Acinetobacter baumannii is one of the most important opportunistic pathogens that causes serious health care associated complications in critically ill patients. In the current study we report on the ...diversity of the clinical multi-drug resistant (MDR) A. baumannii in Kuwait by molecular characterization. One hundred A. baumannii were isolated from one of the largest governmental hospitals in Kuwait. Following the identification of the isolates by molecular methods, the amplified bla OXA-51-like gene product of one isolate (KO-12) recovered from blood showed the insertion of the ISAba19 at position 379 in bla OXA-78. Of the 33 MDR isolates, 28 (85%) contained bla OXA-23, 2 (6%) bla OXA-24 and 6 (18%) bla PER-1 gene. We did not detect bla OXA-58, bla VIM, bla IMP, bla GES, bla VEB, and bla NDM genes in any of the tested isolates. In three bla PER-1 positive isolates the genetic environment of bla PER-1 consisted of two copies of ISPa12 (tnpiA1) surrounding the bla PER-1 gene on a highly stable plasmid of ca. 140-kb. Multilocus-sequence typing (MLST) analysis of the 33 A. baumannii isolates identified 20 different STs, of which six (ST-607, ST-608, ST-609, ST-610, ST-611, and ST-612) were novel. Emerging STs such as ST15 (identified for the first time in the Middle East), ST78 and ST25 were also detected. The predominant clonal complex was CC2. Pulsed-field gel electrophoresis and MLST defined the MDR isolates as multi-clonal with diverse lineages. Our results lead us to believe that A. baumannii is diverse in clonal origins and/or is undergoing clonal expansion continuously while multiple lineages of MDR A. baumannii circulate in hospital ward simultaneously.
This study was to estimate the prevalence and characteristics of
from 1,850 retail meat and meat products in China during July 2011 to June 2016. The samples were collected covering most provincial ...capitals in China, including 604 raw meat, 601 quick-frozen meat, and 645 ready-to-eat meat. Using the qualitative and quantitative methods, all 39 cities had
-positive samples, and
was detected in 35.0% (647/1,850) of the samples. The levels of
in retail meat showed that the MPN value of the majority of the positive samples ranged from 0.3 to 100 MPN/g. Twenty-four antibiotics were used to test all 868
isolates for antibiotic susceptibility. Only 11 isolates (1.26%) were susceptible to all antibiotics, whereas most isolates (821/868, 94.6%) showed resistance or intermediary resistance to more than three or more antibiotics. Of these strains, 104 (12.0%) were resistant to more than 10 antibiotics. However, the most frequent resistance was observed to ampicillin (85.4%), followed by penicillin (84.6%), erythromycin (52.7%), tetracycline (49.3%), kanamycin (45.3%), telithromycin (30.1%), clindamycin (29.6%), streptomycin (21.1%), norfloxacin (20.4%), gentamicin (19.4%), fusidic acid (18.4%), ciprofloxacin (16.9%), chloramphenicol (13.1%), amoxycillin/clavulanic acid (11.0%), and others (<10%). 7.4% of isolates (62/868) were confirmed as methicillin-resistance
(MRSA). By molecular typing analysis, there were 164
types and 111 STs were identified, including 15 novel
types and 65 newly STs by multilocus sequence typing (MLST) and
typing. Despite the wide genetic diversity observed among the 868 isolates, a great proportion of the population belonged to finite number of major clones: ST1-t127 (93/868, 10.7%) and ST7-t091 (92/868, 10.6%), ST5-t002 (42/868, 4.8%), ST398-t034 (40/868, 4.6%), ST188-t034 (38/868, 4.4%), ST59-t437 (30/868, 3.5%), ST6-t701 (29/868, 3.3%), and ST9-t899 (27/868, 3.1%) in China. This study reflects
was readily detected in Chinese retail meat and meat products but the level were not very excessive. In this study, the high antibiotic resistance is alarming and raising public health concern. In additions, most of molecular types of isolates have been linked to human infections around the world, indicating that these types of
in China have a theoretical pathogenic potential.
Methicillin-resistant
(MRSA) is an emerging pathogen that is difficult to treat due to the multiresistance of the bacteria upon infection. From 2011 to 2016, 1581
strains were isolated from 4300 ...samples from retail foods covering most provincial capitals in China. To determine the prevalence of food-related MRSA and its genetic background in China, antibiotic resistance, staphylococcal toxin genes, staphylococcal cassette chromosome
(
) typing,
-typing and MLST were carried out in this study. In total, 108 (7.4%) isolates were confirmed for MRSA by phenotyping (cefoxitin) and genotyping (
gene). A total of 52.8% (57/108) of the MRSA isolates belonged to clonal complex 59 (CC59) (ST59, ST338, and ST3355), which was the predominant clone in this study. These CC59 isolates carried SCC
elements of type IV, V, or III and exhibited
type t437, t441, t543, t163, t1785, or t3485, and half of them carried major virulence genes, such as the Panton-Valentine leucocidin (PVL) gene. The secondary clones belonged to ST9 (15.7%, 17/108) with a type of t899-SCC
III and showed a broader range of antimicrobial resistance. The remaining MRSA isolates (31.5%, 34/108) were distributed in 12 different STs and 18 different
types. All isolates harbored at least one of the enterotoxin genes, whereas only 4 isolates (3.70%) were positive for the toxic shock syndrome toxin
alleles. For antibiotic susceptibility testing, all isolates were resistant to more than three antibiotics, and 79.6% of the isolates were resistant to more than 10 antibiotics. Amoxycillin/clavulanic acid, ampicillin, cefoxitin, penicillin, ceftazidime, kanamycin, streptomycin, clindamycin, and telithromycin was the most common antibiotic resistance profile (55.6%, 60/108) in the study. In summary, the results of this study implied that the major food-related MRSA isolate in China was closer to community-associated MRSA, and some of the remaining isolates (ST9-t899-SCC
III) were supposed to livestock-associated MRSA. In addition, most MRSA isolates showed resistance to multiple drugs and harbored staphylococcal toxin genes. Thus, the pathogenic potential of these isolates cannot be ignored. In addition, further studies are needed to elucidate the transmission routes of MRSA in relation to retail foods and to determine how to prevent the spread of MRSA.
•H. influenzae strains can be identified from sputum using culture-independent MLST.•Culture-independent MLST can be used to screen for H. influenzae cross-infection.•Using MLST, there was no ...evidence of cross-infection of H. influenzae in non-CF bronchiectasis.
Whether cross-infection of respiratory pathogens between patients with non-cystic fibrosis bronchiectasis occurs is debated. Investigation with traditional microbiological culture risks simplifying the lung microbiome. We demonstrate the use of culture-independent Multilocus sequence typing to screen for Haemophilus influenzae strain types in a cohort of twenty-eight patients with non-cystic fibrosis bronchiectasis.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
is one of the most common etiological agents of contagious bovine mastitis worldwide. The purpose of this study was to genetically characterize a collection of
isolates (bovine = 146, human = 12) ...recovered from cases of bovine mastitis and nasal swabs of close human contacts in the dairy environment. Isolates were screened for a combination of clinically significant antimicrobial and virulence gene markers whilst the molecular epidemiology of these isolates and possible inter-species host transmission was investigated using a combination of genotyping techniques. None of the isolates under evaluation tested positive for methicillin or vancomycin resistance encoding genes. Twenty seven percent of the bovine
isolates tested positive for one or more of the pyrogenic toxin superantigen (PTSAg) genes with the
and
genes predominating. Comparatively, 83% of the human
isolates tested positive for one or more PTSAg genes with a greater variety of genes being detected. Genomic DNA macrorestriction followed by pulsed-field gel electrophoresis (PFGE) of the bovine isolates generated 58 electrophoretic patterns which grouped into 10 pulsotypes at an 80% similarity level. The majority of the bovine isolates, 93.2% (136/146), clustered into four major pulsotypes. Seven sequence types (ST) were identified among the representative bovine
isolates genotyped, including: ST8 (CC8), ST97 (CC97), ST351 (CC705), ST352 (CC97), ST508 (CC45), ST2992 (CC97) and a novel sequence type, ST3538 (CC97). Based on PFGE analysis, greater genetic diversity was observed among the human
isolates. Bovine and human isolates from three sampling sites clustered together and were genotypically indistinguishable. Two of the isolates, ST97 and ST352 belong to the common bovine lineage CC97, and their isolation from close human contacts suggests zoonotic transfer. In the context of this study, the third isolate, ST8 (CC8), is believed to be a human clone which has transferred to a dairy cow and has subsequently caused mastitis. The detection of indistinguishable
isolates from bovine and human hosts at three of the sampling sites is suggestive of bacterial transmission and supports the need for vigilant monitoring of staphylococcal populations at the human-animal interface.
serovar Isangi (
. Isangi) is a rare non-typhoidal serovar, related to invasive nosocomial infections in various countries and to increasing antimicrobial resistance rates.
Despite existing reports ...on
. Isangi, there is a lack of information of specific traits regarding this serovar, which could be improved through genomic analyses.
Our goals were to characterize the antimicrobial resistance, virulence potential and genomic relatedness of 11
. Isangi strains from Brazil in comparison to 185 genomes of global isolates using whole-genome sequencing (WGS) data.
Phenotypic resistance was determined by disc-diffusion. The search for resistance genes, plasmids, prophages,
pathogenicity islands (SPIs) and virulence genes, plus multi-locus sequence typing (MLST) and core-genome MLST (cgMLST) were performed using WGS.
Brazilian
. Isangi strains showed phenotypic resistance to nalidixic acid, ciprofloxacin and streptomycin, and harboured antimicrobial resistance
,
,
and heavy metal tolerance (
) genes. Col(pHAD28) and IncFII(S) plasmids, virulence genes related to adherence, macrophage induction, magnesium uptake, regulation and type III secretion systems, 12 SPIs and eight prophages were detected. The 185 additional global genomes analysed harboured resistance genes against 11 classes of antimicrobial compounds, 22 types of plasmids, 32 prophages, 14 SPIs, and additional virulence genes related to serum resistance, stress adaptation and toxins. Sequence type (ST)216 was assigned to genomes from Brazil and other countries, while ST335 was the most frequent ST, especially among South African genomes. cgMLST showed that Brazilian genomes were more closely related to genomes from European and African countries, the USA and Taiwan, while the majority of South African genomes were more closely related among each other.
The presence of
. Isangi strains from Brazil and different countries showing a close genomic correlation, antimicrobial resistance profiles to drugs used in human therapy and a large number of virulence determinants reinforced the need for stronger initiatives to monitor rare non-typhoidal
serovars such as
. Isangi in order to prevent its dissemination among human and non-human sources.
is a significant cause of mortality in piglets and growing pigs worldwide. The species contains pathogenic and commensal strains, with pathogenic strains causing meningitis, arthritis, endocarditis, ...polyserositis, and septicemia. Serotyping and multilocus sequence typing (MLST) are primary methods to differentiate strains, but the information is limited for strains found in the United States. The objective of this study was to characterize the diversity of 208
isolates collected between 2014 and 2017 across North America (mainly the United States) by serotyping and MLST and to investigate associations between subtype and pathotype classifications (pathogenic, possibly opportunistic, and commensal), based on clinical information and site of isolation. Twenty serotypes were identified, and the predominant serotypes were 1/2 and 7. Fifty-eight sequence types (STs) were identified, and the predominant ST was ST28. Associations among serotypes, STs, and pathotypes were investigated using odds ratio and clustering analyses. Evaluation of serotype and ST with pathotype identified a majority of isolates of serotypes 1, 1/2, 2, 7, 14, and 23 and ST1, ST13, ST25, ST28, ST29, ST94, ST108, ST117, ST225, ST373, ST961, and ST977 as associated with the pathogenic pathotype. Serotypes 21 and 31, ST750, and ST821 were associated with the commensal pathotype, which is composed of isolates from farms with no known history of
-associated disease. Our study demonstrates the use of serotyping and MLST to differentiate pathogenic from commensal isolates and establish links between pathotype and subtype, thus increasing the knowledge about
strains circulating in the United States.
ObjectiveThis study aimed to understand the epidemic characteristics of Diarrheagenic Escherichia coli （DEC） in domestic meat products.MethodsThe molecular characteristics of 86 strains of DEC were ...analyzed by whole genome sequencing technology， and the dominant pathological types， STs， and serotypes were identified. The phylogenetic relationship between DEC strains derived from meat products in China was determined through whole genome single nucleotide polymorphism.ResultsThe results showed that the pathological types of DEC in meat products were mainly EAEC. Eighty-six DEC strains were divided into eight virulence genotypes， including 48 ST types （including six new ST types）， and 55 O：H serotypes. ST11 and CC10 were the predominant ST and clonal complex， respectively. O157， O15， and O6 were the predominant serogroups. DEC strains exhibited high genetic heterogeneity， the same pathological type had low homology， and they were in different evolutionary branches.ConclusionThere is no correspondence between DE
The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of
. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and ...the gold standard for
subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare
subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of
characterization and subtyping methods.
To obtain a higher resolution of the phylogenetic relationships of species within a genus or genera within a family, multilocus sequence analysis (MLSA) is currently a widely used method. In MLSA ...studies, partial sequences of genes coding for proteins with conserved functions (‘housekeeping genes’) are used to generate phylogenetic trees and subsequently deduce phylogenies. However, MLSA is not only suggested as a phylogenetic tool to support and clarify the resolution of bacterial species with a higher resolution, as in 16S rRNA gene-based studies, but has also been discussed as a replacement for DNA–DNA hybridization (DDH) in species delineation. Nevertheless, despite the fact that MLSA has become an accepted and widely used method in prokaryotic taxonomy, no common generally accepted recommendations have been devised to date for either the whole area of microbial taxonomy or for taxa-specific applications of individual MLSA schemes. The different ways MLSA is performed can vary greatly for the selection of genes, their number, and the calculation method used when comparing the sequences obtained. Here, we provide an overview of the historical development of MLSA and critically review its current application in prokaryotic taxonomy by highlighting the advantages and disadvantages of the method's numerous variations. This provides a perspective for its future use in forthcoming genome-based genotypic taxonomic analyses.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
PDF
