Population structure of food-borne Staphylococcus aureus in China / 中华流行病学杂志

Objective: To understand the population structure of food-borne Staphylococcus (S.) aureus in China. Methods: Whole genome sequencing was used to analyze 763 food-borne S. aureus strains from 16 provinces in China from 2006 to 2020. Multilocus sequence typing (MLST), staphylococcal protein A gene (spa) typing, and staphylococcal chromosome cassettemec (SCCmec) typing were conducted, and minimum spanning tree based on ST types (STs) was constructed by BioNumerics 7.5 software. Thirty-one S. aureus strains isolated from imported food products were also included in constructing the genome phylogenetic tree. Results: A total of 90 STs (20 novel types) and 160 spa types were detected in the 763 S. aureus isolates. The 72 STs (72/90, 80.0%) were related to 22 clone complexes. The predominant clone complexes were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, accounting for 82.44% (629/763) of the total. The STs and spa types in the predominant clone complexes changed over the years. The methicillin-resistant S. aureus (MRSA) detection rate was 7.60%, and 7 SCCmec types were identified. The ST59-t437-Ⅳa (17.24%, 10/58), ST239-t030-Ⅲ (12.07%, 7/58), ST59-t437-Ⅴb (8.62%, 5/58), ST338-t437-Ⅴb (6.90%, 4/58) and ST338-t441-Ⅴb (6.90%, 4/58) were the main types in MRSA strains. The genome phylogenetic tree had two clades, and the strains with the same CC, ST, and spa types clustered together. All CC7 methicillin sensitive S. aureus strains were included in Clade1, while 21 clone complexes and all MRSA strains were in Clade2. The MRSA strains clustered according to the SCCmec and STs. The strains from imported food products in CC398, CC7, CC30, CC12, and CC188 had far distances from Chinese strains in the tree. Conclusions: In this study, the predominant clone complexes of food-borne strains were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, which overlapped with the previously reported clone complexes of hospital and community-associated strains in China, suggesting that close attention needs to be paid to food, a vehicle of pathogen transmission in community and food poisoning.

Study on the features of Clostridioides difficile infection among diarrhea patients in Kunming from 2018 to 2020 / 中华流行病学杂志

Objective: We analyze the characteristics of Clostridioides difficile (C. difficile) infection among diarrhea patients in Kunming from 2018 to 2020 and provide evidence for follow-up surveillance and prevention. Methods: A total of 388 fecal samples of diarrhea patients from four sentinel hospitals in Yunnan Province from 2018 to 2020 were collected. Real-time quantitative PCR was used to detect the fecal toxin genes of C. difficile. The positive fecal samples isolated the bacteria, and isolates were identified by mass spectrometry. The genomic DNA of the strains was extracted for multi-locus sequence typing (MLST). The fecal toxin, strain isolation, and clinical patient characteristics, including co-infection with other pathogens, were analyzed. Results: Among the 388 fecal samples, 47 samples with positive reference genes of C. difficile were positive, with a total positive rate of 12.11%. There were 4 (8.51%) non-toxigenic and 43 (91.49%) toxigenic ones. A total of 18 strains C. difficile were isolated from 47 positive specimens, and the isolation rate of positive specimens was 38.30%. Among them, 14 strains were positive for tcdA, tcdB, tcdC, tcdR, and tcdE. All 18 strains of C. difficile were negative for binary toxins. The MLST results showed 10 sequence types (ST), including 5 strains of ST37, accounting for 27.78%; 2 strains of ST129, ST3, ST54, and ST2, respectively; and 1 strain of ST35, ST532, ST48, ST27, and ST39, respectively. Fecal toxin gene positive (tcdB+) results were statistically associated with the patient's age group and with or without fever before the visit; positive isolates were only statistically associated with the patient's age group. In addition, some C. difficile patients have co-infection with other diarrhea-related viruses. Conclusions: The infection of C. difficile in diarrhea patients in Kunming is mostly toxigenic strains, and the high diversity of strains was identified using the MLST method. Therefore, the surveillance and prevention of C. difficile should be strengthened.

Pathogenic characterization of Klebsiella pneumoniae resistant to carbapenems and polymyxin / 中华预防医学杂志

Objective: Analysis and investigation of pathogenic characteristics of polymyxin-and carbapenem-resistant Klebsiella pneumoniae (PR-CRKP). Methods: A total of 23 PR-CRKP strains isolated from clinical specimens from the General Hospital of Southern Theater Command from March 2019 to July 2021 were retrospectively collected, Whole-genome sequencing was performed on 23 PR-CRKP strains, resistance genes were identified by comparison of the CARD and the ResFinder database, high-resolution typing of PR-CRKP strains was analyzed by core genomic multilocus sequencing (cgMLST) and single nucleotide polymorphism (SNP); polymyxin resistance genes were determined by PCR and sequencing. Results: All PR-CRKP strains were KPC-2 producing ST11 types. cgMLST results showed that the evolutionary distance between the PR-CRKP strains and Klebsiella pneumoniae in mainland China was 66.44 on average, which is more closely related than foreign strains; the 23 PR-CRKP strains were divided into 3 main subclusters based on SNP phylogenetic trees, with some aggregation among Clade 2-1 in the isolation department and date. The two-component negative regulatory gene mgrB has seven mutation types including point mutations, different insertion fragments and different insertion positions. Conclusion: The close affinity of PR-CRKP strains indicate the possibility of nosocomial clonal transmission and the need to strengthen surveillance of PR-CRKP strains to prevent epidemic transmission of PR-CRKP.

Drug resistance and genomic characteristics of Salmonella enterica serovar London from clinical and food sources in Hangzhou City from 2017 to 2021 / 中华预防医学杂志

Objective: To analyze the drug resistance and genomic characteristics of Salmonella enterica serovar London isolated from clinical and food sources in Hangzhou City from 2017 to 2021. Methods: A total of 91 Salmonella enterica serovar London strains isolated from Hangzhou City from 2017 to 2021 were analyzed for drug susceptibility, pulsed field gel electrophoresis (PFGE) typing and whole genome sequencing. Multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST) and detection of drug resistance genes were performed by using the sequencing data. Phylogenetic analysis was conducted to compare the 91 genomes from Hangzhou City with 347 genomes from public databases. Results: No significant difference in the drug resistance rate was observed between clinical strains and food strains to 18 drugs in Hangzhou City(all P>0.05), and the multidrug resistance (MDR) rate was 75.8% (69/91). Most strains were resistant to 7 drug classes simultaneously. One strain was resistant to Polymyxin E as well as positive for mcr-1.1, and 50.5% (46/91) of the strains were resistant to Azithromycin and were positive for mph(A). All 91 Salmonella enterica serovar London strains were ST155, which were subdivided into 44 molecular types by PFGE and 82 types by cgMLST. Phylogenetic analysis showed that most strains from Hangzhou City (83/91) were clustered together, and a small number of human isolates from Europe, North America and pork isolates from Hubei and Shenzhen were mixed in the cluster. Other strains from Hangzhou City (8/91) were closely related to strains from Europe, America and Southeast Asia. Strains isolated from pork were the most closely related to clinical strains. Conclusion: The epidemic of Salmonella enterica serovar London in Hangzhou City is mainly caused by the spread of ST155 strains, which is mainly transmitted locally. At the same time, cross-region transmission to Europe, North America, Southeast Asia, and other provinces and cities in China may also occur. There is no significant difference in the drug resistance rate between clinical strains and food strains, and a high level of MDR is found in the strains. Clinical infection of Salmonella enterica serovar London may be closely related to pork consumption in Hangzhou City.

Genotyping Characteristics of Human Fecal Escherichia coli and Their Association with Multidrug Resistance in Miyun District, Beijing / 生物医学与环境科学（英文）

OBJECTIVE@#To explore the genotyping characteristics of human fecal Escherichia coli( E. coli) and the relationships between antibiotic resistance genes (ARGs) and multidrug resistance (MDR) of E. coli in Miyun District, Beijing, an area with high incidence of infectious diarrheal cases but no related data.@*METHODS@#Over a period of 3 years, 94 E. coli strains were isolated from fecal samples collected from Miyun District Hospital, a surveillance hospital of the National Pathogen Identification Network. The antibiotic susceptibility of the isolates was determined by the broth microdilution method. ARGs, multilocus sequence typing (MLST), and polymorphism trees were analyzed using whole-genome sequencing data (WGS).@*RESULTS@#This study revealed that 68.09% of the isolates had MDR, prevalent and distributed in different clades, with a relatively high rate and low pathogenicity. There was no difference in MDR between the diarrheal (49/70) and healthy groups (15/24).@*CONCLUSION@#We developed a random forest (RF) prediction model of TEM.1 + baeR + mphA + mphB + QnrS1 + AAC.3-IId to identify MDR status, highlighting its potential for early resistance identification. The causes of MDR are likely mobile units transmitting the ARGs. In the future, we will continue to strengthen the monitoring of ARGs and MDR, and increase the number of strains to further verify the accuracy of the MDR markers.

A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis / 生物医学与环境科学（英文）

OBJECTIVE@#A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis.@*METHODS@#In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.@*RESULTS@#We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.@*CONCLUSION@#This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.

Epidemiological and etiological analysis of two infantile cases of serogroup B epidemic cerebrospinal meningitis epidemics in Shandong Province, 2021 / 中华预防医学杂志

Two cases of epidemic situation of serogroup B meningitis in infants in Shandong Province in 2021 were investigated. Samples of cases and their close contacts were collected for isolation, culture and identification of Neisseria meningitides (Nm). The isolates were subjected to multi-locus sequence typing, outer membrane protein porA and fetA genotyping and drug sensitivity test. Two laboratory-confirmed outbreaks of serogroup B meningitis were reported from Yantai city and Linyi city. The indicated cases were infants aged 5 months and 2 months old respectively. They were not vaccinated with meningitis vaccine. Their epidemiological characteristics and clinical manifestations were similar and the prognosis was good. The same sequence type (ST) of serogroup B Nm strains as the indicated cases was detected in the samples of close family contacts, but without subsequent cases. Among them, Yantai strain was were identified as the type ST-8920, belonging to CC4821 clonal complex, and the genotypes of porA and fetA were p1.21-2, 23 and F3-1. Linyi strain was a new type, belonging to CC4821 clonal complex and the genotypes of porA and fetA were p1.20, 23 and F1-91. The above strains were resistant to penicillin, ciprofloxacin, levofloxacin and Chemitrim, and their sensitivity to cephalosporin decreased. Two cases of infant serogroup B epidemic were relatively rare in China, which were different from the epidemiological and pathogenic characteristics of other Nm serogroups in the past.

Molecular characterization of Staphylococcus aureus ST6 and ST7 isolates from food-borne illness outbreaks / 中华预防医学杂志

Objective: To analyze the Staphylococcal enterotoxins, Staphylococcal enterotoxin genes, drug resistance and molecular typing of 41 Staphylococcus aureus isolates from 2 food-borne illness outbreaks on 21 August and 27 September 2020 in Guangzhou. Methods: A total of 41 Staphylococcus aureus isolates from 2 outbreaks were analyzed by multilocus sequence typing (MLST) and spa typing. The Staphylococcal enterotoxins typing and the Staphylococcal enterotoxin genes of the isolates were analyzed by ELISA and PCR, respectively. The antimicrobial susceptibility of the isolates was performed by disc diffusion. 21 Staphylococcus aureus isolates were characterized using whole genome sequencing (WGS). Based on the whole genome single nucleotide polymorphism (SNP), the phylogenetic tree was constructed by Snippy. Results: 41 Staphylococcus aureus isolates were divided into 2 types by MLST and spa typing: ST6-t701 and ST7-t091. 2 ST7-t091 isolates were identified as methicillin-resistant Staphylococcus aureus (MRSA). 25 ST7-t091 isolates and 14 ST6-t701 isolates were methicillin-sensitive Staphylococcus aureus (MSSA), and were resistant to 7 and 6 antibiotics, respectively. All isolates were positive for sea by PCR. WGS revealed all 21 isolates carried scn, sak, sea, hla, hld, hlgA, hlgB, hlgC, lukD virulence genes. The results showed the isolates contained an immune evasion cluster type D which located in bacteriophage ϕSa3. The SNP phylogenetic tree showed 2 MRSA ST7-t091 were constituted a separate clade from the 12 MSSA ST7-t091 isolates and 7 ST6-t701 isolates showed high similarity to each other. Conclusion: Base on the results of phylogenetic analysis, the 2 food-borne illness outbreaks occurred on 21 August and 27 September 2020 are caused by the combination of the MRSA ST7-t091 strain and the MSSA ST7-t091 strain, and the MSSA ST6-t701 strain, respectively. All isolates have high level of antibiotic resistance and carry high virulent genes.

Portación nasal, antibiotipo y genotipo de cepas de Staphylococcus aureus aisladas en estudiantes de Medicina y de Enfermería Campus San Felipe, Universidad de Valparaíso, Chile, durante el año 2017 / Nasal carriage, antibiotype and genotype of isolated Staphylococcus aureus from Medicine and Nursing students of Campus San Felipe, University of Valparaiso, Chile, during 2017

INTRODUCCIÓN. Staphylococcus aureus es parte de la microbiota nasal en 20-30% de la población general, colonización que constituye un reservorio para su transmisión, lo que es preocupante en cepas resistentes a meticilina (SARM). OBJETIVO: Determinar la prevalencia de S. aureus en estudiantes de Medicina y Enfermería del Campus San Felipe y caracterizar sus aislamientos. MATERIAL Y MÉTODOS: El 2017 se midió la portación nasal a 225 estudiantes, a las cepas aisladas se le analizó su antibiotipo por difusión en agar, la relación clonal por electroforesis de campo pulsado y MLST. En SARM se determinó el cassette SCCmec y gen de la leucocidina de Panton-Valentine. RESULTADOS: 61 estudiantes portaron S. aureus (27,1%) incluyendo dos cepas SARM (0,9%). Staphylococcus aureus mostró resistencia a penicilina (75%), eritromicina (14%) y clindamicina (10%), cloranfenicol (1,6%) y levofloxacina, oxacilina, cefoxitina (3,3%). Se diferenciaron diecinueve pulsotipos y el secuenciotipo coincidió con complejos clonales descritos a nivel mundial en portadores de S. aureus: CC30, CC8, CC97, CC15, CC22 y CC1. Las dos cepas SARM correspondieron con los clones chileno/cordobés y USA100NY/J, ambas del CC5. CONCLUSIÓN: La portación nasal de S. aureus y SARM en los estudiantes coincidió con la portación en la población general y las cepas sensibles a meticilina mostraron diversidad clonal y alta susceptibilidad antimicrobiana, exceptuando a penicilina.

BACKGROUND: Staphylococcus aureus is part of the nasal microbiota in 20-30% of the population. This colonization is also a reservoir for its dissemination, which is worrying in the case of strains with resistance to methicillin (MRSA). AIM: To determine S. aureus nasal carriage in nursing and medical students of San Felipe Campus and characterize theirs isolates. METHODS: During 2017, nasal swabs were taken from 225 students and seeded in salt manitol agar. Antibiotypes were determined by agar diffusion and the genetic clonality was assessed by PFGE and MLST in isolated S. aureus. SCCmec cassette and Panton-Valentine leukocidin gene (pvl) presence were determined in the MRSA isolates. RESULTS: 61 students carried S. aureus (27.1%) including two MRSA strains (0.9%). S. aureus showed resistance to penicillin (75%), erythromycin (14%) and clindamycin (10%), chloramphenicol (1.6%) and levofloxacin, oxacillin, cefoxitin (3.3%). Nineteen PFGE-types were differentiated, and their sequence-types coincided with main clonal complexes described in S. aureus carriers from different places worldwide: CC30, CC8, CC97, CC15, CC22 and CC1. MRSA strains belonged to CC5 and they corresponded to the Chilean/Cordobes and USA100NY/J clones. CONCLUSION: Nasal carriage of S. aureus and MRSA in students, coincided with the general population and sensitive-methicillin strains showed clonal diversity and high antimicrobial susceptibility except for penicillin.

Diseminación clonal de KPC-2 en Klebsiella pneumoniae resistente a carbapenémicos / Clonal dissemination of KPC-2 in carbapenem resistant Klebsiella pneumoniae

Objetivo: Determinar los mecanismos de resistencia antibiótica y la epidemiología molecular de aislados clínicos de Klebsiella pneumoniae resistentes a carbapenémicos. Materiales y métodos: 30 aislados multirresistentes de K. pneumoniae fueron obtenidos a partir de: urocultivo, aspirado traqueal, secreción de herida, sonda vesical, hemocultivo, líquido peritoneal, punta de catéter, colección abdominal y secreción bronquial. Los aislados fueron colectados de noviembre de 2012 a abril de 2013. La identificación y susceptibilidad antibiótica fue determinada por el sistema automatizado VITEK 2. Para la amplificación de genes de resistencia se empleó PCR, la determinación de las Secuencias Tipo (ST) fue obtenida por tipificación multilocus de secuencias (MLST) y la relación clonal fue establecida por electroforesis en gel de campo pulsado (PFGE). Resultados: Todos los aislados mostraron fenotipos multirresistentes, excepto a colistina y tigeciclina. El 100% de los aislados fue productor de la carbapenemasa KPC-2. La determinación de la presencia de genes codificantes de β-lactamasas de Espectro Extendido mostró que el 67% de los aislados fue positivo para el gen blaCTX-M, el 100% fue positivo para el gen blaSHV y 93% fue positivo para el gen blaTEM. El análisis de la relación clonal de los 30 aislados agrupó a 20 en un mismo pulso tipo. El análisis por MLST demostró que la ST predominante fue ST258 presente en el 60% de la población, seguida de ST1199 presente en el 20% de la población analizada. Conclusiones: Los resultados obtenidos demuestran la importancia de implementar y combinar estudios epidemiológicos, clínicos y moleculares para comprender la distribución de la resistencia entre bacterias de interés clínico.

Objective: To determine the mechanism of antibiotic resistance and molecular epidemiology of carbapenem resistant isolates of Klebsiella pneumoniae. Materials and Methods: 30 multidrug resistant isolates of K. pneumoniae were obtained from urine culture, tracheal aspirate, wound secretion, bladder catheter, blood culture, peritoneal fluid, catheter tip, abdominal collection, and bronchial secretion. K. pneumoniae isolates were collected between November 2012 and April 2013. Identification and susceptibility were determined by the VITEK 2 system. Resistance genes were identified by PCR, sequence type (ST) was established by multilocus sequence typing (MLST), and clonal relationship was defined by pulsed field gel electrophoresis (PFGE). Results: All isolates were multidrug resistant and susceptible to colistin and tigecycline. 100% of isolates produced KPC-2 carbapenemase. This study detected Extended Spectrum β-Lactamases enconding genes. 67% of isolates were positive for blaCTX-M, 100% were positive for blaSHV, and 93% of isolates were positive for blaTEM. Analysis of the clonal relationship clustered 20 isolates in the same clonal complex. Multilocus sequence typing showed the predominant sequence type ST 258 in 60% of population. ST 1199 were present in 20% of bacterial population. Conclusion: Molecular epidemiology, clinical research and molecular biology studies improve understanding of mechanisms of resistance distribution among bacteria of clinical interest.

Clinical and microbiological characteristics of cryptococcosis at an university hospital in China from 2013 to 2017

ABSTRACT Background: This study aims to explore the epidemiology, clinical profile and strain characteristics of cryptococcosis from 2013 to 2017 in a major teaching hospital in China. Methods: Trends in antifungal drug susceptibility of 217 consecutive non-repetitive cryptococcal isolates collected from patients of an university hospital in China were analyzed between 2013 and 2017. Of those, 98 isolates were conserved for identification by internal transcribed spacer (ITS) sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. Multilocus sequence typing (MLST) was used to designate molecular types. Clinical characteristics of the 98 patients with cryptococcosis during the period of 2013-2017 were retrospectively evaluated. Results: There was a trend for gradual increase in the MIC range of fluconazole was from 2013 to 2017. The conserved 98 clinical cryptococcal isolates included 97 C. neoformans and one C. gattii, and 90 (91.8%) isolates belonged to ST5 genotype VNI. Out of the 98 patients with cryptococcosis, 28 (28.6%) were HIV-infected and 32 (32.7%) had no underlying diseases. HIV-infected patients had higher mortality than HIV-uninfected patients (28.6% vs 14.3%, p = 0.147). Conclusions: Most of the patients with cryptococcosis were not HIV-infected in this study, while patients with HIV had a higher mortality. Reduced susceptibility to fluconazole was observed among C. neoformans isolates, most of them belonged to ST5 genotype VNI having an impact on the effective dose of fluconazole.

Multilocus sequence typing (MLST) of clinical and environmental isolates of Cryptococcus neoformans and Cryptococcus gattii in six departments of Colombia reveals high genetic diversity

Abstract INTRODUCTION: The average annual incidence of cryptococcosis in Colombia is 0.23 cases per 100,000 inhabitants in the general population, and 1.1 cases per 1000 in inhabitants with Acquired Immune Deficiency Syndrome (AIDS). In addition, the causal fungus has been isolated from the environment, with serotypes A-B and C in different regions. This study aims to determine the genetic association between clinical and environmental isolates of C. neoformans/C. gattii in Colombia. METHODS: Multilocus sequence typing (MLST) was used to identify possible clones, providing information about the epidemiology, ecology, and etiology of this pathogen in Colombia. RESULTS: A total of 110 strains, both clinical (n=61) and environmental (n=49), with 21 MLST sequence types (ST) of C. neoformans (n=14STs) and C. gattii (n=7STs) were identified. The STs which shared clinical and environmental isolate sources were grouped in different geographical categories; for C. neoformans, ST93 was identified in six departments, ST77 in five departments; and for C. gattii, ST25 was identified in three departments and ST79 in two. CONCLUSIONS: High genetic diversity was found in isolates of C. neoformans/gattii by MLST, suggesting the presence of environmental sources harboring strains which may be sources of infection for humans, especially in immunocompromised patients; these data contribute to the information available in the country on the distribution and molecular variability of C. neoformans and C. gattii isolates recovered in Colombia.

Perfil de genes de virulência e diversidade clonal de Escherichia coli produtora de toxina Shiga (STEC) e enteropatogênica atípica (aEPEC) do sorotipo O26: H11 / Virulence gene profile and clonal diversity of Shiga toxin-producing Escherichia coli (STEC) and atypical enteropathogenic (aEPEC) serotype O26: H11

O sorotipo O26:H11 associado às aEPEC e STEC tem sido frequentemente implicado com doenças entéricas em diversos países. Análises comparativas de cepas O26:H11 STEC e aEPEC de vários países indicam que as aEPEC O26:H11 representam clones que perderam os genes stx através da excisão fágica. No Brasil, o isolamento de aEPEC O26:H11 de casos de infecção humana é frequente, sendo este um dos mais importantes sorotipos de aEPEC em nosso meio. O objetivo deste estudo foi investigar e fazer uma análise comparativa sobre a ocorrência de vários genes de virulência, alguns deles altamente específicos para o patotipo STEC, em cepas O26:H11 STEC e aEPEC, além de avaliar a diversidade clonal através das técnicas de PFGE e sequenciamento MLST. Oito das 10 cepas STEC apresentaram o genótipo stx1a, enquanto duas cepas apresentaram stx2a. Este é o primeiro relato sobre a ocorrência de STEC O26:H11 albergando o genótipo stx2a no Brasil. Os genes plasmidiais ehxA, katP, espP e toxB foram encontrados em 8 (80%), 7 (70%), 8 (80%) e 8 (80%) das STEC. Todas as STEC abrigaram os genes efa, escN, nleB, nleE, sen, z2098, z2099, z2121, ureD e terE. Os genes espK e espM1 foram encontrados em igual frequência. Dentre as aEPEC, todas foram positivas para os genes efa, escN, nleB, nleE, sen e z2121. Os genes ehxA, espP, espM1, iha, katP, toxB, z2098, z2099, espK, espV, espN, ureD e terE estiveram presentes em 25 (66%), 25 (66%), 35 (92%), 31(82%), 16 (42%), 18 (47%), 26 (68%), 26 (68%), 31 (82%), 13 (34%), 19 (50%), 26 (68%) e 30 (79%) das cepas, respectivamente. O gene astA foi encontrado em apenas três (8%) aEPEC e nenhuma das cepas estudadas...(AU)

The O26: H11 serotype which is associated with pathotypes aEPEC and STEC, is implicated with enteric diseases in several countries. Comparative analyzes of O26:H11 STEC and aEPEC strains from several countries indicated that many aEPEC strains represent STEC clones that lost the stx genes through phage excision. The aim of this study was to investigate the occurrence of several virulence genes, some of which highly specific for the STEC pathotype, in strains O26:H11 STEC and aEPEC, and to evaluate clonal diversity employing of PFGE and MLST aproches. Eight of the 10 STEC strains presented stx1a subtype, while two strains presented stx2a. This is the first report on the occurrence of STEC O26: H11 harboring the stx2a genotype in Brazil. The plasmidial genes ehxA, katP, espP and toxB were found in 8 (80%), 7 (70%), 8 (80%) and 8 (80%) of STEC. All STECs harbored the efa, escN, nleB, nleE, sen, z2098, z2099, z2121, ureD and terE genes. The espK and espM1 genes were found at the same frequency. Among aEPEC, all were positive for the efa, escN, nleB, nleE, sen and z2121 gene. The genes ehxA, espP, espM1, iha, katP, toxB, z2098, z2099, espK, espV, espN, ureD and terE were present in 25 (66%), 25 (66%), 35 (92%), 31 ( 82%), 16 (42%), 18 (47%), 26 (68%), 26 (68%), 31 (82%), 13 (34%), 19 (50%), 26 (68%) ) and 30 (79%). The astA gene was found in only three (8%) aEPEC and none of these strains showed the presence of cdt-V, etpD and pagC. All STECs presented CRISPR sequences, being C+D CRISPR types. Among the aEPEC in addition to these two polymorphisms associated with CRISPR sequences, type E was also found. PFGE typing revealed a wide genetic diversity both between STEC and aEPEC. MLST typing was performed on 24 strains of aEPEC and STEC, ten STECs and 14 aEPEC, but not all strains had a valid ST through the Enterobase bank, only 18 strains presented ST, and all these ST belonged to the clonal complex 29. ST21 and ST29 occurred equally, in four STECs each. Among the aEPEC, two were ST21 and eight belonged to ST29. Most strains of aEPEC O26: H11 in our study demonstrated several characteristics compatible with STEC and are therefore derived from this pathotype. (AU)

Pyomelanin biosynthetic pathway in pigment-producer strains from the pandemic Acinetobacter baumannii IC-5

BACKGROUND Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.

Livestock-associated methicillin-resistant Staphylococcus aureus in Korea: antimicrobial resistance and molecular characteristics of LA-MRSA strains isolated from pigs, pig farmers, and farm environment

Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital / 中华医学杂志(英文版)

BACKGROUND@#Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) poses distinct clinical challenges due to extensively drug resistant (XDR) phenotype, and sequence type (ST) 11 is the most dominant blaKPC-2-bearing CP-Kp clone in China. The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit (ICU) of a Chinese tertiary hospital.@*METHODS@#Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination, polymerase chain reaction, and pyrosequencing. The six ST11 XDR CP-Kp, as well as three multi-drug resistant (MDR) and four susceptible strains, were sequenced using single-molecule real-time method. Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains.@*RESULTS@#We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital. Functionally, genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains, especially genes correlative with mobile genetic elements (MGEs) such as transposons and prophages. Structurally, eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons, integrons, prophages, genomic islands, and integrative and conjugative elements. Three of them were located on plasmids and eight on chromosomes; five of them were with antimicrobial resistance genes and eight with adaptation associated genes. Notably, a new blaKPC-2-bearing ΔΔTn1721-blaKPC-2 transposon, probably transposed and truncated from ΔTn1721-blaKPC-2 by IS903D and ISKpn8, was identified in all six ST11 XDR CP-Kp strains.@*CONCLUSION@#Our findings suggested that together with clonal spread, MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability, which facilitated their widespread dissemination in hospital.

Molecular epidemiology and characterization of Streptococcus mutans strains in Korea / 대한구강보건학회지

OBJECTIVES: We investigated the characteristics of Streptococcus mutans in the national culture collection from Korea. Twenty-nine (dental plaque, n=27; endodontic infections, n=1; blood, n=1) isolates were included in this study.METHODS: Antimicrobial susceptibilities were tested using the disk diffusion test. Multilocus sequence typing (MLST), serotyping, and collagen-binding genes were used for polymerase chain reaction (PCR) and direct sequencing. A collagen-binding (to assess the adhesion properties) assay was performed. S. mutans demonstrated high susceptibility to antimicrobial agents. Differences in collagen-binding abilities of the cnm-positive and -negative groups were compared using the Mann-Whitney U test (P<0.05).RESULTS: MLST analyses revealed 25 sequence types (STs), 17 of which (ST213-ST229) contained new alleles. The strains were classified into four serotypes with the c type encompassing 79.3% of all strains, while the e, f, and k types representing 6.9% each. Analysis of the cnm and cbm genes, which encode the two surface adhesin components of S. mutans, revealed three cnm-positive strains, each displaying greater adhesion ability than those of the cnm-negative strains.CONCLUSIONS: This study highlights the presence of a wide variety of S. mutans genotypes in Korea. These findings may provide useful information regarding the pathogenesis of infectious diseases, such as dental caries.

Caracterización genética de cepas de Listeria monocytogenes aisladas durante los años 2007-2014 en Chile / Genetic characterization of Listeria monocytogenes strains isolated during 2007-2014 in Chile

Resumen Introducción: Listeria monocytogenes es un patógeno transmitido por alimentos que causa listeriosis, una enfermedad que puede presentarse como gastroenteritis febril o en una forma invasora que tiene altas tasas de mortalidad. Hasta el momento, ha sido poco estudiada la diversidad genética de cepas de L. monocytogenes aisladas desde pacientes, alimentos y fuentes ambientales en Chile. Objetivo: Caracterizar genéticamente cepas de L. monocytogenes de estos tres orígenes recibidas por el Instituto de Salud Pública de Chile (ISP) entre los años 2007 y 2014. Material y Métodos: Se seleccionaron 94 cepas de L. monocytogenes correspondientes a 94 pulsotipos diferentes identificados por electroforesis en gel de campo pulsado (PFGE), se extrajo ADN y se realizó serotipificación mediante reacción de polimerasa en cadena (RPC) y tipificación de secuencias multilocus (MLST). Resultados: El serotipo más común fue 4b (55,3%), seguido de 1/2a (25,5%), 1/2b (17%) y 1/2c (2,2%). Se identificaron 32 secuencias tipo (ST), de las cuales cuatro fueron nuevas, y las predominantes fueron ST1 (28,7%) y ST2 (13,8%). La totalidad de las cepas se agrupó en los Linajes I y II. Conclusiones: Se observó una gran variabilidad genética en las cepas de L. monocytogenes analizadas, siendo predominantes las secuencias tipo ST1 y ST2, ambas pertenecientes al Linaje I. Nuestros resultados contribuyen a conocer la estructura poblacional de este patógeno en Chile y su presencia en muestras clínicas, alimentos y el medio ambiente.

Background: Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a disease that can present as febrile gastroenteritis or as an invasive form that has high mortality rates. So far, the genetic diversity of strains of L. monocytogenes isolated from patients, foods and environmental sources in Chile has been poorly studied. Aim: To characterize genetically L. monocytogenes strains received by the Institute of Public Health of Chile (ISP) between 2007 and 2014. Methods: We selected 94 strains of L. monocytogenes corresponding to 94 different pulsotypes identified by pulsed field gel electrophoresis (PFGE), DNA was extracted and serotyping was performed by polymerase chain reaction (PCR) and multilocus sequence typing (MLST). Results: The most common serotype was 4b (55.3%), followed by serotypes 1/2a (25.5%), 1/2b (17%) and 1/2c (2.2%). 32 sequence-type (ST) were identified, of which 4 were new, and the predominant ones were ST1 (28.7%) and ST2 (13.8%). All the strains of L. monocytogenes were grouped in Lineages I and II. Conclusions: A great genetic variability was observed in the strains of L. monocytogenes analyzed, being predominant the ST1 and ST2, both belonging to Lineage I. Our results contribute to know the population structure of this pathogen in Chile and its presence in clinical samples, food and the environment.

Genetic diversity of Mycoplasma hyopneumoniae in Mendoza province / Diversidad genética de Mycoplasma hyopneumoniae en la provincia de Mendoza

En Argentina, la neumonía enzoótica porcina (NEP) es altamente prevalente y se han identificado diferentes tipos genéticos de Mycoplasma hyopneumoniae. Sin embargo, se carece de información acerca de la prevalencia de NEP y de otros aspectos epidemiológicos de esta entidad en la provincia de Mendoza. En esta investigación se usó un análisis multilocus de regiones repetidas en tándem (MLVA) de los loci P97 R1, P97 R1A y P146 R3 para evaluar la diversidad genética de M. hyopneumoniae a partir de muestras clínicas de cerdos de cinco granjas localizadas en diferentes distritos de la provincia de Mendoza. M. hyopneumoniae pudo ser tipificado a partir de 27 muestras de lavado broncoalveolar (LBA) y se identificaron 8 diferentes MLVA-tipos. Este es el primer informe acerca de la diversidad genética de M. hyopneumoniae en Mendoza. Los resultados obtenidos permiten describir de manera más acabada la diversidad genética de este agente en nuestro país.