Antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby isolates from clinical patients and food sources in Hangzhou / 中华微生物学和免疫学杂志

Objective:To analyze the antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby strains isolated from human and food sources in Hangzhou. Methods:A total of 60 Salmonella enterica serovar Derby strains isolated in Hangzhou during the period from 2015 to 2020 were subjected to antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE) typing and whole-genome sequencing. Multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST) and the identification of antimicrobial resistance genes were performed using the sequencing data. Phylogenetic tree based on the single nucleotide polymorphism (SNP) sites in the 60 genomes from Hangzhou and 379 genomes from public databases was constructed. Results:No significant difference was observed in the drug resistance rates between the clinical strains and food strains in Hangzhou. The multidrug resistance (MDR) rate was 76.7% (46/60). All of the 60 Salmonella Derby strains were positive for the antimicrobial resistance genes aac(6′)- Iaa and fosA7. The 60 strains were subtyped into 46 molecular types by PFGE and 53 molecular types by cgMLST(HC2). Except for one strain belonging to ST3220, the other Salmonella Derby strains were ST40. The phylogenetic analysis showed that some strains isolated in Hangzhou were close to the strains in Southeast Asia, suggesting the possibility of cross-border transmission of ST40 strains, with the main food sources being pork and fish; other strains were close to those circulating in Beijing, Guangzhou, Hubei, Chongqing and other provinces, suggesting the possibility of cross-province transmission of the strains, with the main food sources being pork, beef and chicken. Conclusions:The epidemic of Salmonella Derby in Hangzhou was mainly caused by the spread of ST40 strains and MDR was common. Clinical infections might be closely related to the consumption of pork, beef, chicken and fish. There was the possibility of cross-border transmission of Salmonella Derby between Hangzhou and Southeast Asia and cross-province transmission in China.

Genetic characteristics of multi-locus sequence typing of Brucella isolates in Guizhou Province from 2017 to 2021 / 中华地方病学杂志

Objective:To study the multi-locus sequence typing (MLST) gene characteristics of Brucella isolates in Guizhou Province. Methods:Brucella strains, which were isolated from 2017 to 2021 in Guizhou Province (preserved in the Bacterial and Viral Seed Bank of Guizhou Center for Disease Control and Prevention) were identified Brucella and species/types by BCSP31-PCR and AMOS-PCR methods, respectively. MLST method was used for genotyping, and Biometrics 8.0 software was used for cluster analysis of the typing results. Results:A total of 32 strains of Brucella were isolated in Guizhou Province and identified as Brucella melitensis ( B.melitensis) by BCSP31-PCR and AMOS-PCR methods. These strains were classified into 2 ST types (ST8 and ST39) by MLST method, with 28 strains of ST8 type(87.5%) and 4 strains of ST39 type (12.5%). The 28 strains of ST8 type were distributed in 7 cities (prefectures) of Guizhou Province, while the 4 strains of ST39 type were only found in Qianxinan Buyi and Miao Autonomous Prefecture. The cluster analysis results showed that ST8 and ST39 types strains were clustered in a group with the reference strain of B.melitensis, and there was only one nucleotide site difference between ST39 and ST8 types in the glk gene, indicating a close genetic relationship. Conclusions:B.melitensis is the main pathogen of the brucellosis epidemic in Guizhou Province in recent years. ST8 is the dominant MLST genotype in Guizhou Province.

Multi-locus sequence typing of human Brucella isolated in Sichuan Province from 2014 to 2020 / 中华地方病学杂志

Objective:To learn about the genotyping of human Brucella isolated from Sichuan Province. Methods:BCSP31-PCR and AMOS-PCR were used to identify the genus and biotype of the 66 strains isolated from confirmed human brucellosis cases in Sichuan Province from 2014 to 2020, respectively. The isolated strains were genotyped by multi-locus sequence typing (MLST)-9. The sequence type (ST) was compared trough the online MLST database. A minimum spanning tree (MST) was constructed to cluster the newly discovered and known ST using the BioNumerics software version 7.6.Results:The 66 strains isolated from human cases of brucellosis in Sichuan Province from 2014 to 2020 were Brucella, and 65 of them were Brucella melitensis while one strain was Brucella abortus. The MLST method identified three known STs (ST-8, ST-39 and ST-2) and one newly type (ST-101). Among them, ST-8 was the main ST in Sichuan Province (90.91%, 60/66), another 4 strains of Brucella melitensis were ST-39, and 1 strain of Brucella abortus was ST-2. The newly type ST-101 was isolated from Leshan City in 2019, belonging to the Brucella melitensis and closely related to the evolution of ST-8. Conclusion:Brucella melitensis is the main epidemic Brucella strain in Sichuan Province, ST-8 is predominant genotype, with a small amount of ST-39, ST-101 and ST-2.

Genomic characterization, antimicrobial resistance profiles, enterotoxin, and biofilm production of methicillin-resistant Staphylococcus aureus isolated from clinical and animal products origins in Eastern Turkey

ABSTRACT: Staphylococcus aureus is an opportunistic and ubiquitous pathogen found in the skin, nares, and mucosal membranes of mammals. Increasing resistance to antimicrobials including methicillin has become an important public concern. One hundred and eight (108) S. aureus strains isolated from a total of 572 clinical and animal products samples, were investigated for their biofilm capability, methicillin resistance, enterotoxin genes, and genetic diversity. Although only one strain isolated from raw retail was found as a strong biofilm producer, the percentage of antimicrobial resistance pattern was relatively higher. 17.59% of S. aureus strains tested in this study were resistant to cefoxitin and identified as methicillin-resistant S. aureus (MRSA) isolates. mecA and mecC harboring S. aureus strains were detected at a rate of 2.79% and 0.93%, respectively. In addition, staphylococcal enterotoxin genes including Sea, Seb, Sec, and Sed genes were found to be 18.5%, 32.4%, 6.5% and 3.7%, respectively. The phylogenetic relationship among the isolates showed relationship between joint calf and cow milk isolates. Multi locus sequence typing (MLST) revealed three different sequence types (STs) including ST84, ST829, and ST6238. These findings highlight the development and spread of MRSA strains with zoonotic potential in animals and the food chain throughout the world.

RESUMO: Staphylococcus aureus é um patógeno dúctil e ubíquo encontrado na pele, narinas e membranas mucosas de mamíferos. O aumento da resistência aos antimicrobianos, incluindo a meticilina, tornou-se uma importante preocupação pública. Cento e oito (108) cepas de S. aureus isoladas de um total de 572 amostras clínicas e de produtos animais foram investigadas por sua capacidade de biofilme, resistência à meticilina, genes de enterotoxinas e diversidade genética. Embora apenas uma cepa isolada do cru tenha sido encontrada como forte produtora de biofilme, a porcentagem do padrão de resistência antimicrobiana foi relativamente maior. Parte das cepas (17,59%) de S. aureus testadas neste estudo eram resistentes à cefoxitina e identificadas como isolados de MRSA. mecA e mecC abrigando cepas de S. aureus foram detectados a uma taxa de 2,79% e 0,93%, respectivamente. Além disso, verificou-se que os genes da enterotoxina estafilocócica, incluindo os genes Sea, Seb, Sec e Sed, eram 18,5%, 32,4%, 6,5% e 3,7%, respectivamente. A relação filogenética entre os isolados mostrou relação entre os isolados de bezerro e leite de vaca. A tipagem de sequência multiloco (MLST) revelou três tipos de sequência diferentes (STs), incluindo ST84, ST829 e ST6238. Essas descobertas destacam o desenvolvimento e a disseminação de cepas de MRSA com potencial zoonótico em animais e na cadeia alimentar em todo o mundo.

Genomic characterization, antimicrobial resistance profiles, enterotoxin, and biofilm production of methicillin-resistant Staphylococcus aureus isolated from clinical and animal products origins in Eastern Turkey / Caracterização genômica perfis de resistência antimicrobiana, produção de enterotoxinas e biofilme Staphylococcus aureus resistente à meticilina isolado de origem clínica e de produtos de origem animal no leste da Turquia

Staphylococcus aureus is an opportunistic and ubiquitous pathogen found in the skin, nares, and mucosal membranes of mammals. Increasing resistance to antimicrobials including methicillin has become an important public concern. One hundred and eight (108) S. aureus strains isolated from a total of 572 clinical and animal products samples, were investigated for their biofilm capability, methicillin resistance, enterotoxin genes, and genetic diversity. Although only one strain isolated from raw retail was found as a strong biofilm producer, the percentage of antimicrobial resistance pattern was relatively higher. 17.59% of S. aureus strains tested in this study were resistant to cefoxitin and identified as methicillin-resistant S. aureus (MRSA) isolates. mecA and mecC harboring S. aureus strains were detected at a rate of 2.79% and 0.93%, respectively. In addition, staphylococcal enterotoxin genes including Sea, Seb, Sec, and Sed genes were found to be 18.5%, 32.4%, 6.5% and 3.7%, respectively. The phylogenetic relationship among the isolates showed relationship between joint calf and cow milk isolates. Multi locus sequence typing (MLST) revealed three different sequence types (STs) including ST84, ST829, and ST6238. These findings highlight the development and spread of MRSA strains with zoonotic potential in animals and the food chain throughout the world.

Staphylococcus aureus é um patógeno dúctil e ubíquo encontrado na pele, narinas e membranas mucosas de mamíferos. O aumento da resistência aos antimicrobianos, incluindo a meticilina, tornou-se uma importante preocupação pública. Cento e oito (108) cepas de S. aureus isoladas de um total de 572 amostras clínicas e de produtos animais foram investigadas por sua capacidade de biofilme, resistência à meticilina, genes de enterotoxinas e diversidade genética. Embora apenas uma cepa isolada do cru tenha sido encontrada como forte produtora de biofilme, a porcentagem do padrão de resistência antimicrobiana foi relativamente maior. Parte das cepas (17,59%) de S. aureus testadas neste estudo eram resistentes à cefoxitina e identificadas como isolados de MRSA. mecA e mecC abrigando cepas de S. aureus foram detectados a uma taxa de 2,79% e 0,93%, respectivamente. Além disso, verificou-se que os genes da enterotoxina estafilocócica, incluindo os genes Sea, Seb, Sec e Sed, eram 18,5%, 32,4%, 6,5% e 3,7%, respectivamente. A relação filogenética entre os isolados mostrou relação entre os isolados de bezerro e leite de vaca. A tipagem de sequência multiloco (MLST) revelou três tipos de sequência diferentes (STs), incluindo ST84, ST829 e ST6238. Essas descobertas destacam o desenvolvimento e a disseminação de cepas de MRSA com potencial zoonótico em animais e na cadeia alimentar em todo o mundo.

25S rDNA genotyping and multi-locus sequence typing of Candida albicans of pathogenic and commensal origins in the Klang Valley, Malaysia

@#Candida albicans is an important opportunistic fungal pathogen capable of causing fatal systemic infections in humans. Presently in Malaysia, there is little information available on the genetic diversity of this organism and trends in behavioural characteristics. In this project, three genotyping methods: 25S rDNA genotyping, Alternative Lengthening of Telomerase (ALT) sequence typing and Multi-Locus Sequence Typing (MLST) were applied to study the genetic diversity of strains from infected hospital in-patients and asymptomatic individuals in the community. The results showed that, with the 25S rDNA genotyping, as in other parts of the world, the most common genotype was type A which accounted for approximately 70% of the 111 isolates tested. Further typing with the ALT sequence showed type 3 to be the most common in the isolates tested. MLST analysis revealed many possibly novel sequence types, as well as a statistically significant association between pathogenicity and a group of closely related isolates, most of which were from hospital samples. Further work on genotypes associated with enhanced virulence will help to clarify the value of genotyping for clinical and epidemiological investigations. Keywords:

Genetic Diversity, Antimicrobial Resistance, and Virulence Genes of Isolates from Clinical Patients, Tap Water Systems, and Food / 生物医学与环境科学（英文）

Objective@#This study aimed to evaluate the genetic diversity, virulence, and antimicrobial resistance of isolates from clinical patients, tap water systems, and food.@*Methods@#Ninety isolates were obtained from Ma'anshan, Anhui province, China, and subjected to multi-locus sequence typing (MLST) with six housekeeping genes. Their taxonomy was investigated using concatenated sequences, while their resistance to 12 antibiotics was evaluated. Ten putative virulence factors and several resistance genes were identified by PCR and sequencing.@*Results@#The 90 isolates were divided into 84 sequence types, 80 of which were novel, indicating high genetic diversity. The isolates were classified into eight different species. PCR assays identified virulence genes in the isolates, with the enterotoxin and hemolysin genes , , , and found in 47 (52.2%), 13 (14.4%), 22 (24.4%), and 12 (13.3%) of the isolates, respectively. The majority of the isolates (≥ 90%) were susceptible to aztreonam, imipenem, cefepime, chloramphenicol, gentamicin, tetracycline, and ciprofloxacin. However, several resistance genes were detected in the isolates, as well as a new variant.@*Conclusions@#Sequence type, virulence properties, and antibiotic resistance vary in isolates from clinical patients, tap water systems, and food.

Ultrasound gel as a source of hospital outbreaks: Indian experience and literature review

Purpose: Hospital outbreaks are observed increasingly worldwide with various organisms from different sources such as contaminated ultrasound gel, intravenous (IV) fluids and IV medications. Among these, ultrasound gel is one of the most commonly reported sources for Burkholderia cepacia complex (Bcc) outbreaks. In this study, we describe our experience on investigation and the management of Bcc bacteraemia outbreak due to contaminated ultrasound gel from a tertiary care centre, South India. Materials and Methods: Over a 10-day period in October 2016, seven children in our Paediatric intensive care unit (ICU) were found to have bacteraemia with Bcc isolated from their blood culture. Repeated isolation of the same organism with similar antimicrobial susceptibility pattern over a short incubation period from the same location, confirmed the outbreak. An active outbreak investigation, including environmental surveillance, was carried out to find the source and control the outbreak. Isolates were subjected to multi-locus sequence typing (MLST) and global eBURST (goeBURST) analysis. Results: Environmental surveillance revealed contaminated ultrasound gel as the source of infection. MLST and goeBURST analysis confirmed that the outbreak was caused by a novel sequence type 1362 with the same clonal complex CC517. The outbreak was controlled by stringent infection control measures, withdrawal of contaminated ultrasound gel from regular usage and implementing the practice of using ultrasonogram (USG) probe cover for USG screening and guided procedures. Conclusion: This report highlights the importance of early identification of an outbreak, prompt response of the ICU and infection control teams, sound environmental and epidemiological surveillance methods to identify the source and stringent infection control measures to control the outbreak. Contaminated ultrasound gel can be a potential source for healthcare-associated infection, which cannot be overlooked.

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae strains / 中国感染与化疗杂志

Objective To investigate the distribution of common carbapenem resistance genes and virulence genes in and understand the molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains.Methods A total of 84 non-duplicate CRKP isolates were collected from Renji Hospital,Shanghai Jiao Tong University School of Medicine and Changzheng Hospital,the Second Military Medical University,in 2015.Kirby-Bauer disk diffusion method was used to test their susceptibility to 15 antimicrobial agents.The HM phenotype of K.pneumoniae was determined by string test.Carbapenem-resistant genes and virulence genes were detected by polymerase chain reaction (PCR).The molecular epidemiology of the 84 isolates were further analyzed by multi locus sequence typing (MLST).The population structure of CRKPs was evaluated by eBURST with the results of MLST.Results Antimicrobial susceptibility test showed that 84 isolates were highly resistant to most antimicrobial agents such as carbapenems,penicillins,cephalosporins and aztreonam.More than 90％ of the strains were resistant to most of the antibiotics tested except ciprofloxacin (77.4％,65/84) and amikacin (82.1％,69/84).Two strains showed HM phenotype.PCR results showed that 90.5％ (76/84) of the strains were positive for blaKPC-2,1.2％ (1/84) positive for blaNDM and blaIMP each,but either blaOXA or blaVIM was not identified.The overall prevalence of virulence genes was low except for mrkD (97.6％,82/84),ybtS (92.9％,78/84) and entB (100％,84/84).Eight sequence types (STs) were obtained.The dominant clone was ST11 (84.5％,71/84),and the two strains of HM phenotype were ST11.eBURST analysis identified 2 ST groups among the 84 CRKPs.Each ST group includes 2 ST types (ST11 and ST1869,ST15 and ST709),respectively.The other four ST types were single ST type.In this study,71 strains of ST11,4 ST15 and 4 ST323 belonged to CC258,CC15 and CC163 clones,respectively.Conclusions CRKP is highly resistant to the commonly used antibiotics.The multidrug resistance or pandrug-resistance of K.pneumoniae is mainly associated with the expression of blaKPC-2 gene.Three virulence genes mrkD,ybtS and entB are highly prevalent in the CRKP isolates.The dominant clone of KPC-producing K.pneumoniae is ST11 in both hospitals.

Molecular characteristics of non-O1/O139 Vibrio cholerae in Yunnan Province / 中国人兽共患病学报

Non-O1/O139 group of Vibrio cholerae can cause human acute diarrhea disease,while compared with the O1 and O139 groups;it often ignore the risk of the disease for human being.Therefore,we analyzed the molecular characteristics of 31 V.cholerae isolated from Yunnan Province.We used the agar disc diffusion method (K-B) to carry out the antibiotic sensitivity test;polymerase chain reaction (PCR) amplification for the detection of virulence gene;at the same time,all of strains were performed for pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).The drug sensitivity test showed that 67.74％ strains were resistant to rifampin,29.03％ resistant to nalidixic acid and cotrimoxazole,all of the isolates were sensitive to gentamicin and ciprofloxacin;PCR results showed that all strains had the ompW gene,87.10％ strains had hly gene,25.81％ strains had rstREl tor,16.13％ strains had rstRClassical and tcpAEl tor,while CT rfbO1 and rfbO139 gene were negative;PFGE results showed that 31 strains had a trend of discrete height,the same PFGE identity pattern was not nearly found;for the analysis of MLST,we found the one new alleles of gyrB,four new alleles of mdh gene,six new alleles of metE gene,two new alleles of pntA,three new alleles of purM and four new alleles of pyrC gene.After permutation and combination,we found 17 new ST types for V.cholerae(ST273-ST289).Non-O1/O139 group V.cholerae showed a high degree of diversity,while the non-O1/O139 group of V.cholerae in Yunnan Province has a certain geographical features,which enriched the existing molecular typing system of V.cholerae.

Molecular characteristics of Listeria monocytogenes foodborne isolates in Hangzhou, China / 中国人兽共患病学报

We determined molecular characteristics of Listeria monocytogenes foodborne isolates in Hangzhou and investigated the characterization of local strains.Multi-locus sequence typing(MLST) and pulsed-field gel electrophoresis(PFGE) were applied to identify molecular types of Listeria monocytogenes isolates.Results showed that a total of 133 strains of 6 serotypes were divided into 19 MLST types including a new type ST767.ST9 and ST121 were the major ST types.There were 33 and 45 PFGE patterns characterized by AscⅠ and ApaⅠ.The molecular types of Listeria monocytogenes strains were widely distributed in Hangzhou.It is indicated that the major clusters were Lineage Ⅰ and Lineage Ⅱ which will cause listeriosis.The contamination of Listeria monocytogenes in food is serious in Hangzhou and the surveillance and management should be strengthened to prevent the food borne diseases.

Etiologic characteristics of food-borne Vibrio parahaemolyticus strains isolated in Guangdong,2014 / 中华流行病学杂志

Objective To investigate the serotypes, antimicrobial resistance, virulence genes and molecular characteristics of food-borne Vibrio parahaemolytieus isolated in Guangdong province in 2014.Methods Sixty V.parahaemolyticus strains were tested in this study.The serotyping and antibiotic resistance test were conducted, while the tdh and trh gens of the strains were detected with conventional PCR, and pulsed field gel electrophoresis (PFGE) and multiple locus sequence typing (MLST) were conducted too.Results The 60 strains belonged to 13 serotypes, the major serotypes included O3 : K6, O4: K8, O 1 : K36 and O4: KUT.The antibiotic resistance test indicated the isolates were highly resistant to ampicillin (100.0％), sulfonamides (43.3％) and cefalotin (28.3％).Up to 56.7％(34/60) of the strains were resistant to two or more antibiotics, and 2 strains showed resistance to three antibiotics.The virulence gene detection indicated that 63.3％ (38/60) of the strains carded tdh+trh-, while only 1 strain carried tdh+trh+.The 60 strains digested by Not I belonged to 48 different PFGE patterns and 3 clusters.The cluster B included the strains isolated from sporadic food borne cases with serotype of O3:K6 and similarity of 62.6％-100.0％.The cluster C included O4:K8 strains with the PFGE pattem similarity of 56.7％-62.5％.The MLST indicated that the 60 strains had 26 sequence types (STs).The ST-3 was predominant, including 33 strains (serotypes O3:K6 and O1 : K36).The four O4:K8 strains formed another predominant colony, which was different from ST-3.Conclusion The etiologic characteristics of V.parahaemolyticus varied, which might be one of the reasons for high incidence of food-bome V.parahaemolyticus infection in Guangdong.The molecular characteristics of O4: K8 strain were differem from the other predominant serotypes.Close attention should be paid to the possible outbreak caused by O4: K8 strain in this area.

Virulence gene detection and multi-locus sequence typing of Vibrio parahaemolyticus from patients in Ningbo,China / 中国人兽共患病学报

To investigated the toxin genes distribution and molecular characteristics of Vibrio parahaemolyticus from pa‐tients in Ningbo ,V .parahaemolyticus strains were collected from patients with food poisoning and diarrhea .Thermostable di‐rect hemolysin gene (tdh) and TDH‐related hemolysin gene (trh) were detected by polymerase chain reaction (PCR) .Molecu‐lar characteristics were acquired by multi‐locus sequence typing (MLST ) .Of 248 clinical strains were isolated from 2006 to 2012 .Forty‐eight strains were selected to detect virulence genes and MLST genotyping .Forty‐two isolates were detected as tdh+ and 11 isolates were detected as trh+ .There were 9 STs and one undifferentiated type in Ningbo clinical strains .Thirty‐two strains were classified into ST3 ,5 strains into ST265 and 3 strains into ST120 .ST265 was found in Ningbo strains com‐pared with strains from other regions of China .Strains with tdh+ accounted for the majority in Ningbo clinical strains .Twen‐ty‐five strains of ST3 clone were tdh+ /trh‐.There were 9 STs coexsited in Ningbo clinical strains .ST3 clone was dominant , followed by ST265 and ST120 .Strains with tdh+ /trh‐were dominant in the ST3 clone .The unique ST262 was found in Ning‐bo clinical strains .

rpoB gene sequencing for phylogenetic analysis of avian pathogenic Escherichia coli / 대한수의학회지

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

Characteristics of Metallo-beta-Lactamase-Producing Pseudomonas aeruginosa in Korea / 감염과화학요법

BACKGROUND: The aim of this study was to investigate the molecular epidemiological characteristics of metallo-beta-lactamase (MBL)-producing Pseudomonas aeruginosa clinical isolates in Korea. MATERIALS AND METHODS: Three hundred and twenty nine P. aeruginosa clinical isolates were collected from 23 general hospitals in Korea from March to June 2014. Species were identified by matrix-assited laser desorption/ionization-time of flight and 16S rRNA sequencing. Antimicrobial susceptibility was determined by disk diffusion methods. Further, minimum inhibitory concentrations of carbapenems were determined by Etest. Polymerase chain reaction and sequencing were performed to identify genes encoding MBLs. Multi-locus sequence typing and pulsed-field gel electrophoresis were performed to determine epidemiological characteristics of MBL-producing P. aeruginosa isolates. RESULTS: Of the 329 isolates, 229 (69.6%) were susceptible to the carbapenems tested, including imipenem and meropenem; while 100 (30.4%) were non-susceptible to more than one of the carbapenems. Genes encoding imipenemase-6 (IMP-6) and Verona imipenemase-2 (VIM-2) MBLs were identified in 21 (6.4%) isolates (n = 17 and 4, respectively). All MBL-producing isolates showed multi-drug resistant phenotype, and a majority (n = 19) of the isolates were identified as sequence type 235 (ST235). The remaining isolates (n = 2) were identified as ST309 and ST463. CONCLUSION: P. aeruginosa ST235 might play an important role in dissemination of MBL genes in Korea.

In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences / Análises in silico da filogenia e do perfil de genes associados à virulência, dos genomas de linhagens de Escherichia coli de origem aviária

Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC) associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST) of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli) and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

As infecções causadas por linhagens de Escherichia coli de origem aviária (APEC) são responsáveis por perdas significativas na indústria avícola em todo mundo. Risco zoonótico tem sido atribuído às linhagens APEC, devido às semelhanças existentes entre elas e linhagens de E. coli patogênicas extraintestinais (ExPEC) de origem humana, causadoras de infecções no trato urinário e meningite neonatal. Neste trabalho, apresentamos os resultados de análises in silico feitas a partir dos genomas de linhagens patogênicas de E. coli, incluindo genomas recentemente obtidos de linhagens APEC. Uma árvore filogenética foi obtida, com base na tipagem de sequência multilocus (MLST) de sete genes essenciais, revelando alta diversidade na composição de alelos, mas ainda assim possibilitando o agrupamento dos diferentes patótipos. Foi determinado também, para cada linhagem, o perfil gênico, por meio da presença ou ausência de 83 genes associados à virulência. A árvore filogenética e o perfil gênico demonstraram que existem semelhanças genéticas entre cepas APEC brasileiras, APEC isolada nos Estados Unidos, UPEC (uropathogenic E. coli) e linhagens produtoras de diarreia em humanos. Essa correlação corrobora e reforça a hipótese de que linhagens APEC apresentam potencial risco zoonótico.

Genotyping of Giardia duodenalis Isolates from Dogs in Guangdong, China Based on Multi-Locus Sequence

This study aimed to identify the assemblages (or subassemblages) of Giardia duodenalis by using normal or nested PCR based on 4 genetic loci: glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi), beta-giardin (bg), and small subunit ribosomal DNA (18S rRNA) genes. For this work, a total of 216 dogs' fecal samples were collected in Guangdong, China. The phylogenetic trees were constructed with MEGA5.2 by using the neighbor-joining method. Results showed that 9.7% (21/216) samples were found to be positive; moreover, 10 samples were single infection (7 isolates assemblage A, 2 isolates assemblage C, and 1 isolate assemblage D) and 11 samples were mixed infections where assemblage A was predominant, which was potentially zoonotic. These findings showed that most of the dogs in Guangdong were infected or mixed-infected with assemblage A, and multi-locus sequence typing could be the best selection for the genotype analysis of dog-derived Giardia isolates.

Multiple locus sequence typing of Salmonella Typhi, isolated in north India - a preliminary study.

Background & objectives: In India enteric fever is a major public health problem and Salmonella Typhi is the most common aetiologic agent. Any control strategy for such infections depends to a large extent on the understanding of the disease and relatedness of strains across the world. Multi locus sequence typing (MLST) is one such method of genotyping of bacteria based upon housekeeping genes of known function and chromosome position. MLST data of pathogens are important to determine the molecular evolution by a stable and reproducible method. This study was undertaken to determine the sequence types of representatives S. Typhi isolates obtained from enteric fever patients in a tertiary care centre in north India, over a period of 20 years (1990-2010). Methods: A total of 30 representative isolates of S. Typhi identified by biochemical and serological tests were subjected to multi locus sequence typing (MLST). Seven housekeeping genes of known function and chromosome position were used for the typing by MLST. Sequencing was carried out by using an automated DNA sequencer and results were analyzed to generate phylogenetic tree. Results: MLST pattern grouped S. Typhi into two sequence types- ST1 and ST2. ST1 was predominantly present followed by ST2. Interpretation & conclusions: By MLST the presence of both sequence types, ST1 and ST2, was found in S. Typhi isolates in our region. Predominately ST1 was present followed by ST2. These preliminary results corroborate the global distribution of both sequence types of S. Typhi and also emphasize for the continuous screening of S. Typhi.

Genotyping Klebsiella pneumoniae isolated from hepatic abscesses in three patients from Bogota, Colombia / Genotipificación de Klebsiella pneumoniae aislada de abscesos hepáticos de pacientes de Bogotá, Colombia / Genotipificação de Klebsiella pneumoniae isolada de abscessos hepáticos de pacientes de Bogotá, Colômbia

Pyogenic liver abscess caused by Klebsiella pneumoniae represents an ever increasing entity which has mainly been described as occurring in Asia, even though, on a smaller scale, cases are being more frequently described from the USA and Europe, 13% overall mortality being reached worldwide. Affected patients are severely sick, suffering from fever, sweating, having increased acute phase reactants and risk factors such as Diabetes Mellitus, alcoholism and the inherent characteristics of the bacteria causing the disease. Objective: in this work we used a Multilocus Sequencing Typing (MLST), a nucleotide sequence-based method in order to characterize the genetic relationships among bacterial isolates. Materials and methods: the report is focused on three cases involving patients suffering from pyogenic liver abscess caused by Klebsiella pneumoniae in two hospitals in Bogota, Colombia, where phenotyping and hypermucoviscosity studies were carried out, as well as the genotyping of cultured Klebsiella isolates. Results: it was found that the isolated microorganism in cases I and II corresponded to the same K. pneumoniae strain, having 100% sequence identity for the 5 genes being studied while the strain in Case III was genotypically different. Conclusion: it is important to carry out multidisciplinary studies allowing all pyogenic liver abscess cases reported in Colombia to be complied to ascertain the frequency of microorganisms causing this pathology in our country, as well as a genotyping study of different K. pneumoniae strains to compare them and confirm clonal and pathogenicity relationships through housekeeping gene analysis.

El absceso hepático piógeno causado por Klebsiella pneumoniae representa una entidad descrita con frecuencia en los países asiáticos y, en menor escala, también en Estados Unidos y Europa. En el ámbito mundial su mortalidad alcanza a un 13%. Los pacientes pueden presentar un compromiso severo, el cual cursa con fiebre, sudoración y aumento de reactantes de fase aguda, sobre todo en individuos con factores de riesgo como la diabetes mellitus y el alcoholismo, además de las características inherentes de la bacteria responsable de la infección. Objetivo: a continuación se presentan tres casos de pacientes con absceso hepático piógeno causado por Klebsiella pneumoniae en dos hospitales de Bogotá. Materiales y métodos: se realizó caracterización molecular de los aislados de Klebsiella mediante la técnica de Multilocus Secquence Typing (MLST), análisis fenotípicos y de hipermucoviscosidad. Resultado: se encontró que el microorganismo aislado en los casos I y II corresponde a la misma cepa de K. pneumoniae, que tiene 100% de identidad de secuencia de los 5 genes en estudio mientras que la cepa en Case III fue genotípicamente diferente. Conclusión: es importante llevar a cabo estudios multidisciplinarios que incluyan todos los casos de abscesos hepáticos piógenos reportados en Colombia con el objeto de determinar la frecuencia de los microorganismos causantes de esta patología en nuestro país, así como un estudio de genotipificación de diferentes cepas de K. pneumoniae para confirmar las relaciones clonales y de patogenicidad.

O abscesso hepático piogênico causado por Klebsiella pneumoniae representa uma entidade descrita com frequência nos países asiáticos e, em menor escala, também nos Estados Unidos e na Europa. No âmbito mundial sua mortalidade alcança um 13%. Os pacientes podem apresentar um compromisso severo, o qual cursa com febre, sudoração e aumento de reagentes de fase aguda, especialmente em indivíduos com fatores de risco como a diabetes mellitus e o alcoolismo, além das características inerentes da bactéria responsável da infecção. Objetivo: a continuação apresentamse três casos de pacientes com abscesso hepático piogênico causado por Klebsiella pneumoniae em dois hospitais de Bogotá; Materiais e métodos: realizou-se caracterização molecular dos isolados de Klebsiella mediante a técnica de Multilocus Secquence Typing (MLST), análises fenotípicas e de hipermucoviscosidade. Resultado: encontrou-se que o micro-organismo isolado nos casos I e II corresponde à mesma cepa de K. pneumoniae, que tem 100% de identidade de sequencia dos 5 genes em estudo enquanto a cepa no caso III foi genotipicamente diferente. Conclusão: é importante levar a cabo estudos multidisciplinares que incluam todos os casos de abscessos hepáticos piogênicos reportados na Colômbia com o objeto de determinar a frequência dos micro-organismos causadores desta patologia em nosso país, assim como um estudo de genotipificação de diferentes cepas de K. pneumoniae para confirmar as relações clonais e de patogenicidade.

Molecular characteristics of Salmonella typhi and Salmonella paratyphi A isolates in Hangzhou area / 中华微生物学和免疫学杂志

Objective To determine the molecular characteristics of predominant Salmonella typhi and Salmonella paratyphi A strains prevalent in Hangzhou area from 2002 to 2008.Methods Pulse field gel electrophoresis (PFGE),multi-locus variable-number tandem repeat analysis (MLVA) and multi-locus sequence typing (MLST) were applied for typing as well as analysis of the molecular characteristics of 31 S.typhi isolates and 404 S.paratyphi A isolates from Hangzhou area during 2002 to 2008.Results The 404 S.paratyphi A isolates could be divided into six PFGE types (P1-P6).99.0％ of the S.paratyphi A isolates (400/404) belonged to the same one clone family (P1 and P2 types),in which P1 strains occupied 93.3％ (373/400) of the isolates.The 31 S.typhi isolates displayed a high diversity,which could be classified into 14 PFGE types,28 MLVA types with 90.3％ resolving power and 3 MLST types.The S.typhi strains prevalent in Hangzhou area were similar to those in Southeast Asia but different from those in Europe.The variable number tandem repeat (VNTR) sites with high polymorphism,TR1,TR2 and Sal02,could be used to the markers for diagnosis of S.typhi isolates in the area.The MLST types of 31 S.typhi isolates included all the three types currently found in the world but the ST2 type of S.typhi strains was predominant (23/31,74.2％).Conclusion The paratyphoid A prevalence in Hangzhou area in the recent years is caused by infection of the same clone family of S.paratyphi A whereas the S.typhi strains prevalent in the area display a high diversity.