This study was conducted to investigate the existence and possible transmission routes of CREs during the bovine slaughter process. A total of 600 samples including rectoanal mucosal swaps, bovine ...hides and carcasses were collected weekly, over a 20 week period from three different slaughterhouses in Samsun province and analyzed in terms of CRE. Isolation of CRE was performed using Chromatic CRE Agar. Obtained isolates were identified using PCR and VITEK MS. E-test method was used for screening of carbapenemase production and disk diffusion method was used for detection of phenotypic carbapenem resistance. Presence of five major carbapenemase genes were investigated by PCR and obtained amplicons were sequenced by Sanger sequencing. Clonal relatedness was investigated by Clermont phylo-typing and MLST. Plasmid incompability groups were determined by PCR-based replicon typing. Based on the results, only one bovine hide sample was found positive in terms of CRE and blaKPC-2 harbouring E. coli ST398 (phylogroup A) was identified. E. coli ST398 was found resistant to meropenem, imipenem, ertapenem, doripenem and also tested fluoroquinolones. ST398 was found to harbour three distinct replicons, namely N, FIIK, and FIB KQ. Inc. groups for these replicons were identified as IncN and IncFIIK. On the other hand, no concrete evidence has been obtained to suggest that CREs are spreading at the slaughterhouse level. Conclusively, conducting further studies in areas such as farms, pens, and feedlots is necessary to gain a better understanding of the transmission routes of CREs in livestock.
•Out of a total of 600 samples, CRE was detected in only one bovine hide sample.•E. coli ST398 was found to harbour blaKPC-2 and resistant to all tested carbapenems.•E. coli ST398 was found to contain N, FIIK, and FIB KQ replicons.•Incompatibility groups for detected replicons were identified as IncN and IncFIIK.•Transmission of CRE was not detected among the samples throughout the study period.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
As an opportunistic pathogen worldwide,
Staphylococcus aureus
can cause food poisoning and human infections. This study investigated the sequence typing, the penicillin (blaZ) and methicillin (mec) ...resistance profiles of
S. aureus
from food samples and food poisoning outbreaks in Shijiazhuang City, and the staphylococcal enterotoxin (SE) types of the
S. aureus
isolates from food poisoning. A total of 138 foodborne
S. aureus
isolates were distributed into 8 clonal complexes (CCs) and 12 singletons. CC1, CC5, CC8, CC15, CC97, CC59, CC398, CC88, and CC7 were the predominant CCs of foodborne
S. aureus
isolates. Moreover, CC59, CC15, and CC5 were the most prevalent CCs in food poisoning outbreaks. SEE was the most commonly detected SE in food poisoning isolates. One hundred thirty-three
S. aureus
isolates harbored the penicillin-resistant gene
blaZ
, and nine isolates carried the
mec
gene. The present study further explained the relationship between
S. aureus
and foods and food poisoning and indicated the potential risk of
S. aureus
infection.
Salmonella enterica (
S. enterica
) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health.
Salmonella
typing is ...essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250
S. enterica
isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All
S. enterica
isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in
dnaN
. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,5,12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of
S. enterica
isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of
Salmonella
from different hosts in China in the recent 16 years. These results greatly supplement
Salmonella
strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of
Salmonella
; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot for cruciferous vegetables worldwide, especially for the cole crops such as cabbage and cauliflower. Due to the lack of ...resistant cabbage cultivars, black rot has brought about considerable yield losses in recent years in China. Understanding of the pathogen features is a key step for disease prevention, however, the pathogen diversity, population structure, and virulence are largely unknown. In this study, we studied 50 Xcc strains including 39 Xcc isolates collected from cabbage in 20 regions across China, using multilocus sequence genotyping (MLST), repetitive DNA sequence-based PCR (rep-PCR), and pathogenicity tests. For MLST analysis, a total of 12 allelic profiles (AP) were generated, among which the largest AP was AP1 containing 32 strains. Further cluster analysis of rep-PCR divided all strains into 14 DNA groups, with the largest group DNA I comprising of 34 strains, most of which also belonged to AP1. Inoculation tests showed that the representative Xcc strains collected from diverse regions performed differential virulence against three brassica hosts compared with races 1 and 4. Interestingly, these results indicated that AP1/DNA I was not only the main pathotype in China, but also a novel group that differed from the previously reported type races in both genotype and virulence. To our knowledge, this is the first extensive genetic diversity survey for Xcc strains in China, which provides evidence for cabbage resistance breeding and opens the gate for further cabbage-Xcc interaction studies.
Introduction Acinetobacter baumannii ( A. baumannii ) is an important opportunistic pathogen causing nosocomial infection in the clinic. The occurrence rate of antibiotic resistance is increasing ...year by year, resulting in a highly serious situation of bacterial resistance. Methods To better understand the local epidemiology of multidrug-resistant A. baumannii , an investigation was conducted on the antibiotic resistance of different types of A. baumannii and its relationship with the genes of A. baumannii . Furthermore, the molecular mechanism underlying antibiotic resistance in A. baumannii was investigated through transcriptome analysis. Results These results showed that a total of 9 STs were detected. It was found that 99% of the strains isolated in the hospital belonged to the same STs, and the clone complex CC208 was widely distributed in various departments and all kinds of samples. Furthermore, these A. baumannii strains showed high resistance to ertapenem, biapenem, meropenem, and imipenem, among which the resistance to ertapenem was the strongest. The detection rate of bla OXA –51 gene in these carbapenem resistance A. baumannii (CRAB) reached 100%; Additionally, the transcriptome results showed that the resistance genes were up-regulated in resistance strains, and these genes involved in biofilm formation, efflux pumps, peptidoglycan biosynthesis, and chaperonin synthesis. Discussion These results suggest that the CC208 STs were the main clonal complex, and showed high carbapenem antibiotic resistance. All these resistant strains were distributed in various departments, but most of them were distributed in intensive care units (ICU). The bla OXA –23 was the main antibiotic resistance genotype; In summary, the epidemic trend of clinical A. baumannii in Guiyang, China was analyzed from the molecular level, and the resistance mechanism of A. baumannii to carbapenem antibiotics was analyzed with transcriptome, which provided a theoretical basis for better control of A. baumannii .
•A five locus-based MLST assay was developed for genotyping M. anserisalpingitidis.•MLST assay of 89 different samples yielded 76 unique sequence types.•MLST could identify related samples from ...different geographical locations.•The MSLT scheme provides novel phylogenetic tool for M. anserisalpingitidis.
Mycoplasma anserisalpingitidis infection is associated with the inflammation of the genital tract and cloaca, embryo lethality, and decreased egg production in geese, leading to serious economic losses. M. anserisalpingitidis has been detected mainly in Central and Eastern Europe, especially in Hungary, but the pathogen was identified recently in China, predicting it’s worldwide occurrence. In this study, a novel multilocus sequence typing (MLST) scheme was developed to analyse phylogenetic relationships between M. anserisalpingitidis field isolates and clinical specimens originating from different geographical locations.
Five loci (atpG, fusA, pgiB, plsY, and uvrA) were selected for the final MLST study. The examined 89 M. anserisalpingitidis samples yielded 76 unique sequence types with a 0.994 Simpson’s index of diversity. The samples were originated from Hungary, Poland, Ukraine, China, and Vietnam. Phylogenetic analysis revealed the existence of three distinct clades (A–C) and six subclades within clade C. Generally, samples originating from the same geographical locations or livestock integration clustered together. Isolates in clade A showed the closest relationships to the M. anatis outgroup due to sequence similarity of the plsY locus. The highest genetic distance was observed in 5C among the subclades of clade C, containing the Asian and some Hungarian field isolates.
The developed MLST assay revealed high diversity of the investigated M. anserisalpingitidis samples. The method proved to be a valuable and cost-effective tool for sequence typing of this waterfowl Mycoplasma species, enabling the better understanding of its phylogeny and providing a robust assay for future molecular epidemiological investigations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study explores the prevalence of adherent-invasive Escherichia coli (AIEC) in colorectal cancer (CRC) patients and investigates the potential of effective intracellular antibiotics as a ...therapeutic strategy for CRC patients with AIEC infections. Considering the pivotal role of integrons in bacterial antibiotic resistance, the frequency of class 1 and 2 integrons in AIEC isolated from CRC patients, in one of the referenced 3 gastroenterology clinics in Isfahan, Iran was examined. AIEC strains were isolated from the colorectal biopsies and their antimicrobial sensitivity was assessed using the disc diffusion method. Polymerase chain reaction (PCR) was employed to detect intl1 and intl2 . The multilocus sequence typing (MLST) method was utilized to type 10 selected isolates. Of the 150 samples, 24 were identified as AIEC, with the highest number isolated from CRC2 (33.4%) and CRC1 (29.16%), and the least from the FH group (8.3%) and control group (12.5%). int1 in 79.2% and int2 in 45.8% of AIEC strains were found and 41.6% of strains had both integrons. AIEC isolates with int1 exhibited the highest sensitivity to trimethoprim-sulfamethoxazole (57.9%), while those with int2 showed the highest sensitivity to ciprofloxacin (63.6%). A significant association between resistance to rifampin and integron 2 presence in AIEC isolates was observed. Furthermore, a significant correlation between integron 1 presence, invasion, survival, and replication within macrophages in AIEC strains was identified. MLST analysis revealed ST131 from CC131 with integron 1 as the most common sequence type (ST). The emergence of such strains in CRC populations poses a serious public health threat. The distribution pattern of STs varied among studied groups, with pandemic STs highlighting the importance of examining and treating patients infected with these isolates. Comprehensive prospective clinical investigations are warranted to assess the prognostic value of detecting this pathovar in CRC and to evaluate therapeutic techniques targeting drug-resistant AIECs, such as phage therapy, bacteriocins, and anti-adhesion compounds, for CRC prevention and treatment.
is one of the most important food-borne pathogens globally. It produces various toxins and invasive enzymes and can be found in numerous food products. Milk is an important source of staphylococcal ...food poisoning. After pasteurization, this microorganism or its enterotoxins might still remain in pasteurized milk. Therefore, this study was to investigate the contamination of
in 258 pasteurized milk from 39 cities of China. The prevalence and levels of
in these samples as well as antibiotic susceptibility profiles, virulence genes, biofilm formation, and biofilm related genes,
typing and MLST were used to determine the characterization among the isolates. It was found 3.9% of samples were detected
in 8 of 39 cities in China. The contaminated level were not very excessive which showed the MPN values of the most positive samples (9/10) were less than 1 MPN/g. All pasteurized milk-related
isolates have ability to produce biofilm and harbored
,
genes, other biofilm related genes
were showed in 91.7% of isolates and
gene were showed in 50%, except
gene which were free in all isolates. The antibiotic susceptibility test showed that all isolates were resistant or intermediate-resistant to different concentrations of the antibiotics. Furthermore, 75.0% of the isolates were resistant to three or more antibiotic classes, which indicated multidrug resistance. The isolates had virulence potential, which showed 66.7% (8/12) of the isolates carried one or more virulence-associated genes. Molecular typing by MLST and
typing enabled classification of these isolates into a total of 11 sequence types (STs) and
types, which indicated high genetic diversity. Most of these types were related to various clinical
infections. Thus, the findings of this study reflect the potential risk of
infection in China. Our study also provides comprehensive analysis of the prevalence of
in pasteurized milk and helps ensure more accurate treatment of human infection with effective antibiotics.
The genus Vibrio includes important pathogenic species for human and aquatic organisms such as Vibrio cholera, V. parahaemolyticus, V. vulnificus, V. anguillarum or V. harveyi. At present, ...Vibrionaceae family consists of >190 described species, classified into nine genera. Vibrio are widespread in shellfish, finfish and marine ecosystems and show resourceful ecologies, which recognized as one of the most diverse bacterial groups for illuminating the genome evolution. In the present study, to clarify the relationship among aquatic species in the genus, a multilocus sequence analysis (MLSA) and typing (MLST) approach was applied to characterize 51 Vibrio isolates from Turkish fish farms, 146 strains deposited in the PubMLST database and 59 type strains from GenBank. For all studied isolates (n = 256), diversity analysis, population structure, determination of recombination, demographic history and gene flow were performed based on the MLST scheme. Vibrio isolates, subjected to the study, showed a high diversity within the Vibrio population and also genetic interactions into the genus. We found 17 new described sequence types by MLST analysis that were isolated from rainbow trout, sea bream and sea bass in Turkish fish farms, which clearly indicate that the genes underwent recombination frequently. While predominant sequence types were found in the presented study, differences of genotypes need to be evaluated in a disease situation or preventing measurements. The findings about genetic recombination possibly helps to understand differences of Vibrio infections in fish. Furthermore, elucidating of genetic variability within species shed light on providing effective measurements in aquaculture by vaccine production and drug applications.
•Vibrio isolates (Turkish fish farms), strains from PubMLST and type strains (GenBank) were used for Sequence Typing analysis•17 new described sequence types were found by MLST analysis•This study indicate that a high level of population genetic diversity exists in aquatic Vibrio species•The genetic diversity of Vibrio species addressed to species-specific control such as vaccine production, could be provided
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Shiga toxin–producing Escherichia coli (STEC) is one of the major causes of human gastrointestinal disease and has been implicated in sporadic cases and outbreaks of diarrhoea, haemorrhagic colitis ...and haemolytic uremic syndrome worldwide. In this study, we determined the molecular characteristics and phylogenetic relationship of STEC isolates, and their genetic diversity was compared to that of other E. coli populations. Whole genome sequencing was performed on 132 clinical STEC isolates obtained from the faeces of 129 Dutch patients with gastrointestinal complaints. STEC isolates of this study belonged to 44 different sequence types (STs), 42 serogenotypes and 14 stx subtype combinations. Antibiotic resistance genes were more frequently present in stx1-positive isolates compared to stx2 and stx1 + stx2–positive isolates. The iha, mchB, mchC, mchF, subA, ireA, senB, saa and sigA genes were significantly more frequently present in eae-negative than in eae-positive STEC isolates. Presence of virulence genes encoding type III secretion proteins and adhesins was associated with isolates obtained from patients with bloody diarrhoea. Core genome phylogenetic analysis showed that isolates clustered according to their ST or serogenotypes irrespective of stx subtypes. Isolates obtained from patients with bloody diarrhoea were from diverse phylogenetic backgrounds. Some STEC isolates shared common ancestors with non-STEC isolates. Whole genome sequencing is a powerful tool for clinical microbiology, allowing high-resolution molecular typing, population structure analysis and detailed molecular characterization of strains. STEC isolates of a substantial genetic diversity and of distinct phylogenetic groups were observed in this study.
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