Epidemiological and genetic characterization of multidrug-resistant non-O1 and non-O139 Vibrio cholerae from food in southern China.

This study reports a comprehensive epidemiological and genetic analysis of V. cholerae strains, specifically non-O1/non-O139 serogroups, isolated from animal-derived food samples in Guangdong province from 2015 to 2019. A total of 21 V. cholerae strains were obtained, which exhibited high resistance rates for nalidixic acid (57.14 %, 12/21), ampicillin (33.33 %, 7/21), and ciprofloxacin (19.05 %, 4/21). The quinolone resistance-related gene, qnrVC, was prevalent in 80.95 % (17/21) of the isolates. Additionally, chromosomally mediated quinolone-resistance mutations, including mutations in GyrA at position 83 (S83I) and ParC at position 85 (S85L), were detected in 47.62 % of the isolates. The combination of target mutation and qnrVC genes was shown to mediate resistance or intermediate resistance to ciprofloxacin in V. cholerae. Furthermore, an IncC-type conjugative plasmid carrying thirteen antibiotic resistance genes, including genes conferring resistance to two clinically important antibiotics, cephalosporins and fluoroquinolones, was identified in the shrimp-derived strain Vc516. While none of our food isolates harbored the toxigenic CTX- and TCP-encoding genes, they did possess genes encoding toxins such as HlyA and Autoinducer-2. Notably, some V. cholerae strains from this study exhibited a close genetic relationship with clinical strains, suggesting their potential to cause human infections. Taken together, this study provides a comprehensive view of the epidemiological features and genetic basis of antimicrobial resistance and virulence potential of V. cholerae strains isolated from food in southern China, thereby advancing our understanding of this important pathogen.

Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli.

Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.

An isothermal CRISPR- based lateral flow assay for detection of Neisseria meningitidis.

BACKGROUND: Neisseria meningitidis can cause life-threatening meningococcal meningitis and meningococcemia. Old standard microbiological results from CSF/blood cultures are time consuming. This study aimed to combine the sensitivity of loop-mediated isothermal nucleic acid amplification (LAMP) with the specificity of CRISPR/Cas12a cleavage to demonstrate a reliable diagnostic assay for rapid detection of N. meningitidis. METHODS: A total of n = 139 samples were collected from patients with suspected meningococcal disease and were used for evaluation. The extracted DNA was subjected to qualitative real-time PCR, targeting capsular transporter gene (ctrA) of N. meningitidis. LAMP-specific primer pairs, also targeting the ctrA, were designed and the LAMP products were subjected to CRISPR/Cas12 cleavage reaction. the readout was on a lateral flow strip. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of LAMP-CRISPR/Cas was compared with real-time PCR assays. The limit of detection (LOD) was established with serial dilutions of the target N. meningitidis DNA and calculated by Probit regression analysis. RESULTS: Six LAMP assay-specific primers were developed targeting the ctrA gene of N. meningitidis, which is conserved in all meningococcal serogroups. The LAMP primers did not amplify DNA from other bacterial DNA tested, showing 100% specificity. The use of 0.4 M betaine increased the sensitivity and stability of the reaction. LAMP-CRISPR/Cas detected meningococcal serogroups (B, C, W). The assay showed no cross-reactivity and was specific for N. meningitidis. The LOD was 74 (95% CI: 47-311) N. meningitidis copies. The LAMP-CRISPR/Cas performed well compared to the gold standard. In the 139 samples from suspected patients, the sensitivity and specificity of the test were 91% and 99% respectively. CONCLUSION: This developed and optimized method can complement for the available gold standard for the timely diagnosis of meningococcal meningitis and meningococcemia.

Molecular Characteristics and Virulence Profile of Clinical Listeria monocytogenes Isolates in Northern Taiwan, 2009-2019.

Listeria monocytogenes is a critical foodborne pathogen that causes severe invasive and noninvasive diseases and is associated with high mortality. Information on the prevalence of L. monocytogenes infections in Taiwan is very limited. This study aimed to analyze the molecular epidemiological surveillance and virulence gene distribution of 176 human clinical L. monocytogenes isolates collected between 2009 and 2019 in northern Taiwan. Our results showed that the isolates belonged to 4 serogroups (IIa, IIb, IVb, and IIc), with most isolates in serogroups IIa (81/176, 46%) and IIb (71/176, 40.3%). Multilocus sequence typing analysis revealed 18 sequence types (STs) and 13 clonal complexes (CCs). Eighty-four percent of all isolates belonged to six STs: CC87-ST87 (40/176, 22.7%), CC19-ST378 (36/176, 19.9%), CC155-ST155 (28/176, 15.5%), CC1-ST710 (16/176, 8.8%), CC5-ST5 (16/176, 8.8%), and CC101-ST101 (11/176, 6.1%). Furthermore, our analysis showed the distributions of four Listeria pathogenicity islands (LIPI) among all isolates. LIPI-1 and LIPI-2 existed in all isolates, whereas LIPI-3 and LIPI-4 only existed in specific STs and CCs. LIPI-3 existed in the STs, CC1-ST710, CC3-ST3, CC288-ST295, and CC191-ST1458, whereas LIPI-4 could be found in the STs, CC87-ST87 and CC87-ST1459. Strains containing LIPI-3 and LIPI-4 are potentially hypervirulent; thus, 68/176 isolates (39.1%) collected in this study were potentially hypervirulent. Since L. monocytogenes infections are considered highly correlated with diet, molecular epidemiological surveillance of Listeria in food is important; continued surveillance will provide critical information to prevent foodborne diseases.

A comparative study on the occurrence, genetic characteristics, and factors associated with the distribution of Listeria species on cattle farms and beef abattoirs in Gauteng Province, South Africa.

These cross-sectional studies reported the occurrence, genetic characteristics, and factors associated with the distribution of Listeria species on cattle farms and beef abattoirs in Gauteng Province, South Africa. A total of 328 samples (faeces, feeds, silage, and drinking water) were collected from 23 cattle farms (communal, cow-calf, and feedlot), and 262 samples (faeces, carcass swabs, and effluents) from 8 beef abattoirs (low throughput and high throughput) were processed using standard bacteriological and molecular methods to detect Listeria species. The factors associated with the prevalence of Listeria species were investigated, and multiplex polymerase chain reaction (mPCR) was used to determine Listeria species, the pathogenic serogroups, and the carriage of eight virulence-associated genes by Listeria monocytogenes. The overall prevalence of Listeria species in cattle farms was 14.6%, comprising Listeria innocua (11.3%), Listeria monocytogenes (3.4%), Listeria welshimeri (0.0%) compared with 11.1%, comprising Listeria innocua (5.7%), Listeria monocytogenes (4.6%), Listeria welshimeri (0.8%) for beef abattoirs. Of the three variables (area, type of farm/abattoir, and sample type) investigated, only the sample types at abattoirs had a significant (P < 0.001) effect on the prevalence of L. innocua and L. welshimeri. The frequency of distribution of the serogroups based on 11 L. monocytogenes isolated from farms was 72.7% and 27.3% for the serogroup 1/2a-3a and 4b-4d-4e, respectively, while for the 12 L. monocytogenes isolates recovered from abattoirs, it was 25%, 8.3%, 50% and 16.7% for the serogroup 1/2a-3a, 1/2b-3b, 1/2c-3c, and 4b-4d-4e respectively (P < 0.05). All (100%) isolates of L. monocytogenes from the farms and abattoirs were positive for seven virulence genes (hlyA, inlB, plcA, iap, inlA, inlC, and inlJ). The clinical and food safety significance of the findings cannot be ignored.

Comparative genome analysis of Pasteurella multocida strains of porcine origin.

Pasteurella multocida causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters. In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.

Legionella spp. Monitoring in the Water Supply Systems of Accommodation Facilities in Sardinia, Italy: A Two-Year Retrospective Analysis.

Travel-associated Legionnaires' disease is a significant public health concern worldwide. A high number of cases are reported every year among travellers who stay at guest houses, hotels, and spas. Indeed, hot water systems, showers, and air-conditioning systems can be contaminated by Legionella, which grows at 25-42 °C. Studies have shown that in Sardinia, especially during the summer months, the water circulation in the hotels' pipes is exposed to extremely high temperatures. As a result, this study was conducted to assess the colonization of hotel water systems by Legionella in Sardinia, concerning a recent EU directive 2020/2184 for drinking water with a limit of 1000 CFU /L. Methods. A total of 112 accommodation facilities were analyzed, of which 61.3% were found to be colonized with Legionella, and out of a total of 807 samples, 32.5% were positive for Legionella presence. The results showed a higher number of positive samples in the summer season. This was also associated with the higher concentration presence of >1000 CFU/L in the samples. Consequently, this study confirms that local hotel operators should improve their water safety and prevention plans, especially in spring and summer.

Meningococcal burden of disease in Argentina: 10 years epidemiologic review.

Invasive meningococcal disease (IMD) is an uncommon but serious and potentially fatal condition, mainly affecting infants. In 2017, Argentina introduced a vaccination program against serogroups A, C, W and Y (MenACWY) for infants aged 3, 5 and 15 months and adolescents aged 11 years. The objective of this study was to review the burden of IMD in Argentina in 2010-2019. Data were obtained from national surveillance databases, and the study estimated IMD incidence, mortality, case-fatality rates, and serogroup distributions across age groups. A total of 1,972 IMD cases were reported in the study period, with the highest incidence in infants aged < 1 year. Incidence peaked in 2013 and subsequently declined. Mortality rates were 18 times higher in infants than in other age groups, reflecting the high impact of IMD in this age group. The case-fatality rate was 8.5% on average and increased with age. The proportion of notified cases with serogroup identification increased over the period, reaching 91% in 2019. The most common serogroups over the study period were serogroup B (48%) and serogroup W (42%), with an increase in B relative to W since 2015. In infants aged < 1 year, the proportion of serogroup B increased in recent years, reaching around 70% of characterized cases in 2018-2019. These results show the dynamism of IMD and indicate the importance of vaccination at an early age and offering protection against predominant serogroups. These data are valuable to support evidence-based decision-making in healthcare.

[Epidemiological study and serotyping by multiple PCR of Listeria monocytogenes isolated from food matrices in Argentina]. / Estudio epidemiológico y serotipificación por PCR múltiple de Listeria monocytogenes aislada de matrices alimentarias en Argentina.

Listeria monocytogenes is an opportunistic foodborne pathogen. It can resist stress conditions by adapting through the production of biofilms, which represents a serious problem for the food industry. It is classified into 14 serotypes, although only four (1/2a, 1/2b, 1/2c, and 4b) account for 89.0-98.0% of listeriosis cases worldwide. The objective of this study was to detect and serotype L.monocytogenes isolated from different food matrices from processing plants in Argentina. In the period 2016-2021, 1832 samples (meat, ready-to-eat foods, ice cream, dairy foods, and frozen vegetables) were analyzed, of which 226 (12.34%) isolates compatible with L.monocytogenes were detected. At the same time, environmental and surface samplings were performed in processing plants for ready-to-eat foods, sausages and dairy products, where environmental contamination with L.monocytogenes was detected in numerous critical points of the process, yielding a positivity rate of 22.7%. The molecular analysis of serogroups was performed, where it was observed that serogroup IIb was the most frequent with 66.5% (n=107), and in descending order IIc with 22.3% (n=36), and IIa (n=9) and IVb (n=9) with 5.6%. The serogroup mostly isolated in environmental monitoring was IIb. This work highlights the importance of the detection and serotyping of L.monocytogenes for taking actionable measures and identifying outbreaks, and is the first study in Argentina to describe an extensive study in food matrices.

Trends in Neisseria meningitidis serogroups amongst patients with suspected cerebrospinal meningitis in the meningitis belt of Ghana: a 5-year retrospective study.

BACKGROUND: Serogroup A Neisseria meningitidis was the major cause of meningococcal meningitis epidemics in the African meningitis belt before 2010 when the monovalent meningococcal A conjugate vaccine (MenAfriVac) was introduced in the region. Therefore, this study aimed to establish the trends in N. meningitidis serogroups from 2016 to 2020 in Ghana's meningitis belt. METHODS: Polymerase chain reaction (PCR) confirmed laboratory results of suspected cases of cerebrospinal meningitis from January, 2016 to March, 2020 were obtained from the Tamale Public Health Laboratory. The data were subjected to trend analysis using Statistical Package for the Social Sciences version 25. Differences between discrete variables were analyzed using the Cochran-Armitage trend test. RESULTS: Of the 2,426 suspected cases, 395 (16.3%) were confirmed positive for N. meningitidis using PCR. Serogroup X showed a significant upward trend (P < 0.01), and serogroup W showed a downward trend (P < 0.01). However, no significant trend was observed for any other serogroup. CONCLUSION: This study showed the emergence of serogroup X, a non-vaccine type, as the predominant N. meningitidis serogroup in the wake of a declining serogroup W in Ghana's meningitis belt.

Group B Streptococcus agalactiae resistant to recommended intrapartum antibiotic prophylaxis isolated from the rectovaginal area of 35-37 weeks pregnant women

Aims@#Group B Streptococcus (GBS; Streptococcus agalactiae) is naturally found in the gut of humans and other warm-blooded animals. GBS asymptomatically colonizes the rectovaginal area of pregnant women and it has been identified as a significant risk factor for neonatal disease and mortality. This study was aimed to characterize GBS isolates isolated from pregnant women in Eastern Cape, South Africa.@*Methodology and results @#A total of 82 pregnant women in their third trimester (35-37 weeks) of gestation were screened for GBS. GBS strains were isolated from rectovaginal swabs using standard microbiological methods on Todd-Hewitt broth and blood agar, from which presumptive isolates with β-haemolysis were confirmed by polymerase chain reaction (PCR). The confirmed GBS isolates were further delineated into serogroups by PCR. An antimicrobial susceptibility profiling was carried out on the isolates, followed by resistance gene profiling on resistant isolates by PCR. A total of 49 (60%) out of 82 pregnant women were colonized with GBS. The prevalence of the serogroups that were identified were serogroup Ib 2 (4.8%), serogroup II 20 (40.8%) and serogroup IV 5 (10.2%), and non-typable 22 (44.9%). All confirmed GBS isolates (49) were resistant to erythromycin, tetracycline and clindamycin, and MAR and MARI ranged from 5-7 and 0.4-0.7, respectively. The genes responsible for conferring resistance to erythromycin, tetracycline and penicillin were successfully amplified, while no genes associated with resistance to vancomycin and clindamycin were detected. @*Conclusion, significance and impact of study @#Research findings of this study showed that serogroup Ib 2 (4.8%), serogroup II 20 (40.8%), serogroup IV 5 (10.2%) and non-typable 22 (44.9%) were the prevalent GBS serogroups. A high prevalence of antibiotics resistances was observed among the isolates, thus posing a threat to public health as it limits treatment options.

Antimicrobial resistance, serogroups, virulence gene profiles and MLST of Escherichia coli from giant panda.

Escherichia coli is a major bacterial pathogen which causes diarrhea in the giant panda. This study investigated the biological characteristics of 100 E. coli strains isolated from fecal samples collected from 100 captive giant pandas of different age groups and sexes. A standard Kirby-Bauer disk diffusion antimicrobial susceptibility test was performed with the isolates and we then further evaluated the antibiotic resistance genes (ARGs) by high-throughput quantitative PCR. Additionally, we then analyzed O serogroups through a slide agglutination test, virulence genes and the multi-locus sequence typing (MLST) by PCR. Antimicrobial susceptibility testing demonstrated that the 100 E. coli strains were mainly resistant to ENR (68%), AM (56%), IPM (55%), AMX (54%) and CA (52%), but were susceptible to MEM and FOX. The resistance to TZP, AK, FEP, CAZ, AMS, AZM, AT and IPM was significantly related to age (p < 0.05); the resistance rate of E. coli isolated from female giant pandas to N was significantly higher than in males (p < 0.05). Forty-five different types of ARGs were found, which included a total of 2,258 ARGs, in the 100 E. coli isolates. The top 10 of detection rate of ARGs were: acrA-04, acrA-05, aacC, blaCTX-M-04, ampC-04, blaSHV-01, blaTEM, sul2, blaOXY, tetA-02. ARGs aac (6')I1, blaCTX-M-03, tetD-02, blaSHV-02 and blaOXY were significantly related to age (p < 0.05), blaSHV-02, blaNDM and ampC-04 were related to sex (p < 0.05). Twelve different O serogroups from 32 E. coli isolates were distinguished, including O4, O8, O9, O15, O18, O20, O55, O88, O112, O157, O158, and O167. The most prevalent O serotype was O20, but O28, O45, O101, O149, and O152 were not detected. Fourteen different types of virulence genes were detected in the 100 E. coli isolates, of which papA (99%) were highly detected, while hlyA, elt and estA were not detected. MLST showed that 41 STs, which had one CCs and six groups with SLVs, in the 100 E. coli strains were identified, the main type was ST37. Our results advocate the need of strict biosecurity and surveillance programs in order to prevent the spread of pathogenic bacteria in the captive giant panda population.

Quantification of Total and Viable Cells and Determination of Serogroups and Antibiotic Resistance Patterns of Listeria monocytogenes in Chicken Meat from the North-Western Iberian Peninsula.

Twenty samples of minced chicken meat procured from butcher's shops in León (Spain; 10 samples) and Vila Real (Portugal; 10 samples) were analyzed. Microbial concentrations (log10 cfu/g) of 7.53 ± 1.02 (viable aerobic microbiota), 7.13 ± 1.07 (psychrotrophic microorganisms), and 4.23 ± 0.88 (enterobacteria) were found. The detection method described in the UNE-EN ISO 11290-1 standard (based on isolation from the chromogenic medium OCLA) with confirmation by the polymerase chain reaction (PCR; lmo1030) (OCLA−PCR), revealed Listeria monocytogenes in 14 samples (70.0% of the total), nine of Spanish origin and five of Portuguese (p > 0.05). The levels of viable and inactivated L. monocytogenes in the samples were determined with a q-PCR using propidium monoazide (PMAxx) as a viability marker. Seven samples tested positive both with the OCLA−PCR and with the q-PCR, with estimated concentrations of viable cells varying between 2.15 log10 cfu/g (detection limit) and 2.94 log10 cfu/g. Three samples tested negative both with the OCLA−PCR and with the q-PCR. Seven samples were positive with the OCLA−PCR, but negative with the q-PCR, and three samples tested negative with the OCLA−PCR and positive with the q-PCR. The percentage of viable cells relative to the total ranged between 2.4% and 86.0%. Seventy isolates of L. monocytogenes (five from each positive sample) were classified in PCR serogroups with a multiplex PCR assay. L. monocytogenes isolates belonged to serogroups IIa (52 isolates; 74.3%), IIc (7; 10.0%), IVa (2; 2.9%), and IVb (9; 12.9%). The susceptibility of the 70 isolates to 15 antibiotics of clinical interest was tested. The strains presented resistance to between three and eight antibiotics. The average number of resistances was greater (p < 0.001) among strains isolated from Spanish samples (6.20 ± 1.08), than in those from Portugal (5.00 ± 1.08). In both groups of strains, a prevalence of resistance higher than 95% was observed for oxacillin, cefoxitin, cefotaxime, and cefepime. The need to handle minced chicken meat correctly, taking care to cook it sufficiently and to avoid cross-contamination, so as to reduce the danger of listeriosis, is emphasized. A combination of culture-dependent and culture-independent methods offers complementary routes for the detection in food of the cells of L. monocytogenes in various different physiological states.

Frequency of Salmonella serotypes among children in Iran: antimicrobial susceptibility, biofilm formation, and virulence genes.

BACKGROUND/SIGNIFICANCE: Salmonella gastroenteritis causes significant morbidity among pediatric patients, mainly in developing world, such as the Middle East and North Africa (MENA) region. Concurrently, data from MENA countries like Iran, regarding prevalence of Salmonella serotypes, antimicrobial susceptibility, and biofilm production is scarce. MATERIAL & METHODS: Slide agglutination was used to determine the serogroup of 140 Salmonella isolates recovered from 4477 stool specimens collected from children with gastroenteritis, and isolates were serotyped by PCR assay. The antimicrobial susceptibility of isolates to five first line drugs was assessed by disk diffusion assay using CLSI guidelines. Semi-quantitative evaluation of biofilm production was done by microtiter plate assay followed by PCR detection of biofilm-associated virulence genes csgD, pefA, and bcsA for each isolate. RESULTS: Nearly 94% of Salmonella isolates were recovered from ≤ 5-year-old patients, and 99% of isolates were non-typhoidal. While we found extensive diversity among Salmonella isolates, serogroup D (46%) predominated, and Salmonella Enteritidis (41%) was the most common serotype that showed the highest antimicrobial susceptibility rate (> 96%). For the first time in Iran, S. Newport serotype from human specimens was isolated. Most isolates were sensitive to all test antimicrobials, but 35% of isolates were not-typed (NT) that showed the highest resistance with 48% being resistant to ≥ 1 test antimicrobial. Majority of isolates made weak (or no) biofilm, and we found a weak association between antimicrobial susceptibility, biofilm production, or virulence genes csgD, pefA, and bcsA. CONCLUSIONS: The most effective measure that may control pediatric salmonellosis outbreaks is raising awareness of parents of preschoolers about food safety. Isolation of highly diverse Salmonella serotypes, including many commonly isolated from animals, indicates widespread contamination of the food chain. Majority of serotypes were sensitive to first-line antimicrobials, thus presently, pediatric Salmonella infections in this region may be controlled by conventional antimicrobials. However, despite the current trend, an imminent emergence of resistant Salmonella strains is foreseen, since various serotypes resistant to > 1 antimicrobial agent are typically associated with animals. Our results warrant further investigation that includes correlation analysis of clinical data regarding treatment outcomes, and serotype attributes like virulence genes.

Shiga Toxin Subtypes, Serogroups, Phylogroups, RAPD Genotypic Diversity, and Select Virulence Markers of Shiga-Toxigenic Escherichia coli Strains from Goats in Mid-Atlantic US.

Understanding Shiga toxin subtypes in E. coli from reservoir hosts may give insight into their significance as human pathogens. The data also serve as an epidemiological tool for source tracking. We characterized Shiga toxin subtypes in 491 goat E. coli isolates (STEC) from the mid-Atlantic US region (stx1 = 278, stx2 = 213, and stx1/stx2 = 95). Their serogroups, phylogroups, M13RAPD genotypes, eae (intimin), and hly (hemolysin) genes were also evaluated. STEC-positive for stx1 harbored Stx1c (79%), stx1a (21%), and stx a/c (4%). Those positive for Stx2 harbored stx2a (55%) and Stx2b (32%), while stx2a/stx2d and stx2a/stx2b were each 2%. Among the 343 STEC that were serogrouped, 46% (n = 158) belonged to O8, 20% (n = 67) to 076, 12% (n = 42) to O91, 5% (n = 17) to O5, and 5% (n = 18) to O26. Less than 5% belonged to O78, O87, O146, and O103. The hly and eae genes were detected in 48% and 14% of STEC, respectively. Most belonged to phylogroup B1 (73%), followed by D (10%), E (8%), A (4%), B2 (4%), and F (1%). M13RAPD genotyping revealed clonality of 091, O5, O87, O103, and O78 but higher diversity in the O8, O76, and O26 serogroups. These results indicate goat STEC belonged to important non-O157 STEC serogroups, were genomically diverse, and harbored Shiga toxin subtypes associated with severe human disease.

Molecular characterization and phylogeny of Shiga toxin-producing Escherichia coli derived from cattle farm.

Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen, which can cause diseases such as diarrhea, hemorrhagic enteritis, and hemolytic uremic syndrome in humans. Twelve STEC isolates were collected from beeves and feces of commercial animals in China between 2019 and 2020 for this study. In addition to the determination of serotype and Shiga toxin subtype, whole-genome sequencing (WGS) was used for determining phylogenetic relationships, antimicrobial resistance (AMR), virulence genes, and sequence type (ST) of isolates. A total of 27 AMR genes were detected, and each STEC isolate carried more than 10 AMR genes. Eight STEC isolates from ground beef and four STEC isolated from feces were screened. A total of seven serotypes were identified, and one isolate ONT:H10 was undetermined by SeroTypeFinder. Three O157:H7 strains were confirmed and the remaining five serogroups were confirmed as O26:H11, O81:H31, O105:H8, O178:H19, and O136:H12. The phylogenetic analysis showed that STEC isolates of the same serotype or ST were clustered together based on cgMLST. The comparison of the genomes of 157 STEC reference isolates worldwide with our local STEC isolates showed that STEC isolates screened in China represented various collections and could not form a separate cluster but were interspersed among the STEC reference collection, which suggested that several STEC isolates shared a common ancestor irrespective of STEC serotype isolates. cgMLST revealed that isolates of the same O serotype clustered irrespective of their H type. Further investigation is required to determine the pathogenic potential of other serotypes of STEC, particularly in regard to these rare serotypes.

Prevalence of Neisseria meningitidis serogroups in invasive meningococcal disease in China, 2010 - 2020: a systematic review and meta-analysis.

Invasive meningococcal disease (IMD) caused by Neisseria meningitidis (Nm) continues to be a global public health concern. Understanding the prevalence of Nm serogroups in IMD is critical for developing strategies for meningococcal vaccination. We used the keywords "cerebrospinal meningitis", "meningococcal", "Neisseria meningitidis'', "meningococcal meningitis", "serogroup'' and "China'' to search five databases, including PubMed, CNKI, CBM (Chinese BioMedical Literature Database), WanFang and VIP from 2010 to 2020. The age distributions, proportions of Nm serogroups and serogroup changes in IMD were analyzed. A total of 14 studies were included according to PRISMA guidelines. In China, from 2010 to 2020, the highest proportion of Nm in IMD was NmC, with 49.7% (95% CI: 35.8%-63.5%), followed by NmB with 30.2% (95%CI:17.3%-43.0%) and NmW with 23.8% (95%CI: 7.0-40.7%). Before 2014, NmC was the major circulating serogroup, with 59.6% (95% CI: 43.8%-75.4%), followed by NmW with 24.4% (95% CI: 5.9%-42.9%). After 2015, IMD cases caused by NmB were increasing, the proportion of NmB reached to 52.4% (95% CI: 31.8%-73.1%). The age groups of children from 0 to 5 years and from 6 to 10 years represented, respectively, 29.6% (95% CI: 16.8%-42.4%) and 28.9% (95% CI: 12.1%-45.8%) of all IMD cases were reported. In China, NmB, NmC and NmW were the major serogroups causing IMD between 2010 and 2020. Since 2015, the proportion of NmB increased rapidly. The current serogroup distribution in China highlights the need of replacing the meningococcal polysaccharide vaccines that are being used in the National Immunization Program with more appropriate vaccines.

Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification.

Legionella spp. are Gram-negative bacteria that inhabit freshwater environments representing a serious risk for human health. Legionella pneumophila (Lp) is the species most frequently responsible for a severe pneumonia known as Legionnaires' disease. Lp consists of 15 serogroups (Sgs), usually identified by monoclonal or polyclonal antibodies. With regard to Lp serogrouping, it is well known that phenotyping methods do not have a sufficiently high discriminating power, while genotypic methods although very effective, are expensive and laborious. Recently, mass spectrometry and infrared spectroscopy have proved to be rapid and successful approaches for the microbial identification and typing. Different biomolecules (e.g., lipopolysaccharides) adsorb infrared radiation originating from a specific microbial fingerprint. The development of a classification system based on the intra-species identification features allows a rapid and reliable typing of strains for diagnostic and epidemiological purposes. The aim of the study was the evaluation of Fourier Transform Infrared Spectroscopy using the IR Biotyper® system (Bruker Daltonik, Germany) for the identification of Lp at the serogroup (Sg) level for diagnostic purposes as well as in outbreak events. A large dataset of Lp isolates (n = 133) and ATCC reference strains representing the 15 Lp serogroups were included. The discriminatory power of the instrument's classifier, was tested by Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). All isolates were classified as follows: 12/133 (9.0%) as Lp Sg1 and 115/133 (86.5%) as Lp Sg 2-15 (including both ATCC and environmental Lp serogroup). Moreover, a mis-classification for 2/133 (1.5%) isolates of Lp Sg 2-15 that returned as Lp Sg1 was observed, and 4/133 (3.0%) isolates were not classified. An accuracy of 95.49% and an error rate of 4.51% were calculated. IR Biotyper® is able provide a quick and cost-effective reliable Lp classification with advantages compared with agglutination tests that show ambiguous and unspecific results. Further studies including a larger number of isolates could be useful to implement the classifier obtaining a robust and reliable tool for the routine Lp serogrouping. IR Biotyper® could be a powerful and easy-to-use tool to identify Lp Sgs, especially during cluster/outbreak investigations, to trace the source of the infection and promptly adopt preventive and control strategies.

Escherichia coli serogroups in slaughterhouses: Antibiotic susceptibility and molecular typing of isolates.

This study aimed to investigate the contamination of carcasses and slaughterhouse environment with Escherichia coli O157:H7 and non-O157 serogroups (O45:H2, O103:H2, O121:H19, O145:H28, O26:H11, O111:H8). For this purpose, a total of 150 samples (30 carcasses, 30 shredding units, 30 knives, 30 slaughterhouse waste water and 30 wall surfaces) were collected from 5 different slaughterhouses in Kayseri, Turkey. The conventional and molecular methods were performed in order to detect Escherichia coli and its serogroups. Of the 150 samples, 55 (36%) were found to be contaminated with E. coli. Among isolates, E. coli serogroup (O157:H7) were detected in 2 (11%) carcass and 2 (11%) wastewater samples. None of the E. coli isolates harbored tested genes (stx1, stx2, eaeA, and hylA). Effective infection control measures and antibiotic stewardship programs should be adopted to limit the spread of multidrug-resistant bacteria. It was also deduced that these isolates resistance to different antibiotics could be hazardous for public health.

Serological Diversity of Dichelobacter nodosus in German Sheep Flocks.

Footrot is one of the major causes of lameness in sheep and leads to decreased animal welfare and high economic losses. The causative agent is the Gram-negative anaerobic bacterium Dichelobacter nodosus. The prevalence of D. nodosus in 207 sheep flocks across Germany was 42.9%. Based on the sequence variation in the type IV fimbrial gene fimA, D. nodosus can be subdivided into ten serogroups (A-I and M). There are commercially available vaccines covering nine serogroups, but the efficacy is low compared to bivalent vaccines. The aim of this study was to investigate the diversity of serogroups in Germany at the flock and animal levels. In total, we detected at least one serogroup in 819 samples out of 969 D. nodosus-positive samples from 83 flocks using serogroup-specific singleplex PCR for the serogroups A-I. Serogroup A was most prevalent at the animal level, followed by serogroups B, H and C. At the flock level, serogroups A and B had the highest prevalence, each with 64%, but only 40% of flocks had both. The average number of serogroups per animal was 1.42 (range one to five) and, per flock, 3.10 (range one to six). The serogrouping showed within-flock specific clusters but were widely distributed, with 50 different combinations across the flocks. The factors associated with the number of serogroups per animal and single serogroups were the load of D. nodosus, footrot score, sheep breed and flock. Our results indicate that efficient vaccination programs would benefit from tailor-made flock-specific vaccines and regular monitoring of circulating serotypes in the flock to be able to adjust vaccine formulations for nationwide progressive control of footrot in Germany.