Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

BACKGROUND: The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS: For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS: Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION: COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING: Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.

Antimicrobial resistance among Haemophilus influenzae isolates responsible for lower respiratory tract infections in Poland, 2005-2019.

Haemophilus influenzae is a human-specific pathogen responsible for respiratory tract infections, meningitis, and sepsis. The study aimed to characterize antibiotic resistance in H. influenzae strains isolated from patients with lower respiratory tract infections over 15 years in Poland. The minimum inhibitory concentrations (MICs) of clinically relevant antibiotics were determined by broth microdilution method. Screening for beta-lactam resistance was performed in all isolates following EUCAST recommendation. Finally, relevant changes in penicillin-binding protein 3 (PBP3) were detected by PCR screening. Of the 1481 isolates collected between 2005 and 2019, 12.6%, 0.2%, 17.1%, and 0.2% were resistant to ampicillin, amoxicillin/clavulanate, cefuroxime, and ceftriaxone, respectively. Among them, 74.4% (1102/1481) of isolates were categorized as BLNAS (ß-lactamase negative, ampicillin-susceptible), 13.0% (192/1481) as BLNAS with modified PBP3 (mutations in ftsI gene), 2.6% (39/1481) as BLNAR (ß-lactamase negative, ampicillin-resistant), and 0.2% had PBP3 modifications typical for high-BLNAR. Production of ß-lactamase characterized 9.7% of isolates (8.6% BLPAR-ß-lactamase-positive, ampicillin-resistant, and 1.1% BLPACR-ß-lactamase-positive, amoxicillin-clavulanate resistant). Three isolates with PBP3 modifications typical for high-BLNAR proved resistant to ceftriaxone (MIC > 0.125 mg/L). Resistance to ciprofloxacin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole was observed in 0.1%, 0.5%, 1.6%, and 24.7% of isolates, respectively. This is the first report of Polish H. influenzae isolates resistant to third-generation cephalosporins. Polish H. influenzae isolates demonstrate similar susceptibility trends as in many other countries. The substantial proportion of ß-lactam-resistant isolates and the emergence of those resistant to third-generation cephalosporins are of great concern and should be under surveillance.

Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates.

Recent reports have indicated a rise of invasive disease caused by Haemophilus influenzae serotype a (Hia) in North America and some European countries. The whole-genome sequences for a total of 410 invasive Hia isolates were obtained from 12 countries spanning the years of 1998 to 2019 and underwent phylogenetic and comparative genomic analysis in order to characterize the major strains causing disease and the genetic variation present among factors contributing to virulence and antimicrobial resistance. Among 410 isolate sequences received, 408 passed our quality control and underwent genomic analysis. Phylogenetic analysis revealed that the Hia isolates formed four genetically distinct clades: clade 1 (n = 336), clade 2 (n = 13), clade 3 (n = 3) and clade 4 (n = 56). A low diversity subclade 1.1 was found in clade 1 and contained almost exclusively North American isolates. The predominant sequence types in the Hia collection were ST-56 (n = 125), ST-23 (n = 98) and ST-576 (n = 51), which belonged to clade 1, and ST-62 (n = 54), which belonged to clade 4. Clades 1 and 4 contained predominantly North American isolates, and clades 2 and 3 predominantly contained European isolates. Evidence of the presence of capsule duplication was detected in clade 1 and 2 isolates. Seven of the virulence genes involved in endotoxin biosynthesis were absent from all Hia isolates. In general, the presence of known factors contributing to ß-lactam antibiotic resistance was low among Hia isolates. Further tests for virulence and antibiotic susceptibility would be required to determine the impact of these variations among the isolates.

Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data.

BACKGROUND: Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets, are leading causes of invasive diseases, including bacteraemic pneumonia and meningitis, and of secondary infections subsequent to post-viral respiratory disease. The aim of this study was to investigate the incidence of invasive disease due to these pathogens during the early months of the COVID-19 pandemic. METHODS: In this prospective analysis of surveillance data, laboratories in 26 countries and territories across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae, and N meningitidis from Jan 1, 2018, to May, 31, 2020, as part of the Invasive Respiratory Infection Surveillance (IRIS) Initiative. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for invasive disease due to Streptococcus agalactiae, a non-respiratory pathogen, were collected from nine laboratories for comparison. The stringency of COVID-19 containment measures was quantified using the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed using Google COVID-19 Community Mobility Reports. Interrupted time-series modelling quantified changes in the incidence of invasive disease due to S pneumoniae, H influenzae, and N meningitidis in 2020 relative to when containment measures were imposed. FINDINGS: 27 laboratories from 26 countries and territories submitted data to the IRIS Initiative for S pneumoniae (62 837 total cases), 24 laboratories from 24 countries submitted data for H influenzae (7796 total cases), and 21 laboratories from 21 countries submitted data for N meningitidis (5877 total cases). All countries and territories had experienced a significant and sustained reduction in invasive diseases due to S pneumoniae, H influenzae, and N meningitidis in early 2020 (Jan 1 to May 31, 2020), coinciding with the introduction of COVID-19 containment measures in each country. By contrast, no significant changes in the incidence of invasive S agalactiae infections were observed. Similar trends were observed across most countries and territories despite differing stringency in COVID-19 control policies. The incidence of reported S pneumoniae infections decreased by 68% at 4 weeks (incidence rate ratio 0·32 [95% CI 0·27-0·37]) and 82% at 8 weeks (0·18 [0·14-0·23]) following the week in which significant changes in population movements were recorded. INTERPRETATION: The introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of S pneumoniae, H influenzae, and N meningitidis, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide. FUNDING: Wellcome Trust (UK), Robert Koch Institute (Germany), Federal Ministry of Health (Germany), Pfizer, Merck, Health Protection Surveillance Centre (Ireland), SpID-Net project (Ireland), European Centre for Disease Prevention and Control (European Union), Horizon 2020 (European Commission), Ministry of Health (Poland), National Programme of Antibiotic Protection (Poland), Ministry of Science and Higher Education (Poland), Agencia de Salut Pública de Catalunya (Spain), Sant Joan de Deu Foundation (Spain), Knut and Alice Wallenberg Foundation (Sweden), Swedish Research Council (Sweden), Region Stockholm (Sweden), Federal Office of Public Health of Switzerland (Switzerland), and French Public Health Agency (France).

Relationships among streptococci from the mitis group, misidentified as Streptococcus pneumoniae.

The aim of our study was to investigate phenotypic and genotypic features of streptococci misidentified (misID) as Streptococcus pneumoniae, obtained over 20 years from hospital patients in Poland. Sixty-three isolates demonstrating microbiological features typical for pneumococci (optochin susceptibility and/or bile solubility) were investigated by phenotypic tests, lytA and 16S rRNA gene polymorphism and whole-genome sequencing (WGS). All isolates had a 6-bp deletion in the lytA 3' terminus, characteristic for Mitis streptococc and all but two isolates lacked the pneumococcal signature cytosine at nucleotide position 203 in the 16S rRNA genes. The counterparts of psaA and ply were present in 100% and 81.0% of isolates, respectively; the spn9802 and spn9828 loci were characteristic for 49.2% and 38.1% of isolates, respectively. Phylogenetic trees and networks, based on the multilocus sequence analysis (MLSA) scheme, ribosomal multilocus sequence typing (rMLST) scheme and core-genome analysis, clearly separated investigated isolates from S. pneumoniae and demonstrated the polyclonal character of misID streptococci, associated with the Streptococcus pseudopneumoniae and Streptococcus mitis groups. While the S. pseudopneumoniae clade was relatively well defined in all three analyses, only the core-genome analysis revealed the presence of another cluster comprising a fraction of misID streptococci and a strain proposed elsewhere as a representative of a novel species in the Mitis group. Our findings point to complex phylogenetic and taxonomic relationships among S. mitis-like bacteria and support the notion that this group may in fact consist of several distinct species.

Activity of temocillin against ESBL-, AmpC-, and/or KPC-producing Enterobacterales isolated in Poland.

We evaluated the in vitro effectiveness of temocillin and several commonly used antimicrobials against Enterobacterales bacteria in isolates from Polish patients. We tested 400 isolates: 260 extended-spectrum ß-lactamase (ESBL)- and/or ampC ß-lactamase (AmpC)-producing isolates; 40 Klebsiella pneumoniae carbapenemase (KPC)-producing isolates; and 100 ESBL-, AmpC-, and KPC-negative isolates. The minimal inhibitory concentrations (MICs) of temocillin and 16 other antimicrobials were determined by reference microdilution. We also determined the activities of fosfomycin and ceftazidime/avibactam in KPC-producing isolates. The antibiotic sensitivities were interpreted according to EUCAST, BSAC, and CLSI criteria. Overall, 91% of the isolates were susceptible to temocillin using the urinary tract infection breakpoint (≤ 32 mg/L), and 61.8% were susceptible using the systemic infection breakpoint (≤ 8 mg/L). Meropenem and imipenem were the most active drugs (MIC50 values of 0.06 and 0.5 mg/L, respectively). Colistin and ertapenem (both MIC50 = 0.12 mg/L) were less active than meropenem or imipenem, but some strains were 77% susceptible to each of them. Among the KPC-producing isolates, 42.5% had MIC values of ≤ 32 mg/L (urinary tract infection breakpoint), but 100% were resistant to temocillin (systemic infection breakpoint). Ceftazidime/avibactam was active against 100% of the KPC-producing isolates, and fosfomycin was active against 40%. The empirical susceptibility rate observed among the urinary isolates suggests that temocillin may be considered as an alternative to carbapenems in the absence of KPC-producing bacteria. With regard to isolates from other sources, temocillin might be useful as a documented therapy agent or an empirical treatment in hospitals with a low prevalence of ESBL/AmpC-producing strains.

Genetic variability of Polish serogroup B meningococci (2010-2016) including the 4CMenB vaccine component genes.

Neisseria meningitidis serogroup B (MenB) has recently become the major cause of invasive meningococcal disease in Poland. Therefore, the purpose of this study was to characterize MenB isolates, responsible for invasive meningococcal disease in 2010-2016, by MLST and sequencing of genes encoding proteins used as 4CMenB vaccine antigens. Two methods of coverage estimation were performed: extrapolation of MATS results of Polish meningococci 2010-2011 (exMATS) and gMATS, which combines genotyping and MATS results. Among 662 isolates 20 clonal complexes (CC) were detected, of which the most frequent were CC32, CC41/44 and CC18, accounting for 31.9%, 16.5% and 12.7%, respectively. A total of 111 combinations of PorA variable regions (VR1/VR2) were found, with P1.7,16 (15.0%) and P1.22,14 (13.6%) being prevalent. Vaccine variant VR2:4 was detected in 7.3% of isolates, mainly representing CC41/44 and non-assigned CC. Eighty five fHbp alleles encoding 74 peptide subvariants were revealed. Subvariant 1.1, a component of 4CMenB, was prevalent (24.2%) and found generally in CC32. Typing of the nhba gene revealed 102 alleles encoding 87 peptides. The most frequent was peptide 3 (22.4%), whereas vaccine peptide 2 was detected in 9.8%, mostly among CC41/44. The nadA gene was detected in 34.0% of isolates and the most prevalent was peptide 1 (variant NadA-1; 71.6%), found almost exclusively in CC32 meningococci. Vaccine peptide 8 (variant NadA-2/3) was identified once. Consequently, 292 completed BAST profiles were revealed. Regarding vaccine coverage, 39.7% of isolates had at least one 4CMenB vaccine variant, but according to exMATS and gMATS the coverage was 83.3% and 86.6%, respectively. In conclusion, Polish MenB (2010-2016) was highly diverse according to MLST and gene alleles encoding 4CMenB vaccine antigens. Some correlations between clonal complexes and variants of examined proteins/BAST profiles were revealed and a high coverage of 4CMenB vaccine was estimated.

Pneumococcal meningitis before the introduction of 10-valent pneumococcal conjugate vaccine into the National Childhood Immunization Program in Poland.

BACKGROUND: Poland introduced the 10-valent conjugate pneumococcal vaccine (PCV10) into the childhood immunization program in January 2017. During previous decades, considerable changes had occurred in the surveillance system for invasive pneumococcal disease. Therefore, to provide baseline data on pneumococcal diseases before PCV10 introduction, we evaluated the epidemiology of pneumococcal meningitis (PM), the only syndrome monitored consistently since 1970. METHODS: Based on laboratory-confirmed cases reported during 2005-2015, we calculated the reported rates, serotypes distribution and antimicrobial resistance of pneumococcal meningitis isolates. Data from the mandatory national surveillance system was linked with data on cerebrospinal fluid isolates submitted to the National Reference Centre for Bacterial Meningitis. We used negative binomial regression with Newey West method to test for trend in rates of pneumococcal meningitis notified during 2005-2015 and Chi-squared test to assess changes in the serotype distribution from 2008-2011 to 2012-2015. RESULTS: From 2005 to 2015, the overall reported incidence of PM increased from 0.21 to 0.47 cases per 100,000 population, average yearly increase of 7% (rate ratio 1.07; 95% CI 1.06-1.08). The increase was primarily due to annual increase of 3% (1.02-1.05) among 15-49 years of age, 12% (95% CI: 1.10-1.13) among 50-64 years of age, 18% (95% CI: 1.16-1.19) among persons 65-74 years of age and 9% (95% CI 1.07-1.10) among persons ≥75 years of age. In children <5 years of age, serotypes included in PCV10 and PCV13 accounted for 75% and 80% of reported isolates, respectively. From 2008-2011 to 2012-2015, the proportion of PM cases caused by PCV10 serotypes decreased from 52% to 41% (p < 0.01). Overall, 28% of isolates were resistant to penicillin and 13% were non-susceptible to cefotaxime. CONCLUSIONS: The introduction of PCV10 into national immunization program may have considerable impact on disease burden, especially on number of cases caused by isolates non-susceptible to antimicrobials.

Molecular diversity and antimicrobial susceptibility of Listeria monocytogenes isolates from invasive infections in Poland (1997-2013).

The epidemiology of invasive listeriosis in humans appears to be weakly characterized in Poland, the sixth most populous member state of the European Union. We obtained antimicrobial susceptibility data, PCR-serogroups and genotypic profiles for 344 invasive isolates of Listeria monocytogenes, collected between 1997 and 2013 in Poland. All isolates were susceptible to the 10 tested antimicrobials, except one that was resistant to tetracycline and minocycline and harbored the tet(M), tet(A) and tet(C) genes. Overall, no increasing MIC values were observed during the study period. Four PCR-serogroups were observed: IVb (55.8%), IIa (34.3%), IIb (8.1%) and IIc (1.8%). We identified clonal complexes (CCs) and epidemic clones (ECs) previously involved in outbreaks worldwide, with the most prevalent CCs/ECs being: CC6/ECII (32.6%), CC1/ECI (17.2%), CC8/ECV (6.1%) and CC2/ECIV (5.5%). The present study is the first extensive analysis of Polish L. monocytogenes isolates from invasive infections.

The changing epidemiology of VanB Enterococcus faecium in Poland.

Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation. VanB isolates almost exclusively represented hospital-associated E. faecium, with a significant shift from representatives of 17/18 lineage to 78 lineage after 2005. The vanB determinant, initially located mostly on transferable plasmids of the pRUM-, pLG1-, and pRE25-replicon types, later on was found almost exclusively on the host chromosome. Fifteen different plasmid and chromosomal insertion sites were identified, typically associated with single transposon coupling sequences, mostly not observed before. Our study demonstrates the significant change in the epidemiology of VanB-E. faecium in Poland, associated with the introduction and spread of the lineage 78 of the hospital-adapted E. faecium. These data point to the importance of the lineage 78 for the spread of vancomycin-resistance, determined by the vanB gene cluster, resulting in an increasing VRE prevalence in hospitals. This study also supports the scenario, in which representatives of the hospital-associated E. faecium independently acquire the vanB determinant de novo and spread within and among hospitals, concomitantly undergoing differentiation.

ß-Lactam resistance among Haemophilus influenzae isolates in Poland.

OBJECTIVES: Haemophilus influenzae is a human-specific Gram-negative coccobacillus responsible for a significant number of respiratory tract infections and severe invasive infections such as meningitis and sepsis. The purpose of this study was to characterise the mechanisms of ß-lactam resistance among Polish H. influenzae isolates and to evaluate the resistance detection methods applied. METHODS: This study was conducted on 117 Polish H. influenzae isolates collected in 2012. Minimum inhibitory concentrations were assessed by broth microdilution. All strains were evaluated using the disk diffusion method and the algorithm proposed by the Nordic Committee on Antimicrobial Susceptibility Testing (NordicAST). To detect changes in penicillin-binding protein 3 (PBP3), PCR screening was performed, followed by ftsI gene sequencing. RESULTS: Neither ß-lactamase production nor PBP3 alterations were demonstrated in 76 isolates (65.0%). Susceptibility to ampicillin, amoxicillin, amoxicillin/clavulanic acid, cefuroxime (intravenous) and ceftriaxone was observed in 70.9%, 78.6%, 98.3%, 82.9% and 100% of the isolates, respectively. ß-Lactamase production characterised 21 isolates (17.9%). Screening PCR identified 20 isolates (17.1%) with PBP3 alterations, and according to subsequent ftsI sequencing all these strains were finally recognised as gBLNAR (genetically ß-lactamase-negative, ampicillin-resistant), among which 65.0% were ampicillin-resistant. According to molecular classification of PBP3 alterations, 95.0% of gBLNAR belonged to group II, representing four subgroups IIa-IId. CONCLUSIONS: Haemophilus influenzae resistance to antibiotics requires continuous attention, effective detection methods and a rational policy of antibiotic usage. The algorithm proposed by NordicAST can be applied in routine laboratory work, whereas sequencing of the ftsI gene may be useful in molecular epidemiology studies.

Distribution of antimicrobial resistance determinants, virulence-associated factors and clustered regularly interspaced palindromic repeats loci in isolates of Enterococcus faecalis from various settings and genetic lineages.

Enterococcus faecalis represents an important factor of hospital-associated infections (HAIs). The knowledge on its evolution from a commensal to an opportunistic pathogen is still limited; thus, we performed a study to characterise distribution of factors that may contribute to this adaptation. Using a collection obtained from various settings (hospitalised patients, community carriers, animals, fresh food, sewage, water), we investigated differences in antimicrobial susceptibility, distribution of antimicrobial resistance genes, virulence-associated determinants and phenotypes, and CRISPR loci in the context of the clonal relatedness of isolates. Bayesian Analysis of Population Structure revealed the presence of three major groups; two subgroups comprised almost exclusively HAI isolates, belonging to previously proposed enterococcal high-risk clonal complexes (HiRECCs) 6 and 28. Isolates of these two subgroups were significantly enriched in antimicrobial resistance genes, presumably produced a polysaccharide capsule and often carried the aggregation substance asa1; distribution of other virulence-associated genes, such as esp and cyl, formation of a biofilm and gelatinase production were more variable. Moreover, both subgroups showed a low prevalence of CRISPR-Cas 1 and 3 and presence of small CRISPR2 variants. Our study confirms the importance of HiRECCs in the population of E. faecalis and their confinement to the hospital settings.

Invasive Haemophilus influenzae Serotype f Case Reports in Mazovia Province, Poland.

After successful introduction of anti-Haemophilus influenzae (Hi) serotype b vaccination program in Poland, invasive non-b or nontypeable H. influenzae infections have been reported more frequently alike in other countries all over the world. In this paper, we report 2 cases of H. influenzae serotype f (Hif) meningitis with severe clinical presentations which are rarely seen in previously healthy children.The first case is a 6-year-old girl who was admitted to pediatric ward with signs of meningitis. Laboratory tests confirmed bacteremic meningitis caused by Hif. The girl responded very well to administered treatment and recovered without any further complications. No underlying comorbidities were found. The second patient was a 4-year-old boy who, in course of Hif bacteremic meningitis, developed rapid septicemia and, despite aggressive treatment, died within a few hours of hospitalization. The child's past history was unremarkable.By presenting these cases, we would like to remind clinicians that invasive non-b Hi infections can become fatal not only in the group of the youngest children or children with coexisting comorbidities, as most commonly reported in the worldwide literature. At the same time, we want to emphasize the legitimacy of constant monitoring Hi epidemiology in order to take accurate actions if necessary.

Usefulness of Pneumotest-latex for direct serotyping of Streptococcus pneumoniae isolates in clinical samples.

This study evaluated the usefulness of the Pneumotest-Latex assay for serotyping Streptococcus pneumoniae isolates directly in clinical samples. With an agreement of 88.1% with a PCR-based reference method, this test can be a useful tool for this study purpose, especially in clinical laboratories that do not have access to nucleic acid amplification technologies.

A decade of invasive meningococcal disease surveillance in Poland.

BACKGROUND: Neisseria meningitidis is a leading etiologic agent of severe invasive disease. The objective of the study was to characterise invasive meningococcal disease (IMD) epidemiology in Poland during the last decade, based on laboratory confirmed cases. METHODS: The study encompassed all invasive meningococci collected between 2002 and 2011 in the National Reference Centre for Bacterial Meningitis. The isolates were re-identified and characterised by susceptibility testing, MLST analysis, porA and fetA sequencing. A PCR technique was used for meningococcal identification directly from clinical materials. RESULTS: In the period studied, 1936 cases of IMD were confirmed, including 75.6% identified by culture. Seven IMD outbreaks, affecting mostly adolescents, were reported; all were caused by serogroup C meningococci of ST-11. The highest incidence was observed among children under one year of age (15.71/100,000 in 2011). The general case fatality rate in the years 2010-2011 was 10.0%. Meningococci of serogroup B, C, Y and W-135 were responsible for 48.8%, 36.6%, 1.2% and 1.2% of cases, respectively. All isolates were susceptible to third generation cephalosporins, chloramphenicol, ciprofloxacin, and 84.2% were susceptible to penicillin. MLST analysis (2009-2011) revealed that among serogroup B isolates the most represented were clonal complexes (CC) ST-32CC, ST-18CC, ST-41/44CC, ST-213CC and ST-269CC, and among serogroup C: ST-103CC, ST-41/44CC and ST-11CC. CONCLUSIONS: The detection of IMD in Poland has changed over time, but observed increase in the incidence of the disease was mostly attributed to changes in the surveillance system including an expanded case definition and inclusion of data from non-culture diagnostics.

Insight into antimicrobial susceptibility and population structure of contemporary human Enterococcus faecalis isolates from Europe.

OBJECTIVES: To investigate antimicrobial susceptibility and clonal relatedness of Enterococcus faecalis human isolates recovered recently (2006-09) in six European countries. METHODS: Antimicrobial susceptibility of 386 isolates from Denmark, Germany, Norway, Poland, Spain and The Netherlands, from hospital infections (223 isolates), carriage (82 isolates) and from colonization in the community (81 isolates) was determined by the broth microdilution method. Clonal relatedness of isolates was assessed by multilocus sequence typing. RESULTS: All isolates were susceptible to benzylpenicillin, ampicillin, linezolid, tigecycline and daptomycin. Non-susceptibility to tetracycline (77.6%), rifampicin (57.3%), ciprofloxacin (51.2%), aminoglycosides (43.3% high-level gentamicin resistance, 40.0% high-level streptomycin resistance) was frequent among hospital isolates, while non-susceptibility to glycopeptides was rare and associated mostly with vanA. Multidrug resistance was found in 59.7% of hospital isolates and 16.1% of community isolates. Isolates were classified into 105 sequence types (STs), of which 21 STs, representing more than half of the collected isolates (53.9%), grouped with 6 large E. faecalis clonal complexes (CCs; CC2, CC16, CC21, CC30, CC40 and CC87). Two of these, CC2 (frequently recovered in Spain and The Netherlands) and CC87 (prevalent in Poland), were found almost exclusively in hospitals and included the highest proportion of multiresistant isolates. CONCLUSIONS: While hospital-acquired E. faecalis in Europe remains susceptible to ampicillin and glycopeptides, the high prevalence of strains that are highly resistant to aminoglycosides excludes these antibiotics from combination therapies. Genotyping revealed that nosocomial infections by multiresistant E. faecalis are largely caused by only a few hospital-associated clones.

Efficiency of the Cepheid Xpert vanA/vanB assay for screening of colonization with vancomycin-resistant enterococci during hospital outbreak.

This study aimed to assess the efficiency of the Cepheid Xpert vanA/vanB test for detecting vancomycin-resistant enterococci (VRE) colonization during a VanA Enterococcus faecium outbreak and to compare the Cepheid Xpert vanA/vanB (Cepheid, Sunnyvale, USA) test to a culture method with chromogenic medium chromID VRE agar (bioMérieux). The Cepheid Xpert vanA/vanB assay showed sensitivity 61.5%, specificity 79.2%, positive predictive value 61.5% and negative predictive value 79.2%. The results obtained in this study demonstrate that a positive result in the Cepheid Xpert vanA/vanB test for vanA enables the rapid (less than 1 h) presumptive, prior to culture, recognition of patients colonized with VRE. However, the Cepheid Xpert vanA/vanB assay cannot be the only test used to screen patients during an ongoing VRE outbreak, because additional culturing of all samples negative for both vanA and vanB or positive for vanB should be performed in order to confirm the carrier status of the patient.

[Invasive pneumococcal disease in Poland in 2010]. / Inwazyjna choroba pneumokokowa w Polsce w roku 2010.

UNLABELLED: Streptococcus pneumoniae is the main etiologic agent of community-acquired invasive infections, especially in extreme age groups. Recently, the emergence of pneumococcal conjugate vaccines (PCV) brought a possibility to reduce the number of pneumococcal infections. Their introduction requires a knowledge concerning epidemiology of infections, which in different part of the world differs and changes with time, and therefore must be under permanent surveillance. THE AIM OF THIS STUDY: To characterize invasive pneumococcal disease (IPD) in Poland in 2010 based on data collected by the National Reference Centre for Bacterial Meningitis (NRCBM). MATERIAL AND METHODS: The study was performed on all invasive S. pneumoniae isolates collected in 2010 by the NRCBM. All the strains were identified and serotyped based on routine techniques. Minimal inhibitory concentrations (MICs) were determined by the Etest or M.I.C. Evaluators method. For the incidence rate assessment, cases where the pneumolysin gene was detected by PCR in clinical material were included. RESULTS: The highest IPD incidence rates were among children under 5 years of age (3.43/100,000), and especially among children under 2 years of age (5.17/100,000). The vaccines PCV10 and PCV13 covered 54.9, and 75.4% of all IPD cases, 71.0 and 93.5% of cases among children under 2 years of age, and 71.2 and 92.3% among children under 5 years of age, respectively. Decreased susceptibility to penicillin (MIC > 0.06 mg/l) and cefotaxime (MIC > 0.5 mg/l) was found in 30.7 and 14.8% of isolates, respectively. All isolates were susceptible to rifampicin and vancomycin. Intermediate susceptibility and resistance to meropenem was notified in 6.1 and 5.7% of isolates. Resistance to chloramphenicol, erythromycin, clindamycin, tetracycline and co-trimoxazole was found in 8.0, 36.7, 29.9, 30.7 and 34.5% of isolates, respectively. CONCLUSIONS: Results of the study showed high theoretical coverage of pneumococcal conjugate vaccines among IPD cases in general and especially among infections caused by isolates with decreased susceptibility to antibiotics. Therefore, it seams that the best way to limit invasive pneumococcal disease-associated morbidity and mortality, especially of cases caused by bacteria with decreased susceptibility to antibiotics, is the inclusion of a PCV in the immunization programme in Poland.

The current status of invasive pneumococcal disease in Poland.

The objectives of this study were to assess the incidence of invasive pneumococcal disease (IPD) in Poland (2006-2009), where mass vaccination had not been implemented, and to determine the serotype distribution and antimicrobial susceptibility of Streptococcus pneumoniae isolates. The IPD incidence rates were highest among children under 2 years of age (3.39/100,000 in 2009) and children 2-5 years old (2.44/100,000). The most common serotypes were 14, 3, 1, 4, 19F, 23F, 6B, and 12F (61.7% of all isolates). In children aged less than 5 years, isolates of serotypes 14, 6B, and 19F were most prevalent (52.7% of the IPD cases). The PCV7, PCV10, and PCV13 covered 43.3%, 54.8%, and 68.8% of all IPD cases, and 68.7%, 76.3%, and 86.3% of cases involving children under 5 years of age. Penicillin resistance was found in 21.3% of the isolates responsible for meningitis and in 1.2% of isolates responsible for other invasive infections. Introduction of antipneumococcal conjugated vaccines into the national immunisation programme would likely lead to a significant reduction of IPD-associated morbidity among Polish children in particular, as well as in the population as a whole, especially in cases involving pneumococci with a decreased susceptibility to antibiotics.

First report of Streptococcus pneumoniae serotype 6D isolates from invasive infections.

We report the first invasive Streptococcus pneumoniae isolates of serotype 6D and the first occurrence of this serotype in Europe. Till now, the appearance of serotype 6D pneumococci in nasopharyngeal carriage has been speculated to be associated with a selective pressure from vaccination with the conjugated 7-valent antipneumococcal vaccine. Our observations indicate that this serotype is present also among unvaccinated individuals in the population where mass infant vaccination has not yet been introduced. Importantly, these strains were isolated from invasive infections, indicating the full virulence potential of pneumococci belonging to serotype 6D and its importance for future vaccine formulations.