Sequence Types Types Research Articles

Diversity of Oxacillinases and Sequence Types in Carbapenem-Resistant Acinetobacter baumannii from Austria.

Carbapenem-resistant Acinetobacter baumannii is a significant health problem worldwide. A multicenter study on A. baumannii was performed to investigate the molecular epidemiology and genetic background of carbapenem resistance of A. baumannii isolates collected from 2014–2017 in Austria. In total, 117 non-repetitive Acinetobacter spp. assigned to A. baumannii (n = 114) and A. pittii (n = 3) were collected from four centers in Austria. The isolates were uniformly resistant to piperacillin/tazobactam, ceftazidime, and carbapenems, and resistance to imipenem and meropenem was 97.4% and 98.2%, respectively. The most prominent OXA-types were OXA-58-like (46.5%) and OXA-23-like (41.2%), followed by OXA-24-like (10.5%), with notable regional differences. Carbapenem-hydrolyzing class D carbapenemases (CHDLs) were the only carbapenemases found in A. baumannii isolates in Austria since no metallo-β-lactamases (MBLs) nor KPC or GES carbapenemases were detected in any of the isolates. One-third of the isolates harbored multiple CHDLs. The population structure of A. baumannii isolates from Austria was found to be very diverse, while a total of twenty-three different sequence types (STs) were identified. The most frequent was ST195 found in 15.8%, followed by ST218 and ST231 equally found in 11.4% of isolates. Two new ST types, ST2025 and ST2026, were detected. In one A. pittii isolate, blaOXA-143-like was detected for the first time in Austria.

Prevalence and Genotyping of Campylobacter jejuni and Campylobacter coli from Ovine Carcasses in New Zealand

A pilot survey was performed to determine the prevalence of Campylobacter jejuni and Campylobacter coli on three age classes (lamb, hogget, and mutton) of ovine carcass trim postdressing and prechill. Sampling of hogget carcasses was undertaken 6 months before sampling of lamb and mutton carcasses. A total of 120 trim samples were collected from 11 processing plants across New Zealand. All samples were enriched and screened using PCR for the presence of C. jejuni and C. coli, and isolation was attempted for all screen-positive samples. Enumeration of Campylobacter from lamb trim samples showed that Campylobacter bacteria were present in very low numbers (<10 CFU/g). The overall prevalence of Campylobacter for ovine trim based on PCR detection was 33% (39 of 120 samples), with prevalences for hogget, lamb, and mutton carcass trim of 56% (28 of 50), 11% (4 of 35), and 20% (7 of 35), respectively. Whole genome sequencing was performed on a selection of C. jejuni and C. coli isolates, and the data were used to subtype using multilocus sequence typing (MLST) and whole genome MLST. Twenty-five MLST sequence types (STs) were identified among 44 isolates, including ST42, ST50, ST3222, and ST3072, which have been previously reported to be associated with ruminant sources. Four novel STs were also identified. Whole genome MLST analysis further discriminated isolates within a single ST type and demonstrated a genetic diversity among the ovine isolates collected. Genes associated with the oxacillinase class of β-lactamase enzymes were identified in 41 of 44 Campylobacter isolates. This study provides preliminary data that can be incorporated into existing source attribution models to assist in determining the potential contribution of ovine sources to the burden of campylobacteriosis in New Zealand.

Molecular characterization of clinical isolates from vascular access infection: A single-institution study.

Hemodialysis requires repeated, reliable access to the systemic circulation; therefore, a well‐functioning vascular access (VA) procedure is crucial for stable hemodialysis. VA infections (VAIs) constitute the most challenging complication and cause considerable morbidity, loss of access, and even death. In this study, we investigated the molecular profiles of different bacterial isolates retrieved from various types of VA grafts. We collected clinical isolates from hemodialysis patients with VAIs in our institution for the period between 2013 and 2018. We identified the bacterial isolates using standard biochemical procedures; we used a polymerase chain reaction for coagulase‐negative staphylococci (CoNS) and Burkholderia cepacia complex (BCC) species identification. The antibiotic resistance and molecular profile were analyzed using the disk diffusion method and multilocus sequence typing, respectively. We studied 150 isolates retrieved from patients with VAI and observed that Staphylococcus aureus was the predominant bacterial species, followed by S. argenteus, BCC, and CoNS. According to multilocus sequence typing data, we identified a wide variety of sequence types (STs) in S. aureus isolates, with ST59, ST45, and ST239 being the predominant types. Burkholderia cepacia with two new ST types, namely ST1723 and ST1724, accounted for most of the BCC infections, along with ST102 B. contaminans, which were mainly isolated from infected tunneled‐cuffed catheters. In summary, the increased incidence of S. argenteus and BCC infections provides insights into their potential clinical effects in VAIs. The various STs identified in different bacterial species indicate the high genetic diversity of bacterial species isolated from VAIs in our institution.

Diversity of the diploid sequence type of Candida albicans clinical isolates from a tertiary-care hospital in Mwanza, Tanzania.

Geographical strain variations of Candida albicans causing different clinical conditions in susceptible individuals have been reported. In this study, the distribution of diploid sequence type of C. albicans was investigated in Mwanza, Tanzania. A total of 64 C. albicans were selected on the basis of their antifungal susceptibility patterns, followed by multilocus sequence typing (MLST) to establish the circulating sequence types (STs). Forty-eight MLST were obtained out of 64 isolates amounting to 75% population structure differences. Out of these STs, 27 (56.3%) were new diploid ST types. C. albicans isolates with new ST were more diverse than isolates with known STs (27/29, 93.1% vs. 21/35, 60%, p 0.002). In conclusion, C. albicans from clinical specimens were highly diverse, with more than half of the detected diploid ST not previously reported in the MLST database, thus confirming the genetic differences of C. albicans from different geographical regions.

Insight into Molecular Epidemiology, Antimicrobial Resistance, and Virulence Genes of Extensively Drug-Resistant Acinetobacter baumannii in Thailand.

Extensively drug-resistant Acinetobacter baumannii (XDR-AB) is a major threat to public health worldwide. A retrospective study for 27 XDR-AB isolates from four tertiary hospitals in Thailand was conducted. Beta-lactamase and virulence genes were characterized by PCR. The blaADC, blaOXA-51, and blaOXA-23 were detected in all isolates, whereas blaPER-1 and blaNDM-1 genes were present in 7.4% and 3.7% of isolates. All isolates had virulence genes, including genes in iron acquisition system, biofilm formation and secretion systems. The plasmids in XDR-AB belonged to GR2 (100%), GR6 (40.7%), and GR1 (7.4%). Multilocus sequence typing sequence types (STs) were further investigated. The data demonstrated that XDR-AB isolates had nine STs: ST195 (n = 4), ST208 (n = 4), ST368 (n = 1), ST451 (n = 5), ST457 (n = 2), ST1947 (n = 1), ST1166 (n = 7), including two novel STs namely ST1682 (n = 2) and ST1684 (n = 1). We observed that the majority ST1166 (25.9%) was associated with the prevalence of GR2 and GR6 plasmids and traU virulence gene. Genome-based single nucleotide polymorphism phylogenetic analysis of the isolates with two novel ST types indicated that the two isolates belonged to the international clone II (IC2) within the same cluster. In conclusion, our data showed the dissemination of XDR-AB isolates harbored virulence genes and antibiotic resistance genes among four hospitals in Thailand. The results highlighted the difficulty posed for the empirical treatment of the patients with the A. baumannii infection.

Diphtheria in Metro Manila, the Philippines 2006-2017: A Clinical, Molecular, and Spatial Characterization.

BackgroundDiphtheria is a vaccine-preventable disease that persists as a global health problem. An understanding of the pattern of disease is lacking in low- and middle-income countries such as the Philippines.MethodsWe conducted a retrospective review of the clinical, microbiological, and epidemiological features of patients admitted with a clinical diagnosis of diphtheria to an infectious disease referral hospital in Metro Manila, the Philippines, between 2006 and 2017. Cases were mapped and the distribution was compared with population density. Corynebacterium diphtheriae isolates from between 2015 and 2017 were examined by multilocus sequence typing (MLST).ResultsWe studied 267 patients (range:12−54 cases/year) admitted between 2006 and 2017. The case fatality rate (CFR) was 43.8% (95% confidence interval, 37.8−50.0%). A higher number of cases and CFR was observed among children <10 years. Mortality was associated with a delayed admission to hospital and a lack of diphtheria antitoxin. Between 2015 and 2017 there were 42 laboratory-confirmed cases. We identified 6 multilocus sequence types (STs). ST-302 was the most common (17/34, 48.6%), followed by ST67 (7/34, 20%) and ST458 (5/34, 14%). Case mapping showed a wide distribution of diphtheria patients in Metro Manila. Higher case numbers were found in densely populated areas but with no apparent clustering of ST types.ConclusionsOur analysis indicates that diphtheria remains endemic in Metro Manila and that the infection is frequently fatal in young children. Improved vaccine coverage and a sustainable supply of diphtheria antitoxin should be prioritized.

636. Genome Epidemiology of Carbapenem-Resistant Acinetobacter baumannii (CRAb) in the United States

BackgroundCRAb is a major cause of healthcare-associated infections and is associated with high mortality due to the lack of reliable treatment options. We aimed to elucidate the contemporary population structure of CRAb isolates circulating in US hospitals using whole-genome sequencing (WGS).MethodsA total of 131 CRAb isolates were identified at four tertiary care medical centers located in Ohio, Pennsylvania, Texas and North Carolina between 2017 and 2018. The genomes were sequenced with Illumina NextSeq and de novo assembled. Sequence types (STs) were identified using the Pasteur Institute MLST scheme. β-Lactamase genes were identified by ResFinder and manually curated.ResultsThe 131 isolates belonged to 10 different ST types, including 8 known and 2 novel ones. In this collection, 101 isolates (77.1%) belonged to ST2, the dominant drug-resistant clone in the United States and Europe; 20 isolates belonged to ST499, a less common, but also globally distributed clone. Two isolates each belonged to ST46 and ST79, both common in South America. For the chromosomally encoded blaOXA-51-group genes, 11 variants were identified with blaOXA-66, blaOXA-82, and blaOXA-95 being predominant. For the chromosomally encoded blaADC-group genes, 26 variants were identified, with blaADC-161, blaADC-181, and blaADC-30 being the most common. The most frequent acquired carbapenemase gene was blaOXA-23, which was present in 89 isolates (67.9%). Other acquired blaOXA carbapenemase genes were identified much less frequently and included blaOXA-24, blaOXA-72, blaOXA-207, and blaOXA-237. 17 isolates (13.0%) did not contain any known acquired carbapenemase genes despite resistance to carbapenems.ConclusionST2 is the most prevalent ST type among contemporary CRAb isolates identified in US hospitals, however, new STs are emerging, most notably ST499. Significant diversity was seen among chromosomal blaOXA-51-group carbapenemase, intrinsic blaADC-group cephalosporinase and plasmid-mediated blaOXA-group carbapenemase genes, which likely represented diversification within the STs. Correlations between clinical presentation and outcomes and the genomic features of the infecting isolates are being investigatedDisclosures All authors: No reported disclosures.

Antibiotic resistance and virulence factors of Escherichia coli from eagles and goshawks

One of the major global problems in medicine is microbial resistance to antibiotics (antimicrobial resistance) and this has become an increasingly frequent research topic. This study focuses on antimicrobial resistance, phylogenetic and genetic characterization of Escherichia coli from wild birds: ten isolates from eagles (Aquila chrysaetos), nine from goshawks (Accipiter gentilis) and 24 from broilers in the Slovak Republic. Twenty-two strains with presence of int1 gene were selected and examined for the presence or absence of transposon gene (tn3), genes of antibiotic resistance and virulence factors. We detected sequence type (ST) in eagles ST 442 with genes iss, papC, iutA, cvaC, tsh, fyuA, iroN, kps, feoB, sitA, irp2, ireA for virulence factors and tetA, sul1, sul2, dfrA, aadA for antibiotic resistance; in goshawks ST 1011 with iss, papC, fyuA, iroN, feoB, sitA and qnrS1, tetA, sul1, sul2, dfrA, aadA, respectively. These ST types have been found in humans too and should be evaluated further for possible zoonotic potential and transfer of resistance genes from the environment.

Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017.

Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA’s Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a. Here we described the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010–2017, and determined their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by FDA field labs (ORA), and food testing by a contract company. Only 276 (83%) strains were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% saa (26%)]. Virulence gene prevalence was also determined: stx1 only (19%); stx2 only (66%); and stx1/sxt2 (15%). Our data form a new WGS dataset that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods.

Molecular Epidemiology of Panton-Valentine Leukocidin Harboring Hospital-Associated Methicillin-Resistant Staphylococcus aureus in Septicemic Children, Northeastern Iran, Bojnurd

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for an increasing number of serious hospital- and community-acquired infections in adults and children. Sepsis caused by S. aureus is one of the major health problems associated with treatment failure in adults; however, its clinical outcomes, the rate of treatment failure, and its molecular epidemiology are poorly understood. Objectives: The objective of this study was to evaluate the molecular epidemiology of Panton-Valentine Leukocidin (PVL) harboring MRSA strains isolated from children's blood culture in Bojnurd. Methods: Totally, 58 S. aureus strains were isolated from blood cultures in the major teaching hospital in Bojnurd. After the primary verification of Methicillin resistance by agar screening method, the isolated MRSA strains were confirmed with the detection of the mecA gene. MecA-positive strains evaluated for SCCmec, agr, and toxin profiles. Panton-valentine leucocidin-positive isolates were subjected to be evaluated for spa and sequence type (ST). Results: Our data indicated 53.4% (31) of isolates were MRSA. Twelve (38.7%) of these isolates had PVL gene that 25% (3) of them had tsst-1 gene and 58.3% (7) had etb gene. One (3.2%), 64.5% (20), and 32.2% (10) of these isolates belonged to SCCmec I, III, and IV, respectively. Predominant ST and spa types among PVL positive isolates were ST6 and t304, respectively. Conclusions: We had an uncommon finding because PVL was routinely found in community-acquired MRSA, but in this study we found PVL harboring hospital-associated MRSAs. A notable point about these isolates is that most of them belonged to Asian endemic clones.

Characterization of the clonal profile of methicillin resistant Staphylococcus aureus isolated from patients with early post-operative orthopedic implant based infections

BackgroundTo analyze the molecular epidemiology and to compare between the major methicillin resistant Staphylococcus aureus biotypes for association with patient characteristics who had an implant for closed fracture and developed early post-operative wound infections (POWI) in a tertiary care hospital of India.MethodsPulsed-field gel electrophoresis (PFGE), antimicrobial resistance, accessory gene regulator (agr) and staphylococcal cassette chromosome mec (SCCmec) types, Paton–Valentine leukocidin (PVL) gene, toxin gene profiling, biofilm formation and patient demographics were correlated with MLST clonal complexes (CC).FindingsOverall eight different sequence types (STs) were detected with a predominance of ST239 (66%), ST22 (18%) and some minor types ST772, ST30 (4% each) ST1, ST642, ST6, ST107 (2% each). All ST239 isolates belong to CC239 and SCCmec III whereas ST22 isolates belong to CC22 and SCCmec IV. The isolates varied in the distribution of various toxin genes. With 63.63% biofilm formers ST239 were all multidrug resistant with frequent resistance to erythromycin, clindamycin, gentamicin, cefuroxime, amoxyclav and ciprofloxacin indicating doxycycline, amikacin, vancomycin and linezolid can be the drug of choice.ConclusionThis study shows that ST239 MRSA is still most prevalent strain with new emergence of ST642 and ST107 isolates in association with orthopedic implant based POWI. As compare to other ST types ST239 strain was associated with adverse treatment outcomes. This highlights the importance of improving nosocomial infection control measures in this unit.

Extremely Low Prevalence of Erythromycin-Resistant Streptococcus pyogenes Isolates and Their Molecular Characteristics by M Protein Gene and Multilocus Sequence Typing Methods

Background: Group A streptococci (GAS) are notorious bacteria causing a wide variety of clinical manifestations ranging from mild, acute streptococcal pharyngitis to chronic non-suppurative diseases and immunological sequelae. They are further complicated by the global rise on the emergence of macrolide resistance among these bacteria in which several M protein gene (emm) and sequence types are associated with invasive diseases. Objectives: The current study aimed at determining the erythromycin resistance patterns and molecular characteristics of GAS clinical strains by emm and multilocus sequence typing (MLST) methods. Methods: Thirty-five GAS clinical isolates were subjected to antibiotic susceptibility testing by disk diffusion method. The minimum inhibitory concentration (MIC) of erythromycin against GAS by E-test was determined. Clinical and laboratory standards institute (CLSI) guideline was used for the interpretation of results. Detection of ermA, ermB, and mefA genes by polymerase chain reaction (PCR) was performed and emm typing was done by amplification and sequencing of emm genes per standard protocol. Allele and sequence type (ST) of GAS were obtained using the S. pyogenes MLST database. Results: All the isolates were sensitive to erythromycin, penicillin, clindamycin, chloramphenicol, and vancomycin (100%). Resistance to tetracycline was 54.3%. The mefA gene was found in one erythromycin susceptible isolate. No other erythromycin resistance genes were detected in the isolates. Twenty different emm types were found and the most frequent emm types/subtypes detected were emm1, emm18.21, emm28.5, emm97.4, and emm102.2 (each 8.6%). However, no new emm type was detected. A total of 15 sequence types (STs), eight clonal clusters (CCs), and eight singletons were identified among 21 representative isolates. Three isolates exhibited CC1 (ST28/emm1). Conclusions: High susceptibility of GAS isolates against erythromycin could be due to low antibiotic selective pressure in Malaysian clinical settings. High diversity of emm and ST types revealed the heterogenic nature of the strains circulating in Malaysian hospitals. Continuous epidemiological monitoring by molecular typing methods is warranted to improve the management strategies of GAS infections in future.

Investigation of molecular epidemiology of methicillin-resistant staphylococcus aureus in department of critical care medicine

Objective: To investigate the feature of antimicrobial resistance, homology and other molecular epidemiology of methicillin-resistant staphylococcus aureus(MRSA) in Department of Critical Care Medicine(ICU). Methods: From October 2010 to December 2011, 149 strains of MRSA were collected and identified through sputum culture of patients from 10 ICUs of 10 teaching hospitals distributed in 9 chinese central city of China. Susceptibility testing to 18 kinds of antibiotic was performed, the method of pulsed field gel electrophoresis (PFGE) was used to analyze the homology, and the technique of multilocus sequencing typing (MLST) was used to identify the sequence type (ST). Results: Antibiotic susceptibility testing implied that vancomycin, daptomycin and linezolid are 100% sensitive to collected 149 strains of MRSA. Cotrimoxazole resistance rate is about 0-11.1%. Rifampicin resistant rate was less than 25% in 2 hospitals; the resistance rate of gentamicin and moxifloxacin were more than 80% besides of 50% to70% in 3 hospitals; beta lactam resistant rate was 100%. In 149 strains of MRSA, the main types of PFGE were J (28.9%), C (19.5%), G (10.7%), F (8%)types. J, C, G types mainly distributed in the North, while the F type only distributed in the Guiyang region. The MLST type: 8 ST types were determined ultimately. In which, was dominated by ST-239(67 strains, 45%), distributed in the South and North; followed by ST-5 (54 strains, 36.2%), mainly in the Northeast region (χ2=26.42, P<0.01). Conclusions: Vancomycin, daptomycin and linezolid are 100% sensitive drugs to MRSA in ICU; Higher regional homology for MRSA were observed and it is probably that homologic disseminated infection exited in ICU. It is necessary to enhance continuous monitoring and take effective nosocomial infection control action to avoid MRSA homologic outbreak.

Multilocus Sequence Types and Virulence Determinants of Hypermucoviscosity-Positive Klebsiella pneumoniae Isolated from Community-Acquired Infection Cases in Harbin, North China.

We investigated the molecular epidemiologic characteristics and virulence of hypermucoviscosity-positive Klebsiella pneumoniae in mainland China. We detected 16 hypermucoviscosity-positive strains in 65 total clinical isolates (24.62%). We found that 68.75% (11/16) of the positive strains had K2 genotype and carried the rmpA and iucA genes. Multilocus sequence typing revealed 5 sequence types (STs): ST65 [7], ST23 [4], ST86 [3], ST412 [1], ST375 [1], whereas the remaining 4 isolates were defined as other STs. The order of the median lethal dose values for the ST types was ST23 (2.19 × 10(3) CFU/mouse) < ST86 (1.70 × 10(4) CFU/mouse) < ST65 (5.05 × 10(7) CFU/mouse) < the other STs (1.90 × 10(8) CFU/mouse). In conclusion, the K2 with ST65 carrying rmpA and iucA was the most predominant among the hypermucoviscosity-positive K. pneumoniae strains obtained from community-acquired infection cases in Harbin, North China. Sequence types are a valuable tool to predict the risk of K. pneumoniae infection.

Multilocus Sequence Types of Campylobacter jejuni Isolates from Different Sources in Eastern China.

Campylobacter jejuni is a major food-borne pathogen that causes human gastroenteritis in many developed countries. In our study, we applied multilocus sequence typing (MLST) technology to 167 C. jejuni isolates from diverse sources in Eastern China to examine their genetic diversity. MLST defined 94 sequence types (STs) belonging to 18 clonal complexes (CCs). Forty-five STs from 60 isolates (36%) and 22 alleles have not been previously documented in an international database. One hundred and two isolates, accounting for 61.1% of all isolates, belonged to eight clonal complexes. The eight major CCs were also the most common complexes from different sources. The most common ST type of isolates from human and food was ST-353. The dominant ST type in chicken and foods was ST-354. Among 21 STs that contained two or more different sources isolates, 15 STs contained human isolates and isolates from other sources, suggesting that potentially pathogenic strains are not restricted to specific lineages.

Identification and characterization of cfr-positive Staphylococcus aureus isolates from community-onset infectious patients in a county hospital in China.

The cfr gene was detected in 14 meticillin-susceptible Staphylococcus aureus isolates recovered from outpatients with community-onset infections in a county hospital in China. The MIC of linezolid was 4 μg ml- 1 in eight isolates and 2 μg ml- 1 in six isolates. All isolates were susceptible to vancomycin and teicoplanin, but had elevated MICs for penicillin (0.5-128 μg ml- 1), chloramphenicol (2-32 μg ml- 1), clindamycin (0.5-128 μg ml- 1) and erythromycin (4-128 μg ml- 1). Nine isolates had mutations on domain V of 23S rRNA and/or the ribosomal L proteins that were not located close to the linezolid-binding pocket. Southern blotting experiments demonstrated that the cfr genes in all 14 isolates resided on plasmids. Sequence analysis of the 5.6 kb cfr-carrying plasmid segment revealed 99 % identity to the corresponding sequences in plasmid pSS-01 from animal staphylococci and plasmid pRM-01 from human staphylococci. Five isolates belonged to sequence type (ST)188 and three to ST965; the two ST types were previously reported in isolates of animal origin in some areas of China. These results indicate that the cfr-carrying plasmids in this study are likely of animal origin. The present study shows that cfr-harbouring S. aureus isolates have emerged in some areas of China and that cfr-carrying isolates may be transmitted between animals and humans.

Predominant Campylobacter jejuni sequence types persist in Finnish chicken production.

Consumption and handling of chicken meat are well-known risk factors for acquiring campylobacteriosis. This study aimed to describe the Campylobacter jejuni population in Finnish chickens and to investigate the distribution of C. jejuni genotypes on Finnish chicken farms over a period of several years. We included 89.8% of the total C. jejuni population recovered in Finnish poultry during 2004, 2006, 2007, 2008, and 2012 and used multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) to characterize the 380 isolates. The typing data was combined with isolate information on collection-time and farm of origin. The C. jejuni prevalence in chicken slaughter batches was low (mean 3.0%, CI95% [1.8%, 4.2%]), and approximately a quarter of Finnish chicken farms delivered at least one positive chicken batch yearly. In general, the C. jejuni population was diverse as represented by a total of 63 sequence types (ST), but certain predominant MLST lineages were identified. ST-45 clonal complex (CC) accounted for 53% of the isolates while ST-21 CC and ST-677 CC covered 11% and 9% of the isolates, respectively. Less than half of the Campylobacter positive farms (40.3%) delivered C. jejuni-contaminated batches in multiple years, but the genotypes (ST and PFGE types) generally varied from year to year. Therefore, no evidence for a persistent C. jejuni source for the colonization of Finnish chickens emerged. Finnish chicken farms are infrequently contaminated with C. jejuni compared to other European Union (EU) countries, making Finland a valuable model for further epidemiological studies of the C. jejuni in poultry flocks.

Multilocus Sequence Types of Invasive and Colonizing Neonatal Group B Streptococci in Poland

Objectives: The present study aimed to investigate the molecular characterization of Streptococcus agalactiae (group B streptococcus; GBS) strains isolated from newborns with invasive neonatal infections and healthy newborns in Poland. Materials and Methods: Forty-two GBS isolates were characterized by combining different typing methods, i.e. multilocus sequence typing (MLST), molecular serotyping and protein gene profiling. Results: Using MLST, a total of 16 sequence types (STs) were identified, and among these, 11 were clustered into the following 5 clonal complexes (CCs): CC23 (20; 49%), CC19 (7; 17%), CC17 (4; 10%), CC10 (4; 10%) and CC1 (1; 2%). A statistically significant relationship between ST-17 and invasive isolates (p = 0.0398) and ST-23 and colonizing strains (p = 0.0034) was detected. Moreover, 2 novel STs were detected (ST-637 and ST-638). Molecular serotyping showed that in the invasive isolates serotype III was predominant (11; 50%), followed by serotypes II (6; 27%), V (3; 14%) and Ia (2; 9%). In healthy newborns, serotype III was also dominant (12; 60%), followed by serotypes Ia (4; 20%), II (2; 10%), V (1; 5%) and Ib (1; 5%). Protein gene profiling indicated that the rib gene was predominant in the invasive strains (11; 59%), followed by bca (5; 22%), alp2 (2; 9%), alp3 (1; 5%) and epsilon (1; 5%), while in colonizing strains the alp2 gene was most common (10; 50%), followed by epsilon (5; 25%), rib (2; 10%), bca (2; 10%) and alp3 (1; 5%). A statistically significant relationship was noted between the rib gene and invasive GBS (p = 0.0329), whereas alp2 was related to the colonizing strains (p = 0.0495). Conclusions: The investigated GBS isolates originating from infections in newborns and healthy neonates represented serotype III in more than half of the cases and differed from one another in terms of resistance to macrolides, ST type affiliation and the presence of genes encoding surface proteins from the Alp family. Further comparative genetic research on a larger number of strains is necessary for epidemiological investigation and vaccine development.

Infections caused by fluoroquinolone-resistant Escherichia coli following transrectal ultrasound-guided biopsy of the prostate.

An increase in the number of infections with fluoroquinolone (FQ)-resistant Escherichia coli following transrectal ultrasound-guided biopsy of the prostate (TRUBP) was observed in Louis Stokes Cleveland Department of Veterans Affairs Medical Center. This study investigated whether these infections were caused by a single strain of E. coli possessing distinct resistance and virulence determinants. Of 15 patients with urinary tract infection, 5 were complicated with bacteraemia and 1 with prostate abscess. Thirteen FQ-resistant isolates demonstrated mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC but did not contain plasmid-mediated quinolone resistance determinants; blaCTX-M and blaCMY as well as genes coding for extended-spectrum β-lactamases were also absent. Genes encoding aminoglycoside-modifying enzymes were discovered in an isolate that was gentamicin-resistant. The most prevalent sequence type (ST) was ST43 (n = 7), corresponding to ST131 in Achtman's multilocus sequence typing (MLST) scheme. These isolates (i) were distinguished as >95% similar by repetitive sequence-based PCR (rep-PCR), (ii) belonged to the virulent phylogenetic group B2 and (iii) contained plasmid types FIB, FIA and Frep. Several other strain types were present (ST2, ST27, ST30, ST44, ST472, ST494, ST511 and ST627). Non-ST43 isolates infected patients with more co-morbidities but contained similar virulence factors (kpsMTII, iutA, papAH/papC and sfa/focDE). In our hospital, E. coli isolates causing TRUBP-related infection are quite heterogeneous (ST131 and other ST types) and are part of phylogenetic groups containing multiple virulence factors.

Comparison of ompP5 sequence-based typing and pulsed-filed gel electrophoresis for genotyping of Haemophilus parasuis

In this study, comparison of the outer membrane protein P5 gene (ompP5) sequence-based typing with pulsed-field gel electrophoresis (PFGE) for the genotyping of Haemophilus parasuis, the 15 serovar reference strains and 43 isolates were investigated. When comparing the two methods, 31 ompP5 sequence types (STs) and 43 PFGE types were identified withompP5 STs A16 and A28 being the dominant ompP5 ST types, while no predominant PFGE type was found. The discriminatory indices were 0.95 for ompP5 sequence-based method and 0.98 for PFGE, and the two techniques were proved to be 70.7% congruent. Therefore,ompP5 sequence-based typing was a simple and inexpensive method, enabling it as a preliminary technique to research the molecular differentiation of H. parasuis. Key words: Haemophilus parasuis, ompP5-based typing method, PFGE, molecular typing.