Changes In Molecular Epidemiology Research Articles

Changes in molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in the intensive care units of a Greek hospital, 2018-2021.

The spread of multi-drug resistant (MDR) Gram-negative bacteria, including Klebsiella pneumoniae, constitutes a global threat. The most frequent mechanism of acquired carbapenem resistance is the production of carbapenemases, especially KPC, NDM, VIM, IMP and OXA-48. We analyzed the epidemiological trend of carbapenem resistance genes of carbapenem-resistant K. pneumoniae (CRKP) strains isolated from critically ill patients in a Greek tertiary hospital. The study included 150 CRKP isolates collected from 116 (77.4%) patients hospitalized in the adult ICU and 17 (11.3%) each in the pediatric and the two neonatal ICUs between March 2018 and March 2021. Identification and antimicrobial susceptibility testing were performed using VITEK-2. A multiplex lateral flow immunoassay was used for the detection of carbapenemases, while the detection of bla VIM, bla KPC, bla NDM, bla IMP and bla OXA-48-like genes was achieved by multiplex PCR. The bla NDM was mainly detected in adults (54/116, 46.9%), while in children the most often detected gene was bla KPC (24/34, 70.6%). The predominant carbapenem resistance gene during 2018-2019 was bla KPC alone or in combination with bla VIM, reaching 44.4% in 2019, while during 2020-2021 the detection of bla NDM prevailed significantly, reaching 45.5 and 60.7% for 2020 and 2021, respectively. A shift in the molecular epidemiology of CRKP was seen during 2018-2021, which is probably associated with the recent excessive empiric use of newer antimicrobials. Surveillance studies and proper and strict implementation of infection control measures are highly needed to decrease the spread of MDR bacteria, including CRKP.

Novel reassortant swine H3N2 influenza A viruses in Germany

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology. The data indicate that a novel reassortant, Rietberg/2014-like swine H3N2, emerged in February 2014 in Northern Germany. It is comprised of a hemagglutinin gene of seasonal H3N2 (A/Denmark/129/2005-like), a neuraminidase gene of Emmelsbuell/2009-like swine H1N2 and the internal gene cassette of pandemic H1N1 viruses. Together with Danish swine H3N2 strains of 2013–2015 with identical genome layout, the Rietberg/2014-like viruses represent a second swine H3N2 lineage which cocirculates with a variant of the Gent/1984-like swine H3N2 lineage. This variant, named Gent1984/Diepholz-like swine H3N2, has a Gent/1984-like HA and a Diepholz/2008-like NA; the origin of the internal gene cassette likely derived from avian-like swine H1N1. The first isolate of the Gent1984/Diepholz reassortant emerged in Northern Germany in September 2011 whereas the last German Gent/1984-like isolate was collected in October 2011.

Changes in epidemiologic characteristics and antimicrobial resistance of Streptococcus pyogenes isolated over 10 years from Japanese children with pharyngotonsillitis.

Introduction. Pharyngotonsillitis caused by Streptococcus pyogenes (group A streptococci, or GAS) is among the most common infections treated with antibiotics in pediatric patients.Aim. This study aimed to analyse changes in molecular epidemiology and antibiotic susceptibility among GAS isolates in three study periods spanning 10 years.Methodology. GAS isolated from paediatric patients with pharyngotonsillitis during Period I (mid-2007 to 2008, n=235), Period II (2012, n=210), and Period III (2018, n=189) were analysed for emm type, multilocus sequence type (MLST), antibiotic susceptibility, and macrolide (ML)- and quinolone (QL)-resistance genes.Results. Over 20 % of isolates represented emm1 and emm12 types, remaining common in all three periods. Among other emm types, emm4 was common in Period I, emm28 and emm89 in Period II, and emm3 and emm89 in Period III. All isolates remained highly susceptible to penicillins and cephalosporins. Isolates possessing mefA, ermA, or ermB genes mediating ML resistance increased from 34.9 % in Period I to 60.9 % in Period II, but fell to 27.5 % in Period III. QL-resistant isolates with amino acid substitutions affecting ParC and/or GyrA gradually increased from 11.5 to 14.3 %. Specific sequence types identified by MLST and emm typing were associated closely with ML or QL resistance.Conclusion. Our findings indicate that even in ambulatory care, antibiotic choice for these infections should be based on rapid identification and characterization of causative pathogens.

2404. Molecular Epidemiology of Clostridioides difficile in the United States, 2017

BackgroundIn 2009, the Centers for Disease Control and Prevention (CDC) implemented Clostridioides difficile infection (CDI) surveillance through the Emerging Infections Program (EIP) to monitor the incidence and evolving epidemiology of CDI in the United States. Since 2012, ribotypes (RTs) 027, 106, 002, 014, and 020 have constituted the top five strain types among both US community- and healthcare-associated isolates. Here we describe the changes in molecular epidemiology of C. difficile isolates collected in the United States in 2017.MethodsIn 2017, CDI surveillance was conducted at 10 EIP sites (CA, CO, CT, GA, MD, MN, NM, NY, OR, and TN). A convenience sample of clinical laboratories across EIP sites submitted C. difficile-positive stool specimens to the MN Department of Health Public Health Laboratory and Hines VA Hospital (IL) for culture. Isolates were forwarded to CDC and characterized by capillary-based PCR-ribotyping and PCR detection of tcdA, tcdB, cdtA, cdtB, and deletions in tcdC.ResultsIn 2017, 1,051 C. difficile isolates were submitted; the total number of isolates received from each site ranged from 11 to 286 with a median of 85.5. In total, 143 RTs were observed, with the majority of isolates harboring toxin genes tcdA and tcdB (95%) and a wild-type tcdC sequence (71%). Among 556 healthcare-associated isolates, RT 027 was the most prevalent and the top RT at 5 sites (CA, GA, MD, NM, TN). Ribotype 106 was the most prevalent among 495 community-associated CA isolates and the top RT at 6 sites (CO, CT, GA, MD, MN, TN). Ribotype 027 significantly decreased from 2012 to 2017 among both healthcare-associated (21% vs 15%; p = 0.02) and community-associated isolates (17% vs 6%; P < 0.0001). Among healthcare-associated isolates, RT 076, which was observed in 8 EIP sites, increased from 2% in 2016 to 5% in 2017 (p = 0.05) and replaced RT 020 as one of the top 5 healthcare-associated RTs in 2017.ConclusionDespite an overall decline since 2012, RT 027 remained the most prevalent RT among healthcare-associated isolates submitted in 2017. The increased frequency of RT 076 among healthcare-associated isolates submitted in 2017 highlights the evolving molecular epidemiology of C. difficile and the need for continued surveillance to monitor potential emerging strains.Disclosures All authors: No reported disclosures.

Changes in molecular epidemiology and antimicrobial resistance profiles of Clostridioides (Clostridium) difficile strains in the United States between 2011 and 2017

PCR ribotyping and antimicrobial susceptibility testing were used to characterize 940 Clostridioides (Clostridium) difficile isolates collected from 26 U S. hospitals over three time periods from 2011 to 2017. The proportion of ribotype (RT) 027 isolated during the three surveys decreased significantly over time from 31% in 2011–2012, to 22% in 2013–2014, and to 14% in 2015–2017 (p < 0.001 and p = 0.010, respectively), while we observed an increase in prevalence of RT106, that rose from 7% in our first survey to 19% of isolates in our last survey (p < 0.001). In addition, both RT056 and RT002 rose from 3% to 10% (p < 0.001). The proportions of all other ribotypes remained steady over time, and RT014/020 was the third most common strain type in our convenience sample in the final survey. Overall, resistance to moxifloxacin, rifampin, and vancomycin decreased during our studies, mainly due to the decline in RT027 isolates. A decrease in moxifloxacin resistance and an increase in tetracycline resistance were found among RT027 strains isolated in the last survey. Although the proportion of RT027 isolates declined, multidrug resistance among this ribotype continues to be common.

Distribution of Hepatitis C Virus Genotypes and Related Risk Factors Among Iranian Blood Donors: A Penalized Logistic Regression

Background: The hepatitis C virus (HCV) is a blood born virus and the major cause of liver diseases worldwide. Distribution of HCV genotypes varies depending on geographical regions and routes of infection. Knowledge regarding the distribution of HCV genotypes and related risk factors plays an essential role in the control of HCV infection in the community. Objectives: The current study aimed at determining the current distribution of HCV genotypes and related risk factors among Iranian blood donors. Methods: In the current analytical, cross sectional study, 106 HCV-infected blood donors with detectable HCV RNA over the country were interviewed by trained physicians through a post-donation questionnaire on demographic, medical, and risk history from November 2015 to May 2017. The hepatitis C virus genotype was determined by sequencing of a segment of non-structural 5B region in HCV genome. Penalized logistic regression model was used for statistical analysis through STATA software. Results: Hepatitis C virus genotype was determined in all subjects, and the genotype 3a was the most frequent (65, 61.32%), followed by 1a (31, 29.25%), and 1b (10, 8.49%). Based on the multivariable analysis results, tattooing (adjusted odds ratio: 2.76; 95% confidence interval: 1.03 - 7.37) was associated with HCV genotype 3a. Conclusions: According to the results, it seems that changes in molecular epidemiology of HCV infection and replacement of HCV genotype 1a with 3a, characterized by an increase in genotype 3a and decrease in genotype 1a have occurred over the last decade among Iranian blood donors. Tattooing was an independent risk factor for HCV infection by genotype 3a.

Clinical and Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit in the Decade following Implementation of an Active Detection and Isolation Program.

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent source of infection in the neonatal intensive care unit (NICU), often associated with significant morbidity. Active detection and isolation (ADI) programs aim to reduce transmission. We describe a comprehensive analysis of the clinical and molecular epidemiology of MRSA in an NICU between 2003 and 2013, in the decade following the implementation of an MRSA ADI program. Molecular analyses included strain typing by pulsed-field gel electrophoresis, mec and accessory gene regulator group genotyping by multiplex PCR, and identification of toxin and potential virulence factor genes via PCR-based assays. Of 8,387 neonates, 115 (1.4%) had MRSA colonization and/or infection. The MRSA colonization rate declined significantly during the study period from 2.2 to 0.5/1,000 patient days (linear time, P = 0.0003; quadratic time, P = 0.006). There were 19 cases of MRSA infection (16.5%). Few epidemiologic or clinical differences were identified between MRSA-colonized and MRSA-infected infants. Thirty-one different strains of MRSA were identified with a shift from hospital-associated to combined hospital- and community-associated strains over time. Panton-Valentine leukocidin-positive USA300 strains caused 5 of the last 11 infections. Staphylococcal cassette chromosome mec (SCCmec) types II and IVa and agr groups 1 and 2 were most predominant. One isolate possessed the gene for toxic shock syndrome toxin; none had genes for exfoliative toxin A or B. These results highlight recent trends in MRSA colonization and infection and the corresponding changes in molecular epidemiology. Continued vigilance for this invasive pathogen remains critical, and specific attention to the unique host, the neonate, and the distinct environment, the NICU, is imperative.

Changes in Molecular Epidemiology of Streptococcus pneumoniae Causing Meningitis following Introduction of Pneumococcal Conjugate Vaccination in England and Wales

The introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in September 2006 has markedly reduced the burden of invasive pneumococcal disease (IPD) including meningitis in England and Wales. This study examined changes in the molecular epidemiology of pneumococcal isolates causing meningitis from July 2004 to June 2009. The Health Protection Agency conducts enhanced pneumococcal surveillance in England and Wales. In addition to serotyping, pneumococcal isolates causing meningitis were genotyped by multilocus sequence typing (MLST). A total of 1,030 isolates were both serotyped and genotyped over the 5-year period. Fifty-two serotypes, 238 sequence types (STs), and 87 clonal complexes were identified, with no significant difference in the yearly Simpson's diversity index values (range, 0.974 to 0.984). STs commonly associated with PCV7 serotypes declined following PCV implementation, with a proportionally greater decline in ST124 (commonly associated with serotype 14). No other ST showed significant changes in distribution, even within individual serotypes. Replacement disease following PCV7 introduction was mainly due to serotypes 1, 3, 7F, 19A, 22F, and 33F through clonal expansion. A single instance of possible capsule switching was identified where one ST4327 clone expressed a serotype 14 capsule in 2005 and a serotype 28A capsule in 2009. In 2008 to 2009, ST191 (7F) became the most prevalent clone causing meningitis (10.3%). Case fatality (145 fatalities/1,030 cases; 14.1%) was high across all age groups and serotype groups. Thus, the introduction of PCV7 resulted in an increase in non-PCV7 serotypes, including some not covered by the 13-valent vaccine, such as serotypes 22F and 33F, emphasizing the importance of long-term epidemiological and molecular surveillance.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus in a Spanish hospital over a 4-year period: clonal replacement, decreased antimicrobial resistance, and identification of community-acquired and livestock-associated clones

This study was carried out on 189 methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates collected in a third-level hospital in Valladolid, Spain, between 2005 and 2008 in order to investigate the changes in molecular epidemiology and genetic backgrounds associated with the changes in resistance phenotypes produced over time. The MRSA isolates were classified as belonging to 10 different clones, including the identification of a novel MRSA clone, ST2422-MRSA-IV, belonging to CC121; 1 CA-MRSA strain from a USA300 clone; another from ST97-MRSA-IV, associated with clones adapted to livestock (LA-MRSA); and 2 strains belonging to a new spa type (t10258) related to the ST8-MRSA-IV clone. Sixty-two percent of the strains belonging to Spanish-prevalent MRSA sequence type ST125 harboured composite or multiple SCCmec elements including SCCmec type IV plus ccrA/B4 (ST125-SCCmec IV/VI). In the years studied, it was observed that ST125-SCCmec IV/VI replaced the multiresistant ST228-SCCmec I previously prevalent, and, as a consequence, decreased gentamicin and clindamycin resistance was further observed.

Clonal nature and diversity of resistance, toxins and adhesins genes of meticillin-resistant Staphylococcus aureus collected in a Spanish hospital

In this study we determined the prevalence of genes coding for antimicrobial resistance, toxins, enzymes, immunoevasion and adhesins factors among 189 meticillin-resistant Staphylococcus aureus (MRSA) strains isolated from a third level hospital in Valladolid (Spain) between 2005 and 2008 in order to examine the relationship between these pathogenicity determinants, both individually and in combination, and the genetic background of main MRSA strains that are presents in Spanish hospitals. MRSA isolates were first characterised epidemiologically by a combination of molecular typing strategies like spa, SCCmec and multilocus sequence typing, and then, a cluster analysis based on pathogenicity factors genes was performed according to the hybridisation pattern of 65 virulence, 36 resistance, 15 adhesins, and 11 set/ssl genes on a Diagnostic DNA microarray (Alere StaphyType DNA microarray Jena, Germany). CC5-agr type II [ST125-SCCmecIV/VI (32.2%) or ST125-IV (19.1%), ST228-I (19.1%), ST146-IV (13.7%) and ST5- IV (0.5%)] isolates was widely distributed. CC8-agr type I [ST8-IV (11.5%), USA300 clone (0.5%), and ST239-III (1.1%)]; CC45-agr type II [ST45- IV (1.6%)], and the CC97-agr type I [ST97-IV] were also detected. We identified 42 different resistance genes profiles, 22 set/ssl genes profiles, and 91 different virulence profiles. However although the high genetic diversity of MRSA strains, mainly with respect to virulence factors genes, the results of the simultaneous assessment of resistance and virulence genes and the genetic background illustrated a correspondence relationship (p<0.001) between the different clones and same resistance and virulence genes or clusters of them. During the study period we observed changes in molecular epidemiology of MRSA isolates and as a consequence we report the changes of the resistance and virulence potential of MRSA strains produced over time in our institution.

Changes in molecular epidemiology of community-associated and health care–associated methicillin-resistant Staphylococcus aureus in Korean children

Widespread emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has changed the epidemiology of S. aureus infections. We examined the molecular types and antibiotic susceptibility of CA-MRSA and health care–associated MRSA (HA-MRSA) among Korean children. MRSA isolates were obtained from patients admitted to university-affiliated tertiary hospitals in Korea, between 2006 and 2010. Molecular studies including multilocus sequence typing, SCCmec typing, and polymerase chain reaction amplification of PVL genes and antibiotic susceptibility tests were performed. SCCmec type IV was most frequently found for both CA-MRSA (80.0%) and HA-MRSA (56.4%). ST72-MRSA-SCCmec type IV and its single-locus variants were the most prevalent MRSA clones in the Korean pediatric population, both in community and in health care settings. The PVL genes were detected in 10% (4/40) of CA-MRSA isolates. Most of the clinical MRSA isolates showed vancomycin MIC ≥1.0 μg/mL. In conclusion, the molecular characteristics of HA-MRSA have been changing and CA-MRSA genotype overtook HA-MRSA genotype in health care settings.

Changes in antibiotic susceptibility and ribotypes in Clostridium difficile isolates from southern Scotland, 1979–2004

An increase in the incidence of clinical cases of Clostridium difficile infection has been reported in recent years, but few studies have examined changes in molecular epidemiology and antibiotic resistance over a long period of time. A collection of 179 isolates of C. difficile obtained from symptomatic adult patients in southern Scotland between 1979 and 2004 was used to determine changes in the prevalence of epidemiological types and antibiotic susceptibilities to common antibiotics. PCR ribotyping and MIC determination were performed on all isolates. A total of 56 different ribotypes were identified, among which ribotype 002 was the commonest type overall (14 .0%), followed by ribotypes 014 (7.3 %), 012 (5 .0%), 015 (5.0 %), 020 (5 .0%) and 001 (4.5 %). Ribotype 078 was also identified. The 10 commonest ribotypes comprised 55 % of the total isolates. Ribotype 001 increased in prevalence from 1.5 to 12.2 % over the study years, whereas the prevalence of ribotype 012 decreased from 8.7 to 2 .0%. Resistance to clindamycin, erythromycin and ceftriaxone was found in 95.5, 14.0 and 13.4 % of isolates, respectively. Resistance to vancomycin or metronidazole was not detected. Thirty-two (17.9 %) and 14 (7.8 %) isolates were resistant to two and three or more antibiotics, respectively. Ribotype 001 displayed maximum resistance, with 50 % of isolates resistant to erythromycin, moxifloxacin and ceftriaxone, and 100 % resistant to clindamycin. Over the 26 years of the study, antibiotic resistance and ribotype prevalence have changed, and antibiotic pressures may have been the major driver of this change.

Factors affecting the changes in molecular epidemiology of acute hepatitis B in a Southern Italian area

To explore changes in molecular epidemiology of acute viral hepatitis B (AVH-B), hepatitis B virus (HBV) genotypes were determined by direct sequencing of the Pre-S-S region in 123 consecutive patients, with AVH-B observed in Naples or its surroundings in the last decade (group AVH-B) and in 123 HBV chronic carriers [chronic carrier of HBV (CC-B) group] from the same areas, who had been hepatitis B surface antigen-positive for more than 10 years. Genotype D was less frequently detected in patients with AVH-B than in those in the CC-B group (76.4%vs 97.5%, P < 0.0001). In the AVH-B group, intravenous drug addiction (IVDA) was the prevalent risk factor (55.3%) for acquiring HBV in the 94 patients with HBV genotype D, but it was rarely recorded (6.9%) in the 29 patients with genotypes non-D (P < 0.0001); unsafe sexual intercourse was prevalent in patients with genotype non-D (72.3%) and less frequent in those with genotype D (28.8%, P < 0.005). In the AVH-B group, the prevalence of non-D genotypes increased during the observation period from 11.1% in 1999-2003 to 41.1% in 2004-2008 (P < 0.0005), paralleling the increase in the prevalence of patients with unsafe sexual intercourse; similarly, the progressive decrease in IVDA paralleled the decrease in the prevalence of genotype D (from 88.3% in 1999-2003 to 11.7% in 2004-2008). The prevalence of HBV non-D genotypes recorded in the last 10 years in AVH-B in this area shows a progressive increase, most probably because of recent changes in HBV epidemiology, namely, the HBV mass vaccination campaign and increased immigration from areas with high HBV endemicity.

P63 Dynamic changes in molecular epidemiology of Clostridium difficile from inpatients at Canadian hospitals, 2005 to 2008

This study aimed to identify the molecular determinants responsible for antibiotic resistance among human wound isolates in Cambodia. Staphylococcus spp. (n = 10) and a variety of Gram-negative isolates (n = 21) were taken from a larger collection of wound isolates collected during 2011–2013 and were analysed for the presence of >230 resistance determinants using a broad-spectrum DNA microarray. These isolates were chosen to represent the species most commonly found in wound isolates referred during this time and to include some of the most resistant strains. Resistance determinants detected among the staphylococci included blaZ (90%), mecA (100%), erm(B) (70%), erm(C) (20%), tet(38) (90%), tet(K) (40%), tet(Lp) (10%), tet(M) (20%), lnu(A)/lin(A) and lnu(B)/lin(B) (10% each), msr(A)/msr(B)/msr(SA) (10%), norA (80%) and dfrA (10%). Eleven different β-lactamase genes were detected among the Gram-negative bacteria, including genes encoding the TEM (48%), CTX-M-1 (48%), CTX-M-9 (5%), SHV (5%) and VEB (10%) families of broad-spectrum and extended-spectrum β-lactamase enzymes, as well as the carbapenemase gene blaOXA-23. Forty additional genes were also detected in the Gram-negative isolates conferring resistance to aminoglycosides (11 genes), phenicols (5 genes), macrolides [4 genes, including mph(A)/mph(K) (10%)], lincosamides [lnu(F)/lin(F), lnu(G)/lin(G)], tetracycline (4 genes), rifampicin [arr (29%)], quaternary amines [qacEΔ1 (43%)], quinolones [qnrS (14%) and qnrB (5%)], sulfonamides [sul1 (29%), sul2 (38%) and sul3 (10%)], streptothricin (sat2) and trimethoprim (6 genes). The results obtained here provide a snapshot of the broad variety of resistance determinants currently circulating within Cambodia.