RAD in late summer 2022. The percentage of positive RV/EV test results in national laboratory-based surveillance and the percentage of positive EV-D68 test results in pediatric sentinel surveillance also increased during this time. Previous increases in EV-D68 respiratory illness have led to substantial resource demands in some hospitals and have also coincided with increases in cases of AFM (2), a rare but serious neurologic disease affecting the spinal cord. Therefore, clinicians should consider AFM in patients with acute flaccid limb weakness, especially after respiratory illness or fever, and ensure prompt hospitalization and referral to specialty care for such cases. Clinicians should also test for poliovirus infection in patients suspected of having AFM because of the clinical similarity to acute flaccid paralysis caused by poliovirus. Ongoing surveillance for EV-D68 is critical to ensuring preparedness for possible future increases in ARI and AFM.

S8.1b Is a search and destroy strategy still feasible for Candida auris in South Africa?

S8.1 Tackling Candida auris in resource-limited settings, September 23, 2022, 3:00 PM - 4:30 PM Candida auris was prospectively detected as a healthcare-associated pathogen in South Africa in 2014. However, a retrospective review of a culture collection from national laboratory-based surveillance for Candidaemia in 2009-10 showed that earlier cases had been missed owing to species misidentification. National surveillance, which was repeated during 2016-17, revealed that C. auris caused >10% of cases of Candidaemia in South Africa, with most (86%) cases detected in the Gauteng Province. We recommended all hospitals to passively monitor cases of C. auris disease and colonization by each maintaining a line list of culture-confirmed cases. Facilities were thus classified into three tiers. Tier 1 (‘green status’) included facilities with no prior known cases. Such facilities were requested to report their first cases for urgent intervention. This included active colonization surveys, isolation and/or cohorts of infected or colonized patients as well as intensified infection prevention and control and antifungal stewardship activities. Tier 2 (‘orange status’) included facilities with sporadic cases defined arbitrarily as fewer than 12 cases in the past 6 months and/or fewer than three units affected. Such facilities were requested to report any increase in the number of cases compared with a baseline, clinical units affected for the first time, or apparent case clustering within the facility for investigation. Tier 3 (‘red status’) included facilities with a relative endemicity defined as >12 cases and/or >3 units with cases in the last 6 months. Tier 3 facilities were only requested to report increases over a baseline or apparent clustering within the facility. Owing to limited resources, colonization screening of newly-admitted patients was not recommended in acute-care facilities in South Africa. During 2019-21, the proportion attributable to C. auris increased even further to 25% (of 12 959 national cases of Candidaemia), with a concomitant reduction in cases caused by C. parapsilosis. This suggested a concerning replacement of multidrug-resistant C. auris in an ecological healthcare niche previously occupied by azole-resistant C. parapsilosis. An epidemiological shift was also observed with an expanding number of acute healthcare facilities outside Gauteng Province reporting C. auris and large persistent healthcare-associated infection outbreaks in neonatal units, particularly in the under-resourced public health sector.

Acinetobacter baumannii complex, national laboratory-based surveillance in South Africa, 2017 to 2019.

ObjectiveWe aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa.Materials and methodsABC surveillance was conducted from 1 April 2017 to 30 September 2019 at 19 hospital sites from blood cultures of any age and sex. Organism identification was performed using the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for whole-genome sequencing.ResultsDuring the study period, we identified 4822 cases of ABC, of which 2152 cases were from 19 enhanced surveillance sites were reported during the enhanced surveillance period (1 August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR), with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmid- and chromosomal- mediated were not observed. Although all isolates had, nine efflux pump genes related to antimicrobial resistance.ConclusionOur surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates were resistant to colistin.

The association between area deprivation and COVID-19 incidence: a municipality-level spatio-temporal study in Belgium, 2020\u20132021

BackgroundIn Belgium, current research on socio-economic inequalities in the coronavirus disease 2019 (COVID-19) crisis has mainly focused on excess mortality and data from the first epidemiological wave. The current study adds onto this by examining the association between COVID-19 incidence and area deprivation during the first five wave and interwave periods, thus adding a temporal gradient to the analyses.MethodsWe use all confirmed COVID-19 cases between March 2020 and June 2021 in Belgium, aggregated at the municipality-level. These data were collected by the national laboratory-based COVID-19 surveillance system. A level of area deprivation was assigned to each Belgian municipality using data of three socio-economic variables: the share of unemployed persons in the active population, the share of households without a car and the share of low-educated persons. The spatio-temporal association between COVID-19 incidence and area deprivation was assessed by performing multivariate negative-binomial regression analyses and computing population attributable fractions.ResultsA significant association between COVID-19 incidence and area deprivation was found over the entire study period, with the incidence in the most deprived areas predicted to be 24% higher than in the least deprived areas. This effect was dependent on the period during the COVID-19 crisis. The largest socio-economic inequalities in COVID-19 infections could be observed during wave 2 and wave 3, with a clear disadvantage for deprived areas.ConclusionOur results provide new insights into spatio-temporal patterns of socio-economic inequalities in COVID-19 incidence in Belgium. They reveal the existence of inequalities and a shift of these patterns over time.

1333. A National Outbreak of Respiratory Syncytial Virus Associated with Emergence of a Genetically Distinct ON1 variant

BackgroundA national outbreak of respiratory syncytial virus (RSV) has been observed in the community since Fall 2020 in Taiwan.MethodsWe reviewed a national laboratory-based surveillance network established over 20 years by Taiwan Centers for Disease Control (TCDC) for respiratory viral positivity rate and viral pathogen in outpatient department and hospitalized patients. A retrospective study of children younger than 5 years old hospitalized with RSV infections at Chang Gung Memorial Hospital (CGMH) including Lin Kou and Kaohsiung branch between 2018 and 2020 was conducted. Samples positive for RSV A were sequenced. Patients’ clinical data was obtained from medical files and stratified by genotype and year.Results2020 showed a 4-fold surge in RSV cases in Taiwan, in which surpassed both 2011 (the appearance of ON1 strain in Taiwan) and 2013 (ON1 strain predominates in Taiwan)(Figure1,Table1). Phylogenetic analysis of G protein sequences showed that most strains in 2020 were clustered apart from 2018, 2019 seasons and other ON1 reference strains between 2011 and 2016, indicating a novel ON1 variant had been circulating in the community(Figure2). The novel ON1 variants carried six amino acid changes, of which T113I,V131D, H258Q,H266L,Y304H located in the mucin domains and N178G in central conserved domain. These changes emerged gradually in 2019 and showed a high consistency in 2020. The unique amino acid substitution E257K in the second mucin domain was noticed in 2020 exclusively. Besides, 10 substitutes in F protein were appeared between 2018 and 2020, of which R213S and N276S were in antigenic sites. Furthermore, substitutes T12I and H514N in F protein were first emerged since 2020. On multivariate analysis, age (OR 0.97; 95% CI 0.94-0.99; p 0.02) and ON1 variant in 2020 (OR 2.52; 95% CI 1.13-5.63; p 0.025) were independently associated with oxygen saturation < 94% during hospitalization (Table 2). Figure 2. The phylogenetic tree of G protein sequences including ON1 strains in our study from 2018 to 2020 and reference strains from 2011 to 2016 The phylogenetic tree showed that most strains of the 2020 season clustered apart from those of the previous seasons, which indicated there was a novel ON1 variant circulating in the community associated with 2020 RSV epidemic. Variables with p<0.1 in the univariate analysis were included in the multivariate analysis.ConclusionAn unprecedented RSV epidemic within the last 10 years caused by a novel ON1 variant has occurred in 2020 (Figure 1), suggesting the sets of mutations may confer fitness advantage. Further studies on viral replication, infectivity and virulence is needed to understand the evolution and spread of RSV. Disclosures All Authors: No reported disclosures

One year of laboratory-based COVID-19 surveillance system in Belgium: main indicators and performance of the laboratories (March 2020\u201321)

BackgroundWith the spread of coronavirus disease 2019 (COVID-19), an existing national laboratory-based surveillance system was adapted to daily monitor the epidemiological situation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the Belgium by following the number of confirmed SARS-CoV-2 infections, the number of performed tests and the positivity ratio. We present these main indicators of the surveillance over a one-year period as well as the impact of the performance of the laboratories, regarding speed of processing the samples and reporting results, for surveillance.MethodsWe describe the evolution of test capacity, testing strategy and the data collection methods during the first year of the epidemic in Belgium.ResultsBetween the 1st of March 2020 and the 28th of February 2021, 9,487,470 tests and 773,078 COVID-19 laboratory confirmed cases were reported. Two epidemic waves occurred, with a peak in April and October 2020. The capacity and performance of the laboratories improved continuously during 2020 resulting in a high level performance. Since the end of November 2020 90 to 95% of the test results are reported at the latest the day after sampling was performed.ConclusionsThanks to the effort of all laboratories a performant exhaustive national laboratory-based surveillance system to monitor the epidemiological situation of SARS-CoV-2 was set up in Belgium in 2020. On top of expanding the number of laboratories performing diagnostics and significantly increasing the test capacity in Belgium, turnaround times between sampling and testing as well as reporting were optimized over the first year of this pandemic.

Genome-Enabled Molecular Subtyping and Serotyping for Shiga Toxin-Producing Escherichia coli

Foodborne pathogens are a major public health burden in the United States, leading to 9.4 million illnesses annually. Since 1996, a national laboratory-based surveillance program, PulseNet, has used molecular subtyping and serotyping methods with the aim to reduce the burden of foodborne illness through early detection of emerging outbreaks. PulseNet affiliated laboratories have used pulsed-field gel electrophoresis (PFGE) and immunoassays to subtype and serotype bacterial isolates. Widespread use of serotyping and PFGE for foodborne illness surveillance over the years has resulted in the accumulation of a wealth of routine surveillance and outbreak epidemiological data. This valuable source of data has been used to understand seasonal frequency, geographic distribution, demographic information, exposure information, disease severity, and source of foodborne isolates. In 2019, PulseNet adopted whole genome sequencing (WGS) at a national scale to replace PFGE with higher-resolution methods such as the core genome multilocus sequence typing. Consequently, PulseNet's recent shift to genome-based subtyping methods has rendered the vast collection of historic surveillance data associated with serogroups and PFGE patterns potentially unusable. The goal of this study was to develop a bioinformatics method to associate the WGS data that are currently used by PulseNet for bacterial pathogen subtyping to previously characterized serogroup and PFGE patterns. Previous efforts to associate WGS to PFGE patterns relied on predicting DNA molecular weight based on restriction site analysis. However, these approaches failed owing to the non-uniform usage of genomic restriction sites by PFGE restriction enzymes. We developed a machine learning approach to classify isolates to their most probable serogroup and PFGE pattern, based on comparisons of genomic k-mer signatures. We applied our WGS classification method to 5,970 Shiga toxin-producing Escherichia coli (STEC) isolates collected as part of PulseNet's routine foodborne surveillance activities between 2003 and 2018. Our machine learning classifier is able to associate STEC WGS to higher-level serogroups with very high accuracy and lower-level PFGE patterns with somewhat lower accuracy. Taken together, these classifications support the ability of public health investigators to associate currently generated WGS data with historical epidemiological knowledge linked to serogroups and PFGE patterns in support of outbreak surveillance for food safety and public health.

Unprecedented Outbreak of Respiratory Syncytial Virus in Taiwan Associated with ON1 Variant Emergence between 2010 and 2020

Background: A national outbreak of respiratory syncytial virus (RSV) has been observed in the community since August 2020 in Taiwan even under strict COVID-19 related public health measures.Methods: We reviewed a national laboratory-based surveillance network established by Taiwan Centers for Disease Control for respiratory viral pathogens between 2010 and 2020. A retrospective study of 257 children Findings: National data from 2020 showed an enormous increase in RSV case numbers. The RSV positivity rate in 2020 had an approximately 4-fold surge compared to 2010 in Taiwan (OR 3.79; 95% CI, 3.06–4.69; p Interpretation: The unprecedented 2020 RSV epidemic caused by novel ON1 variants suggests that the mutations may confer a fitness advantage over other genotypes. Further studies on viral replication, antigenic changes, and virulence are required.Funding: This work was supported by the Chang Gung Memorial Hospital in Taiwan [Grant CMRPG3K1011 and CMRPG3K1141 ]; Ministry of Science Technology in Taiwan [MOST 108-2314-B-182A-156-MY3]; China Medical University, Taiwan [Grant CMU 108-S-23, CMU109-MF-111]Declaration of Interests: No potential conflict of interest was reported by the authors.Ethics Approval Statement: This study was approved by the Research and Ethics Committee of Chang Gung Memorial Hospital (IRB:202100450B0, 202100569A3).

In Vitro Antifungal Resistance of Candida auris Isolates from Bloodstream Infections, South Africa.

Candida auris is a multidrug-resistant fungal pathogen that is endemic in South African hospitals. We tested bloodstream C. auris isolates that were submitted to a reference laboratory for national laboratory-based surveillance for candidemia in 2016 and 2017. We confirmed the species identification by phenotypic/molecular methods. We tested susceptibility to amphotericin B, anidulafungin, caspofungin, micafungin, itraconazole, posaconazole, voriconazole, fluconazole, and flucytosine using broth microdilution and Etest methods. We interpreted MICs using tentative breakpoints. We sequenced the genomes of a subset of isolates and compared them to the C. auris B8441 reference strain. Of 400 C. auris isolates, 361 (90%) were resistant to at least one antifungal agent, 339 (94%) to fluconazole alone (MICs of ≥32 µg/ml), 19 (6%) to fluconazole and amphotericin B (MICs of ≥2 µg/ml), and 1 (0.3%) to amphotericin B alone. Two (0.5%) isolates from a single patient were pan-resistant (resistant to fluconazole, amphotericin B, and echinocandins). Of 92 isolates selected for whole-genome sequencing, 77 clustered in clade III, including the pan-resistant isolates, 13 in clade I, and 2 in clade IV. Eighty-four of the isolates (91%) were resistant to at least one antifungal agent; both resistant and susceptible isolates had mutations. The common substitutions identified across the different clades were VF125AL, Y132F, K177R, N335S, and E343D in ERG11; N647T in MRR1; A651P, A657V, and S195G in TAC1b; S639P in FKS1HP1; and S58T in ERG3. Most South African C. auris isolates were resistant to azoles, although resistance to polyenes and echinocandins was less common. We observed mutations in resistance genes even in phenotypically susceptible isolates.

Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates

ABSTRACT In South Africa, Candida auris was the third most common cause of candidemia in 2016–2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hospitals and a colonization study during a neonatal unit outbreak. The first known South African C. auris strain from 2009 clustered in clade IV. Overall, 98 strains clustered within clade III (85%), 14 within clade I (12%) and three within clade IV (3%). All environmental and colonizing strains clustered in clade III. We also identified known clade-specific resistance mutations in the ERG11 and FKS1 genes. Identification of clade I strains between 2016 and 2018 suggests introductions from South Asia followed by local transmission. SNP analysis characterized most C. auris strains into clade III, the clade first reported from South Africa, but the presence of clades I and IV strains also suggest early introductions from other regions.

Patterns of resistance to antimicrobials in serovars of Salmonella enterica in Peru, 2012-2015

Salmonellosis is a universal zoonosis, causing frequent outbreaks of foodborne illness; Salmonella enterica is the species with the highest prevalence, a progressive increase in its resistance to antimicrobials is described. To determine the frequency of serovars and antimicrobial resistance patterns in S. enterica isolates submitted to the National Institute of Health, Lima, Peru. This is a cross-sectional study. All strains referred as part of national laboratory-based surveillance between 2012 and 2015 were included in the study. Strains were confirmed by conventional tests and serotyped by the Kauffmann-White scheme; antimicrobial susceptibility and confirmation of the BLEE phenotype was performed according to the method of Kirby-Bauer and Jarlier's method. A total of 540 strains of S. enterica were included in the study, where 96% (520/540) corresponded to human strains and 4% (20/540) to non-human strains (birds, food and environmental). In human samples, the most frequent serovar was S. Infantis (57%), followed by S. Enteritidis (27%) and S. Typhimurium (6%). High resistance to nitrofurantoin (74%), nalidixic acid (64%), ciprofloxacin (63%), tetracycline (63%), ampicillin (56%), sulfamethoxazole-trimethoprim (56%), cefotaxime (53%) and chloramphenicol (50%) was detected. In non-human samples, the most frequent serotype was S. Infantis (45%), followed by S. Typhimurium (40%) and S. Enteritidis (10%); a high resistance to nalidixic acid (55%), ciprofloxacin (45%), sulfamethoxazole-trimethoprim (40%), nitrofurantoin (40%), tetracycline (40%) was found. 65% of all strains had resistance to more than two antibiotics, 43,3% were ESBL producers and 99% of these had resistance between six and eight antibiotics. We found a high frequency of S. Infantis producing ESBL with multi-resistance to the antimicrobials in human and nonhuman samples received by the National Institute of Health.

Dynamic changes in paediatric invasive pneumococcal disease after sequential switches of conjugate vaccine in Belgium: a national retrospective observational study

Ten-valent and 13-valent pneumococcal conjugate vaccines (PCVs) have shown important benefits by decreasing invasive pneumococcal disease caused by vaccine serotypes. Belgium had an uncommon situation with sequential use of PCV7, PCV13, and PCV10 in the childhood vaccination programmes between 2007 and 2018. We aimed to analyse the changes in incidence of invasive pneumococcal disease and serotype distribution in children throughout this period. Streptococcus pneumoniae isolates were obtained from patients with invasive pneumococcal disease in Belgium between 2007 and 2018 by the national laboratory-based surveillance. Paediatric invasive pneumococcal disease incidence, serotype distribution, and antimicrobial susceptibility were analysed in periods during which PCV7 (2009-10), PCV13 (2013-14), both PCV13 and PCV10 (2015-16), and PCV10 (2017-18) were used. Incidence rates and trends were compared. Vaccination status was collected. For a subset of serotype 19A isolates, multilocus sequence type was identified. After a decrease in PCV7 serotype invasive pneumococcal disease was observed during the PCV7 period, total paediatric invasive pneumococcal disease incidence significantly declined during the PCV13 period (-2·6% monthly, p<0·0001). During the PCV13-PCV10 period (2015-16), the lowest mean in paediatric invasive pneumococcal disease incidence was achieved, but the incidence increased again during the PCV10 period (2017-18), especially in children younger than 2 years (+1·7% monthly; p=0·028). This increase was mainly due to a significant rise in serotype 19A invasive pneumococcal disease incidence in the PCV10 period compared with the PCV13 period (p<0·0001), making serotype 19A the predominant serotype in paediatric invasive pneumococcal disease in the PCV10 period. Genetic diversity within the 2017-18 serotype 19A collection was seen, with two predominant clones, ST416 and ST994, that were infrequently observed before PCV10 introduction. In 2018, among children younger than 5 years with invasive pneumococcal disease who were correctly vaccinated, 37% (37 of 100) had PCV13 serotype invasive pneumococcal disease, all caused by serotype 19A and serotype 3. After a significant decrease during the PCV13 period, paediatric invasive pneumococcal disease incidence increased again during the PCV10 period. This observation mainly resulted from a significant increase of serotype 19A cases. During the PCV10 period, dominant serotype 19A clones differed from those detected during previous vaccine periods. Whether changes in epidemiology resulted from the vaccine switch or also from natural evolution remains to be further elucidated. The Belgian National Reference is funded by the Belgian National Institute for Health and Disability Insurance and the whole genome sequencing by an investigator-initiated research grant from Pfizer.

Contribution of Enteroviruses to Acute Central Nervous System or Systemic Infections in Northern Italy (2015-2017): Is It Time to Establish a National Laboratory-Based Surveillance System?

Background Enteroviruses (EVs) can cause infections and outbreaks of mild to severe diseases, such as central nervous system (CNS) and systemic infections. The contribution of EVs to acute CNS/systemic infections requiring hospitalization was assessed by analysing data extracted from virology laboratory database. Methods Real-life data obtained from two molecular virology laboratories located in Northern Italy were retrieved from databases and analysed retrospectively. The queries used to extract the data were (i) requests for EV-RNA detection in clear cerebrospinal fluid (CSF) specimens collected from hospitalized patients with suspected acute CNS (including aseptic meningitis, encephalitis, and acute flaccid myelitis/paralysis) or systemic infections (sepsis-like illness or fever (≥ 38°C) of unknown origin), (ii) CSF samples collected from January 1st, 2015, to December 31st, 2017. Results 582 requests of EV-RNA detection in CSF samples collected from as many patients of any age were recorded. EV-RNA was detected in 4.5% of the CSF samples; 92.3% of EV-positive cases were patients < 15 years, 58.3% of whom were < 3 months. EVs circulated all-year-round, and the highest EV-positive rates were observed from May to August. The risk of EV infection and the relative illness ratio value among children < 1 − year − old were significantly higher than those observed for older patients. Conclusions EV surveillance should be carried out for all pediatric patients < 15 years and especially children less than 1 year of age with clinically suspected CNS infection/systemic infections. The implementation of a laboratory-based surveillance established for analysing the virological data provided by laboratories that routinely perform EV molecular testing may enable us to determine the impact of EVs that can cause infections requiring hospitalization.

Epidemiologic Shift in Candidemia Driven by Candida auris, South Africa, 2016–20171

Abstract Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national laboratory-based surveillance in South Africa during 2016–2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris. The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2–86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 [95% CI 0.8–2.3]). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non–C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.

Epidemiologic Shift in Candidemia Driven by Candida auris, South Africa, 2016-20171.

Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national laboratory-based surveillance in South Africa during 2016–2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris. The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2–86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 [95% CI 0.8–2.3]). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non–C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.

Antimicrobial resistance trends in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis urinary isolates from Switzerland: retrospective analysis of data from a national surveillance network over an 8-year period (2009-2016).

We analysed data from routinely collected Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis urinary samples from community and hospital settings in Switzerland. The data were collected by ANRESIS, the national laboratory-based antimicrobial resistance surveillance system. Our analyses focused on resistance to antibiotics commonly prescribed for UTIs for the period 2009&ndash;2016. Only the first isolate per patient per year was included. 297,200 urinary samples were included in the analysis, of which 246,656 (83.0%) were E. coli isolates. Overall, E. coli showed high susceptibility to 3rd/4th-generation cephalosporins, nitrofurantoin and fosfomycin, with the annual proportions of resistant isolates &lt;6%, &lt;5% and &lt;2%, respectively, for all study years. Resistance to fluoroquinolones was &gt;14% and increased over time (from 14.5% in 2009 to 19.3% in 2016). Resistance to cotrimoxazole was &gt;20% for the whole study period. K. pneumoniae (n = 32,757; 11.0%) showed low resistance to cotrimoxazole and quinolones (&lt;11% and &lt;12%, respectively), while for P. mirabilis (n = 17,787; 6.0%) the proportion of resistant isolates was &lt;35% for cotrimoxazole and &lt;18% for quinolones. Even though quinolone resistance remained low for both pathogens (&lt;12% for K. pneumoniae and &lt;18% for P. mirabilis), it increased significantly over time. Proportions of isolates resistant to 3rd/4th generation cephalosporins remained low (&lt;5% for K. pneumoniae and &lt;2% for P. mirabilis), but in the case of K. pneumoniae they increased over time. Swiss surveillance data confirm that resistance among uropathogenic E. coli isolates to nitrofurantoin and fosfomycin remains low. While resistance to 3rd/4th-generation cephalosporins also remains relatively low, it has been increasing and needs further surveillance. As for K. pneumoniae and P. mirabilis, high levels of susceptibility to 3rd-generation cephalosporins and quinolones were confirmed, while high prevalences of resistance to nitrofurantoin and fosfomycin discourage their use as first-line therapies for these pathogens. &nbsp.