One hundred and forty two Listeria monocytogenes strains isolated from different food matrices in Switzerland between 2011 and 2014 were characterized with respect to their genotypic and phenotypic ...properties. Analyzed strains originated from various meat, milk, plant-associated food products and production environments as well as from other types of foods including fish, seafood, and ready to eat (RTE) products. The collection included serotype 1/2a (64%), 4b (15%), 1/2c (12%), 1/2b (7%) and 3c (3%). The strains were genetically diverse representing 61 MLST sequence types (ST) including 24 new STs. The most frequent clonal complexes (CC) were CC9 (15%) and CC121 (12%). PCR screening detected presence of the stress survival islet (SSI-1) in 50% of the strains. Phenotypic resistance to benzalkonium chloride (BC) was detected in 18% of the strains. The BC resistance genetic determinants qacH and bcrABC were detected in 80% and 12% of the strains, respectively. Most (n = 129) of the strains isolated from Swiss food matrices exhibited poor biofilm formation capacity and there were no correlations detected between strain serotypes, genotypes and biofilm production.
•142 Listeria monocytogenes strains isolated from various food matrices were characterized.•The collection included serotype 1/2a, 4b, 1/2c, 1/2b and 3c strains.•Strains were genetically diverse representing 61 MLST sequence types.•The most frequent clonal complexes (CC) were CC9 (15%) and CC121 (12%).•Phenotypic resistance to benzalkonium chloride was detected in 18% of the strains.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Verona integron-encoded metallo-β-lactamase-producing Pseudomonas aeruginosa (VIM-PA) outbreaks are frequently linked to contaminated sink-drains in the intensive care unit (ICU).
This study aims to ...investigate a VIM-PA outbreak occurring at four ICUs in a Belgian university center.
Between the 1st January 2019 and the 30th July 2023, data were retrospectively retrieved. Whole genome sequencing of VIM-PA was carried out for available clinical and sink-drains isolates and the core genome multilocus sequencing typing (cgMLST) was used to confirm clonality. New case incidence was estimated by analyzing the weekly data of at-risk and VIM-PA colonized patients, fitting a gamma regression with a log link.
Fifty-one patients were colonized, among them 32 (63%) were infected by VIM-PA, which contributed to 7 deaths. The outbreak investigation showed that 19 (47%) of the examined sink-drains grew at least once a VIM-PA. Two major clusters were observed by cgMLST: ST 111 (59 clones with 40 clinical isolates), and ST17 (8 clones with 6 clinical isolates). The estimated incidence rate of new cases was significantly higher in one ICU.
A five-year prolonged outbreak at the ICU of the UZ Brussel was caused by only two VIM-PA clones, both linked to sink-drains, with minimal mutations occurring throughout the years. Statistical modelling found different incidence rates between units. Tailored interventions were hence prioritized.
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•Outbreak investigation at one Belgian university center with four ICUs•two VIM-PA clones linked to sink-drains caused 5-year outbreak•Statistical models estimate higher colonization rates in one unit•Plumbing system studies provided key insights during outbreak investigation
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Recently, pathogenic
Leptospira
culture isolation is an extremely rare phenomenon in Russia.
The aim of our work
was to synthesize the lessons learned at the Irkutsk Anti-Plague Institute from
...Leptospira
culture isolation and identification since 2011.
Materials and methods
. Material from eight individuals with suspected leptospirosis and from 942 small mammals (SM) was examined using PCR and microscopic agglutination test (MAT), from humans and 260 SM, applying bacteriological method. Bacteriological temperature test, MAT, PCR, MLST and MALDI-TOF mass spectrometry with the original
Leptospira
protein profiles base were used to identify cultures. Six complete genomes were generated at the Central Research Institute of Epidemiology of the Rospotrebnadzor.
Results and discussion
. Leptospira have not been isolated from humans against the background of taking antibiotics, despite the positive PCR and MAT results. Four cultures of
Leptospira borgpetersenii
of the
Javanica
serogroup and three
L. kirschneri (Grippotyphosa
) have been isolated from SM. The results of identification using MLST scheme No. 1 and MALDI-TOF MS are identical. MLST in silico has shown the uniformity of two
Grippotyphosa
serogroup strains from Primorie and Khabarovsk with a sequence-type (ST) profile 110:100:94. ST146 is determined in four
Javanica
serogroup strains according to scheme No. 1, and unique single nucleotide polymorphisms are detected according to schemes No. 2–3. Thus, in Siberia and the Far East, between 2012 and 2016, seven pathogenic
Leptospira
cultures were isolated from carriers in natural foci; carrier infection rate being12.0–48.9 %.
Javanica
serogroup strains differ in the MLST profile characteristics and adapt to nutrient media for a longer time than
Grippotyphosa
serogroup strains.
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.
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.
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.
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.
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.
High-resolution and efficient typing for Laribacter hongkongensis (L. hongkongensis) is essential for epidemiological investigation of such emerging foodborne pathogens. Clustered regularly ...interspaced short palindromic repeats (CRISPR) typing is an innovative molecular method that shows great promise for L. hongkongensis typing. Here, we explored the CRISPR typing method by combining CRISPR1 and CRISPR2 loci to characterize a collection of 109 L. hongkongensis isolates from humans and animals and compared it to current molecular methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The results showed that all three methods have high discriminatory power (diversity index was 0.9902 for PFGE, 0.9663 for CRISPR and 0.9562 for MLST); strong congruence was observed between them (Rand index was 0.969 between CRISPR and PFGE, 0.953 between CRISPR and MLST, 0.958 between PFGE and MLST). CRISPR typing could well distinguish the isolates in the same STs or PFGE profiles, and the genetic information contained by the CRISPR array is useful for deep phylogenetic typing. We demonstrate that rapid CRISPR typing is a practical genetic fingerprinting tool with high resolution, comparable ease of use and lower cost, ability to track the source of various groups of L. hongkongensis strains and indication of genetic characteristics.
•CRISPR typing is congruent with PFGE and MLST with great discriminating power.•All the three approaches are suitable for L. hongkongensis transmission analyses.•CRISPR typing is faster, easier of use and lower cost than other two approaches.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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