Browsing by Author "Savicka, Oksana"

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    Circulation and Codetections of Influenza Virus, SARS-CoV-2, Respiratory Syncytial Virus, Rhinovirus, Adenovirus, Bocavirus, and Other Respiratory Viruses During 2022-2023 Season in Latvia
    (2024-10) Kampenusa, Inara; Niedre-Otomere, Baiba; Trofimova, Julija; Pole, Ilva; Pakarna, Gatis; Savicka, Oksana; Nikisins, Sergejs; Department of Infectology
    This retrospective study analysed the routine data obtained by multiplex real-time RT-qPCR methods for respiratory virus detection. A total of 4814 respiratory specimens collected during 1 September 2022-31 August 2023 were included in the study. A total of 38% of the specimens were positive for at least one target, with the incidence maximum (82%) for the small children (age group 0-4 years). The five dominant virus groups were rhinovirus (RV, 12%), influenza virus A (IAV, 7%), adenovirus (AdV, 6%), respiratory syncytial virus (RSV, 5%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 5%). The specimens with multi-detections represented 19% of the positives, unevenly distributed (n = 225, 56, 43, 24) among the age groups 0-4, 5-14, 15-64, and 65< years, respectively. The dominant virus groups in multi-positive specimens were RV (53%), AdV (43%), and bocavirus (BoV, 35%)-in mutual pairs as well as all three together-followed by RSV (21%), and IAV (15%). Our study focused on the specimens with codetections and provides an insight into the variety of the respiratory virus interactions in Latvia during the first year since pandemic-related social restriction measures were eased. The observations also emphasise the need to consider the differentiation between rhinoviruses and enteroviruses, especially for the youngest patients in the age group 0-4.
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    First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity
    (2021) Zrelovs, Nikita; Ustinova, Monta; Silamikelis, Ivars; Birzniece, Liga; Megnis, Kaspars; Rovite, Vita; Freimane, Lauma; Silamikele, Laila; Ansone, Laura; Pjalkovskis, Janis; Fridmanis, Davids; Vilne, Baiba; Priedite, Marta; Caica, Anastasija; Gavars, Mikus; Perminov, Dmitry; Storozenko, Jelena; Savicka, Oksana; Dimina, Elina; Dumpis, Uga; Klovins, Janis; Rīga Stradiņš University
    Remaining a major healthcare concern with nearly 29 million confirmed cases worldwide at the time of writing, novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 920 thousand deaths since its outbreak in China, December 2019. First case of a person testing positive for SARS-CoV-2 infection within the territory of the Republic of Latvia was registered on 2nd of March 2020, 9 days prior to the pandemic declaration by WHO. Since then, more than 277,000 tests were carried out confirming a total of 1,464 cases of coronavirus disease 2019 (COVID-19) in the country as of 12th of September 2020. Rapidly reacting to the spread of the infection, an ongoing sequencing campaign was started mid-March in collaboration with the local testing laboratories, with an ultimate goal in sequencing as much local viral isolates as possible, resulting in first full-length SARS-CoV-2 isolate genome sequences from the Baltics region being made publicly available in early April. With 133 viral isolates representing ~9.1% of the total COVID-19 cases during the "first coronavirus wave" in the country (early March, 2020-mid-September, 2020) being completely sequenced as of today, here, we provide a first report on the genetic diversity of Latvian SARS-CoV-2 isolates.
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    Genomic and phenotypic inconsistencies in Pseudomonas aeruginosa resistome among intensive care patients
    (2024-06-21) Dolguševs, Mihails; Jain, Nityanand; Savicka, Oksana; Vangravs, Reinis; Bodrenko, Jevgenijs; Bergmanis, Edvins; Zemite, Dace; Selderina, Solvita; Reinis, Aigars; Rozentāle, Baiba; Department of Doctoral Studies; Statistics Unit; Department of Infectology; Department of Biology and Microbiology; Department of Public Health and Epidemiology
    Objective: Pseudomonas aeruginosa, a difficult-to-manage nosocomial pathogen, poses a serious threat to clinical outcomes in intensive care (ICU) patients due to its high antimicrobial resistance (AMR). To promote effective management, it is essential to investigate the genomic and phenotypic differences in AMR expression of the isolates. Methods: A prospective observational study was conducted from July 2022 to April 2023 at Liepaja Regional Hospital in Latvia. The study included all adult patients who were admitted to the ICU and had a documented infection with P. aeruginosa, as confirmed by standard laboratory microbiological testing and short-read sequencing. Since ResFinder is the only sequencing-based database offering antibacterial susceptibility testing (AST) data for each antibiotic, we conducted a comparison of the resistance profile with the results of phenotypic testing, evaluating if ResFinder met the US Food and Drug Administration (FDA) requirements for approval as a new AMR diagnostic test. Next, to improve precision, AST data from ResFinder was compared with two other databases – AMRFinderPlus and RGI. Additionally, data was gathered from environmental samples to inform the implementation of appropriate infection control measures in real time. Results: Our cohort consisted of 33 samples from 29 ICU patients and 34 environmental samples. The presence of P. aeruginosa infection was found to be associated with unfavourable clinical outcomes. A third of the patient samples were identified as multi-drug resistant isolates. Apart from resistance against colistin, significant discrepancies were observed when phenotypic data were compared to genotypic data. For example, the aminoglycoside resistance prediction of ResFinder yielded a major errors value of 3.03% for amikacin, which was marginally above the FDA threshold. Among the three positive environmental samples, one sample exhibited multiple AMR genes similar to the patient samples in its cluster. Conclusion: Our findings underscore the importance of utilizing a combination of diagnostic methods for the identification of resistance mechanisms, clusters, and environmental reservoirs in ICUs.
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    Hepatitis A virus subgenotypes in Latvia, 2008-2021
    (2023-09) Savicka, Oksana; Dusacka, Diana; Zeltmatis, Reinis; Nikisins, Sergejs; Azina, Inga; Ivancenko, Ludmila; Tolmane, Ieva; Rozentale, Baiba; Department of Infectology; Department of Public Health and Epidemiology
    BACKGROUND: In Latvia outbreaks of the HAV were observed between 2008 and early 2010 and again in 2017-2018. However, the risks of introducing and spreading infection still exist, as the virus spreads easily when personal hygiene is not followed. METHODS: To determine the spread of HAV subgenotypes in the territory of Latvia the VP1/P2A genomic region of HAV was amplified and sequenced for 259 case serum samples. The study carried out a molecular biological investigation and molecular epidemiological investigation. Demographic data (sex, age), disease data (hepatitis symptoms, hospitalization, vaccination) and epidemiology data (part of the outbreak, possible source of infection, recent travel) were collected. Based on the obtained sequences, the phylogenetic tree was built and analyzed for the homology and belonging to different isolated HAV clusters from other countries. RESULTS: From the obtained data, it was concluded that HAV subgenotype IA had 13 clusters and 12 sporadic cases, HAV subgenotype IB had eight clusters and 11 sporadic cases, HAV subgenotype IIIA had one cluster and nine sporadic cases. It was found that the sources of infection among the investigated cases were different, they were mostly associated with contact with a patient with HAV, travel, as well as between persons who inject drugs and men who have sex with men, and the prevalence of HAV similar sequences was observed in different years. It was concluded that patients with HAV subgenotype IA had the longest hospitalization duration and averaged 9.3 days, while patients with subgenotype IB - 7.3 days, subgenotype IIIA - 7.7 days. Analyzing the data on vaccination, it was found that mostly all were not vaccinated or had an unknown vaccination status. CONCLUSIONS: All of this has led to the conclusion that the application of molecular biological methods of the HAV and a careful analysis of epidemiological data can help to better understand the ways of spreading the infection, investigate local outbreaks, detect cases of imported infection and track the recirculation of the virus.
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    Molecular Epidemiological Characterisation of Hepatitis A Virus in Latvia. Summary of the Doctoral Thesis
    (Rīga Stradiņš University, 2024) Savicka, Oksana; Storoženko, Jeļena
    The doctoral thesis “Molecular Epidemiological Characterization of Hepatitis A Virus in Latvia” is devoted to the viral hepatitis A disease in Latvia, principles of diagnosis and epidemiological monitoring. The incidence of viral hepatitis A in European countries, as well as in the world, is variable. Until the mid -1990s, viral hepatitis A was a very common infectious disease in Latvia. Already in 2000, the number of sick people decreased and the incidence continued to decrease until 2007, when the number of confirmed cases was the lowest (0.66 cases per 100 000 inhabitants). Outbreaks of the hepatitis A were observed between 2008 and early 2010 and again in 2017–2018. Therefore, the risk of infection introducing and spreading remains. The aim of the thesis was to determine the distribution of hepatitis A virus subgenotypes in the territory of Latvia. Based on the obtained sequences and the structure of the phylogenetic tree, to analyze the homology and belonging to different isolated hepatitis A virus clusters from other countries, to identify the sources of infection, to improve laboratory – epidemiological monitoring tactics. In the study, molecular biological investigation and molecular epidemiological investigation were performed in 259 patients whose data were analyzed retrospectively. Demographic data (gender, age; country of birth, country of residence), clinical data of the disease (date of illness, laboratory – confirmed case, hepatitis symptoms, hospitalization, vaccination) and epidemiological data (part of the outbreak, possible source of infection) were collected. As a result of the analysis, it was established that hepatitis A virus subgenotypes IA, IB and IIIA circulate in Latvia, which are also the most common in the world. From the obtained data, it was concluded that hepatitis A virus subgenotype IA has 13 clusters and 12 sporadic cases, hepatitis A virus subgenotype IB has eight clusters and 11 sporadic cases, hepatitis A virus subgenotype IIIA has one cluster and nine sporadic cases. Sequencing data helps to track the spread of infection and any new cases of hepatitis A could be quickly decipherable by phylogenetic tree and already known clusters. It was found that the sources of infection among the investigated cases are different, they were mostly associated with contact with a hepatitis A patient, travel, also occur among people who inject drugs and men who have sex with men. In Latvia, the spread of hepatitis A virus has been observed regularly, but with different intensity, which may indicate the local circulation of the virus. Analyzing the gender of the patients, the majority of patients 54 % were men and 46 % were women, which does not differ from the literature data available to us. But when comparing the age of the patients at the time of diagnosis, the majority of patients were in the age group from 20 to 29 years old, which differs from the general data from the countries of the European Union and the European Economic Area, where from 2008 to 2021, the majority of patients were in the age group from 5 years to 14 years and from 0 years to 4 years. In the analysis, it was established that all patients had symptoms of hepatitis. Average patients were hospitalized 6.9 sick days after the date of illness, with a mean hospitalization of 8.7 days. It was concluded that patients with hepatitis A virus subgenotype IA had the longest number of days of hospitalization with an average of 9.3 days, while patients with hepatitis A virus subgenotype IB 7.3 days, hepatitis A virus subgenotype IIIA 7.7 days. Analysis of our data showed that the median time from the symptom onset to laboratory – confirmed hepatitis A case was 7.9 days. Analysis of vaccination data revealed that 89.6 % of patients included in the study were not vaccinated, 10.0 % had unknown vaccination status, and 0.4 % of patients had received one vaccine dose after contact with a hepatitis A virus patient. All of this has led to the conclusion that the application of molecular biological methods of the hepatitis A virus and the careful analysis of epidemiological data can help to better understand the ways of spread of the infection, investigate local outbreaks, detect cases of imported infection and track the circulation of the virus. This makes it possible to ensure timely and adequate preventive measures against the spread of infection.
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    Molecular epidemiology of hepatitis A outbreaks and sporadic cases, Latvia, 2017 to 2019
    (2022-03-17) Savicka, Oksana; Zeltmatis, Reinis; Storoženko, Jeļena
    Background Hepatitis A is an acute infection of the liver caused by hepatitis A virus (HAV). Molecular detection and typing of the HAV VP1/P2A genomic region is used for genotyping and outbreak investigations. After a large hepatitis A outbreak in Latvia in 2007–08, only sporadic cases were registered until 2017 when a rise in cases occurred. During 2017–19, 179 laboratory-confirmed hepatitis A cases were notified in Latvia. Aim To investigate the observed increase in hepatitis A cases during 2017 and to determine whether these cases were linked to one another, to risk groups, or to other outbreaks. The majority of HAV samples (69.8%) were typed. Methods The VP1/P2A genomic region of HAV was amplified and sequenced for 125 case serum samples. Information about hepatitis-related symptoms, hospitalisation, vaccination, a possible source of infection and suspected countries of origin of the virus were analysed for sequenced cases. Results Most HAV strains were subgenotype IA (n = 77), of which 41 were strains circulating among men who have sex with men (MSM) populations in Europe (VRD_521_2016 (n = 32), RIVM-HAV16–090 (n = 7) or V16–25801 (n = 2)). Forty-four cases were subgenotype IB and four cases subgenotype IIIA. However, other clusters and sporadic cases were detected with or without identifying the epidemiological link. Conclusion This work represents molecular epidemiological data of hepatitis A cases in Latvia from 2017 to 2019. Molecular typing methods allow identification of clusters for public health needs and establishing links with other outbreaks, and to compare Latvian strains with reported strains from other countries.
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    Molekulāri epidemioloģiskais A hepatīta vīrusa raksturojums Latvijā. Promocijas darba kopsavilkums
    (Rīgas Stradiņa universitāte, 2024) Savicka, Oksana; Storoženko, Jeļena
    Promocijas darba “Molekulāri epidemioloģiskais A hepatīta vīrusa raksturojums Latvijā” ir veltīts A vīrushepatīta slimībai, diagnostikas un epidemioloģiskās uzraudzības principiem Latvijā. Saslimstība ar A vīrushepatītu Eiropas valstīs un visā pasaulē ir variabla. Līdz 20. gadsimta 90. gadu vidum A vīrushepatīts bija ļoti izplatīta infekcijas slimība Latvijā. Jau 2000. gadā saslimušo skaits samazinājās, un arī turpmāk saslimstība turpināja samazināties līdz 2007. gadam, kad apstiprināto gadījumu skaits bija viszemākais (0,66 gadījumi uz 100 000 iedzīvotāju). Laikā no 2008. līdz 2010. gada sākumam un pēc tam, 2017.–2018. gadā, tika novēroti A hepatīta uzliesmojumi. Tāpēc infekcijas ieviešanās un izplatīšanās risks joprojām pastāv. Darba mērķis bija noteikt A hepatīta vīrusa subgenotipu izplatību Latvijas teritorijā. Pēc iegūtām sekvencēm un filoģenētiskā koka uzbūves analizēt homoloģiju un piederību pie dažādiem izdalītiem A hepatīta vīrusa klasteriem no citām valstīm, apzināt infekcijas avotus, pilnveidot laboratoriski epidemioloģisko uzraudzības taktiku. Pētījumā tika veikta molekulāri bioloģiskā izmeklēšana un molekulāri epidemioloģiskā izmeklēšana 259 pacientiem, kuru dati analizēti retrospektīvi. Tika apkopoti demogrāfiskie dati (dzimums, vecums; dzimtā valsts, uzturēšanās valsts), dati par slimības klīnisko norisi (saslimšanas datums, laboratoriski apstiprināts gadījums, hepatīta simptomi, hospitalizācija, vakcinācija) un epidemioloģiskie dati (daļa no uzliesmojuma, iespējamais inficēšanas avots). Darba rezultātā tika noskaidrots, ka Latvijā cirkulē A hepatīta vīrusa subgenotipi IA, IB un IIIA, kuri arī ir visizplatītākie pasaulē. No iegūtajiem datiem secināts, ka A hepatīta vīrusa subgenotipam IA ir 13 klasteri un 12 sporādiskie gadījumi, A hepatīta vīrusa subgenotipam IB ir astoņi klasteri un 11 sporādiskie gadījumi, A hepatīta vīrusa subgenotipam IIIA ir viens klasteris un deviņi sporādiskie gadījumi. Sekvencēšanas dati palīdz izsekot infekcijas izplatību, un visi jaunie A hepatīta gadījumi varētu būt ātri atšifrējami pēc filoģenētiskā koka un jau zināmiem klasteriem. No izmeklētajiem gadījumiem konstatēts, ka inficēšanas avoti ir dažādi, pārsvarā kontakts ar A vīrushepatīta pacientu, ceļošana, iespējama izplatība starp injicējamo narkotiku lietotājiem un vīriešiem, kuriem ir sekss ar vīriešiem. Latvijā A hepatīta vīrusa izplatība ir novērota regulāri, bet ar dažādu intensitāti, kas var liecināt par vīrusa vietējo cirkulāciju. Analizējot pacientu dzimumu, lielākā daļa pacientu – 54 % – bija vīrieši un 46 % – sievietes, kas neatšķiras no mums pieejamiem literatūras datiem. Bet, salīdzinot pacientu vecumu diagnozes noteikšanas brīdī, lielākā pacientu daļa bija vecumgrupā no 20 līdz 29 gadiem, kas atšķiras no kopējiem Eiropas Savienības un Eiropas Ekonomikas zonas valstu datiem. Pēc šiem datiem, no 2008. līdz 2021. gadam lielākā daļa pacientu bija vecumgrupā no 5 līdz 14 gadiem un no 0 līdz 4 gadiem. Darbā gaitā tika konstatēts, ka visiem pacientiem bija novēroti hepatīta simptomi. Vidējie pacienti tika hospitalizēti 6,9. slimības dienā pēc saslimšanas datuma ar vidējo hospitalizācijas dienu skaitu 8,7 dienas. Secināts, ka pacientiem ar A hepatīta vīrusa subgenotipu IA bija ilgākais hospitalizācijas dienu skaits – vidēji 9,3 dienas, bet pacientiem ar A hepatīta vīrusa subgenotipu IB – 7,3 dienas, A hepatīta vīrusa subgenotipu IIIA – 7,7 dienas. Analizējot mūsu datus, tika secināts, ka vidējais laiks no simptomu parādīšanās līdz laboratoriski apstiprinātam A vīrushepatīta gadījumam bija 7,9 dienas. Veicot datu analīzi par vakcināciju, tika noskaidrots, ka 89,6 % no pētījumā iekļautiem pacientiem nebija vakcinēti, 10,0 % bija nezināms vakcinācijas statuss un 0,4 % pacientu bija saņemta viena potes deva pēc kontakta ar A hepatīta vīrusa pacientu. Minētie dati ļāva secināt, ka A hepatīta vīrusa molekulāri bioloģisko metožu lietošana un rūpīga epidemioloģisko datu analīze var palīdzēt labāk izprast infekcijas izplatīšanās ceļus, izmeklēt lokālus uzliesmojumus, atklāt ievestās infekcijas gadījumus un izsekot vīrusa cirkulāciju. Tas dod iespēju nodrošināt savlaicīgas un adekvātas infekcijas izplatības preventīvās darbības.
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    Molekulāri epidemioloģiskais A hepatīta vīrusa raksturojums Latvijā. Promocijas darbs
    (Rīgas Stradiņa universitāte, 2024) Savicka, Oksana; Storoženko, Jeļena
    Promocijas darba “Molekulāri epidemioloģiskais A hepatīta vīrusa raksturojums Latvijā” ir veltīts A vīrushepatīta slimībai, diagnostikas un epidemioloģiskās uzraudzības principiem Latvijā. Saslimstība ar A vīrushepatītu Eiropas valstīs un visā pasaulē ir variabla. Līdz 20. gadsimta 90. gadu vidum A vīrushepatīts bija ļoti izplatīta infekcijas slimība Latvijā. Jau 2000. gadā saslimušo skaits samazinājās, un arī turpmāk saslimstība turpināja samazināties līdz 2007. gadam, kad apstiprināto gadījumu skaits bija viszemākais (0,66 gadījumi uz 100 000 iedzīvotāju). Laikā no 2008. līdz 2010. gada sākumam un pēc tam, 2017.–2018. gadā, tika novēroti A hepatīta uzliesmojumi. Tāpēc infekcijas ieviešanās un izplatīšanās risks joprojām pastāv. Darba mērķis bija noteikt A hepatīta vīrusa subgenotipu izplatību Latvijas teritorijā. Pēc iegūtām sekvencēm un filoģenētiskā koka uzbūves analizēt homoloģiju un piederību pie dažādiem izdalītiem A hepatīta vīrusa klasteriem no citām valstīm, apzināt infekcijas avotus, pilnveidot laboratoriski epidemioloģisko uzraudzības taktiku. Pētījumā tika veikta molekulāri bioloģiskā izmeklēšana un molekulāri epidemioloģiskā izmeklēšana 259 pacientiem, kuru dati analizēti retrospektīvi. Tika apkopoti demogrāfiskie dati (dzimums, vecums; dzimtā valsts, uzturēšanās valsts), dati par slimības klīnisko norisi (saslimšanas datums, laboratoriski apstiprināts gadījums, hepatīta simptomi, hospitalizācija, vakcinācija) un epidemioloģiskie dati (daļa no uzliesmojuma, iespējamais inficēšanas avots). Darba rezultātā tika noskaidrots, ka Latvijā cirkulē A hepatīta vīrusa subgenotipi IA, IB un IIIA, kuri arī ir visizplatītākie pasaulē. No iegūtajiem datiem secināts, ka A hepatīta vīrusa subgenotipam IA ir 13 klasteri un 12 sporādiskie gadījumi, A hepatīta vīrusa subgenotipam IB ir astoņi klasteri un 11 sporādiskie gadījumi, A hepatīta vīrusa subgenotipam IIIA ir viens klasteris un deviņi sporādiskie gadījumi. Sekvencēšanas dati palīdz izsekot infekcijas izplatību, un visi jaunie A hepatīta gadījumi varētu būt ātri atšifrējami pēc filoģenētiskā koka un jau zināmiem klasteriem. No izmeklētajiem gadījumiem konstatēts, ka inficēšanas avoti ir dažādi, pārsvarā kontakts ar A vīrushepatīta pacientu, ceļošana, iespējama izplatība starp injicējamo narkotiku lietotājiem un vīriešiem, kuriem ir sekss ar vīriešiem. Latvijā A hepatīta vīrusa izplatība ir novērota regulāri, bet ar dažādu intensitāti, kas var liecināt par vīrusa vietējo cirkulāciju. Analizējot pacientu dzimumu, lielākā daļa pacientu – 54 % – bija vīrieši un 46 % – sievietes, kas neatšķiras no mums pieejamiem literatūras datiem. Bet, salīdzinot pacientu vecumu diagnozes noteikšanas brīdī, lielākā pacientu daļa bija vecumgrupā no 20 līdz 29 gadiem, kas atšķiras no kopējiem Eiropas Savienības un Eiropas Ekonomikas zonas valstu datiem. Pēc šiem datiem, no 2008. līdz 2021. gadam lielākā daļa pacientu bija vecumgrupā no 5 līdz 14 gadiem un no 0 līdz 4 gadiem. Darbā gaitā tika konstatēts, ka visiem pacientiem bija novēroti hepatīta simptomi. Vidējie pacienti tika hospitalizēti 6,9. slimības dienā pēc saslimšanas datuma ar vidējo hospitalizācijas dienu skaitu 8,7 dienas. Secināts, ka pacientiem ar A hepatīta vīrusa subgenotipu IA bija ilgākais hospitalizācijas dienu skaits – vidēji 9,3 dienas, bet pacientiem ar A hepatīta vīrusa subgenotipu IB – 7,3 dienas, A hepatīta vīrusa subgenotipu IIIA – 7,7 dienas. Analizējot mūsu datus, tika secināts, ka vidējais laiks no simptomu parādīšanās līdz laboratoriski apstiprinātam A vīrushepatīta gadījumam bija 7,9 dienas. Veicot datu analīzi par vakcināciju, tika noskaidrots, ka 89,6 % no pētījumā iekļautiem pacientiem nebija vakcinēti, 10,0 % bija nezināms vakcinācijas statuss un 0,4 % pacientu bija saņemta viena potes deva pēc kontakta ar A hepatīta vīrusa pacientu. Minētie dati ļāva secināt, ka A hepatīta vīrusa molekulāri bioloģisko metožu lietošana un rūpīga epidemioloģisko datu analīze var palīdzēt labāk izprast infekcijas izplatīšanās ceļus, izmeklēt lokālus uzliesmojumus, atklāt ievestās infekcijas gadījumus un izsekot vīrusa cirkulāciju. Tas dod iespēju nodrošināt savlaicīgas un adekvātas infekcijas izplatības preventīvās darbības.
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    Streptococcus pneumoniae serotypes and factors associated with antimicrobial resistance in Invasive pneumococcal disease cases in Latvia, 2012–2022
    (2025-03-12) Savrasova, Larisa; Villeruša, Anita; Zeltiņa, Indra; Krūmiņa, Angelika; Čupeca, Hedija; Balasegaram, Sooria; Grēve, Māra; Savicka, Oksana; Selderina, Solvita; Galajeva, Jelena; Dushacka, Diana; Institute of Public Health; Department of Infectology; Department of Human Physiology and Biochemistry; Statistics Unit
    Background: Streptococcus pneumoniae is a major cause of Invasive pneumococcal disease (IPD), including bacteremic pneumonia, septicemia, and meningitis. The introduction of pneumococcal conjugate vaccines (PCVs) has significantly reduced the incidence of IPD caused by vaccine-covered serotypes. However, serotype replacement and antimicrobial resistance remain concerns. In Latvia, vaccination against pneumococcal disease was introduced into the NIP in 2010 with PCV7, later transitioning to PCV10 in 2012 and to PCV15 in 2024. This study aims is to determine the changes in S. pneumoniae antimicrobial resistance and its association with PCV10 serotypes in Latvia. Materials and methods: We conducted a population-based cross-sectional study using IPD surveillance data from Latvia over an 11-year period (2012–2022). IPD cases were defined according to the European Union case definition. Serotyping and antimicrobial susceptibility testing were performed on isolates from normally sterile sites. We analyzed the differences in IPD incidence, serotype distribution, and antimicrobial resistance using chi-square tests and multivariable logistic regression was used to determine associations between antimicrobial resistance and risk factors. Results: A total of 811 IPD cases were reported, with significant differences observed across the study period (p < 0.001). The most common serotypes were 3 and 19A. The proportion of IPD cases caused by PCV10 serotypes significantly decreased over the years, while cases caused by PCV13, PCV15, and PPPV23 serotypes increased. Antimicrobial susceptibility testing revealed resistance rates of 3.8% to penicillin, 5.4% to erythromycin, and 1.2% to cefotaxime/ceftriaxone. Erythromycin resistance showed significant variation over time (p = 0.016), decreasing from 7.1% in 2012 to 4.8% in 2022. Multivariable logistic regression indicated that IPD cases with S. pneumoniae PCV10 serotypes and meningitis were significantly associated with an increased likelihood of penicillin and erythromycin resistance. Conclusion: The study highlights a decrease in erythromycin resistance in IPD cases over time and significant associations between PCV10 serotypes and meningitis in IPD cases and penicillin and erythromycin resistance. The findings underscore the importance of continuous surveillance of S. pneumoniae serotypes and antimicrobial resistance patterns to inform treatment guidelines and vaccination policies. Further research is needed to assess the long-term impact of the PCV15 vaccine on S. pneumoniae serotype distribution and resistance.