Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp.

BACKGROUND: Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant Campylobacter spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide. METHODS: We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant Campylobacter poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids. RESULTS: Overall, 22 different resistance genes and gene variants (e. g. erm(B), aph(3')-IIIa, aph(2'')-If, catA, lnu(C), blaOXA, sat4) and point mutations in three distinct genes (gyrA, 23S rRNA, rpsL) associated with AMR were present in the Campylobacter isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify tet(O) and aadE, when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel tet(W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable aad9, due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in Campylobacter. CONCLUSIONS: The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in Campylobacter strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant Campylobacter spp. that may pose a challenge to global food safety.

Prospective One Health genetic surveillance in Vietnam identifies distinct blaCTX-M-harbouring Escherichia coli in food-chain and human-derived samples.

OBJECTIVES: We performed a One Health surveillance in Hanoi-a region with a high-density human population and livestock production, and a recognized hotspot of animal-associated antimicrobial resistance (AMR)-to study the contribution of blaCTX-M-carrying Escherichia coli and plasmids from food-animal sources in causing human community-acquired urinary tract infections (CA-UTIs). METHODS: During 2014-2015, 9090 samples were collected from CA-UTI patients (urine, n = 8564), pigs/chickens from farms and slaughterhouses (faeces, carcasses, n = 448), and from the slaughterhouse environment (surface swabs, water, n = 78). E. coli was identified in 2084 samples. Extended-spectrum ß-lactamase (ESBL) production was confirmed in 235 and blaCTX-M in 198 strains by PCR with short-read plasmid sequencing. Fourteen strains were long-read sequenced to enable plasmid reconstruction. RESULTS: The majority of the ESBL-producing E. coli strains harboured blaCTX-M (n = 198/235, 84%). High clonal diversity (48 sequence types, STs) and distinct, dominant STs in human sources (ST1193, n = 38/137; ST131, n = 30/137) and non-human sources (ST155, n = 25/61) indicated lack of clonal transmission between habitats. Eight blaCTX-M variants were identified; five were present in at least two sample sources. Human and food-animal strains did not show similar plasmids carrying shared blaCTX-M genes. However, IS6 elements flanking ISEcp1-blaCTX-M-orf477/IS903B structures were common across habitats. CONCLUSIONS: In this study, animal-associated blaCTX-ME. coli strains or blaCTX-M plasmids were not direct sources of CA-UTIs or ESBL resistance in humans, respectively, suggesting evolutionary bottlenecks to their adaptation to a new host species. Presence of common IS6 elements flanking blaCTX-M variants in different plasmid backbones, however, highlighted the potential of these transposable elements for AMR transmission either within or across habitats.

Elucidating the difference in the kinetics of antibody titres of infants in Belgium and Vietnam.

Serological results obtained in a single laboratory from twin-studies on maternal immunisation, in Vietnam and Belgium offer the opportunity to compare antibody kinetics in infants before and after infant vaccination in the presence of vaccine-induced maternal antibodies. Nonlinear mixed-effects models (NLMMs) making use of a hypothesised dynamic evolution that captures the change in antibody titres over time, were employed to model anti-PT and anti-Prn antibody dynamics. Our proposed modelling approach provided useful insight into understanding the differences in the infants' antibody kinetics in both countries since NLMMs offer the possibility of pooling all data in one analysis and incorporate relevant covariates of interest. In both controlled cohort studies, pregnant women were vaccinated with a tetanus, diphtheria, acellular pertussis (Tdap) vaccine (Boostrix®, Belgium; Adacel®, Vietnam), and children were followed before and after primary vaccination, and before and after booster vaccination (Infanrix hexa®). From our models, both anti-PRN and anti-PT antibody titres at birth of Vietnamese infants were significantly lower than those of Belgian infants born to vaccinated women groups. Even though the antibody titres in the cord at birth of Belgian infants were also higher than those of Vietnamese infants born to the control women groups, the difference was not significant. The significant difference between infants born to vaccinated women in the two countries was likely due to the use of different vaccine brands in pregnant women and the different vaccination histories of women in these two countries. Our analyses also suggested that the blunting effect was present during the primary immunisation but went away afterward for anti-PT data. In contrast, for anti-PRN antibodies, the blunting effect persisted after the primary vaccination and possibly went away after the booster dose. Countries should be aware of the regional situation in view of recommending maternal immunization.

Macrolide-Resistant Bordetella pertussis, Vietnam, 2016-2017.

Macrolide-resistant Bordetella pertussis emerged in Vietnam during 2016-2017. Direct analyses of swab samples from 10 patients with pertussis revealed a macrolide-resistant mutation, A2047G, in the 23S rRNA. We identified the MT104 genotype of macrolide-resistant B. pertussis (which is prevalent in mainland China) and its variants in these patients.

Child Overweight or Obesity Is Associated with Modifiable and Geographic Factors in Vietnam: Implications for Program Design and Targeting.

Child overweight or obesity is increasing in most countries, including Vietnam. We sought to elucidate the drivers of child overweight or obesity in Vietnam and understand how they vary geographically. We compiled nationally representative cross-sectional data from the Vietnam Nutrition Surveillance Survey collected annually between 2012-2015 and household income data from the General Statistics Office. We used a quasi-Poisson log link function to calculate relative risks (RRs) of under-five child overweight or obesity for 13 variables and stratified analyses by child age (<2 y and 2-5 y) and region. Additional analysis included log-log linear regression to assess the relationship between average provincial monthly per capita income and child overweight or obesity. The strongest associations with child overweight or obesity included birthweight >4000 g (RR: 1.66; 95% confidence interval (CI): 1.48, 1.86), maternal body mass index (BMI) ≥27.5 compared with BMI <23 (RR: 1.62; 95% CI: 1.47, 1.78), and living in the Southeast (RR: 2.06; 95% CI: 1.84, 2.30), Mekong River Delta (RR: 1.58; 95% CI: 1.41, 1.77), or Central South (RR: 1.54; 95% CI: 1.37, 1.74) compared with the Central Highland. A 20% higher provincial average monthly per capita income was associated with a 17.4% higher prevalence in child overweight or obesity (P < 0.0001, Adjusted R2 = 0.36). High birthweight and maternal BMI were strongly associated with child overweight or obesity but are not likely primary drivers in Vietnam, given their low prevalence. C-section delivery, sedentary lifestyle, high maternal education, urbanicity, and high household income affect a large proportion of the population and are, therefore, important risk factors. Policies and programs should target these factors and regions at greatest risk of overweight or obesity, particularly the Southeast and Mekong River Delta.

Molecular epidemiology of Leptospira interrogans in Rattus norvegicus in Hanoi, Vietnam.

Leptospirosis is a zoonotic disease that is caused by pathogenic spirochaetes of Leptospira spp. and it has become a public health concern in urban localities in the tropics. Rats are important reservoir animals for the transmission of leptospirosis in urban areas. Leptospirosis is considered endemic in Vietnam. However, information on the causative Leptospira genotypes and serotypes in the country is limited. We investigated the carrier status of Leptospira spp. in rats captured in Hanoi by culturing and DNA detection. Isolates were characterized using a serological method and multiple-locus variable-number tandem repeat analysis (MLVA). We captured 144 rats (1 Rattus argentiventer, 135 R. norvegicus, and 8 R. rattus) and obtained 17 L. interrogans, determined by rrs sequencing, from R. norvegicus (12.6%). Sixteen of the isolates were serogroup Bataviae. Five of the 16 isolates exhibited an MLVA type identical to that of the serovar Bataviae reference strain Van Tienen, while there were nine repeats for the other 11 isolates at VNTR31 compared with the reference strain. The remaining isolate grew poorly, and we were unable to determine its serogroup. However, it had an MLVA type matching those of serogroup Pomona strains isolated from R. norvegicus in Japan. Three different flaB sequences were detected in 23 out of 81 R. norvegicus kidney tissue samples (28.4%) using nested PCR followed by DNA sequencing. Two of the sequences were identical with those of serogroups Bataviae and Pomona, and no strain with another sequence was detected in the present study. The present study reveals a high prevalence rate of L. interrogans among R. norvegicus in Hanoi, Vietnam, indicating a potential risk of rat-borne leptospirosis in the area. The present study also demonstrates that a fastidious L. interrogans strain circulates among rats and that molecular detection is crucial in facilitating the accurate determination of reservoir animals.

Pertussis vaccination during pregnancy in Vietnam: Results of a randomized controlled trial Pertussis vaccination during pregnancy.

A pertussis vaccination during pregnancy has recently been adopted in several countries to indirectly protect young infants. This study assessed the effect of adding a pertussis component to the tetanus vaccination, in the pregnancy immunization program in Vietnam. A randomized controlled trial was performed. Pregnant women received either a Tdap (tetanus, diphtheria acellular pertussis) vaccine or a tetanus only vaccine between 19 and 35 weeks' gestational age. Immunoglobulin G (IgG) against tetanus (TT), diphtheria (DT), pertussis toxin (PT), filamentous hemaglutinin (FHA) and pertactin (Prn) were measured using commercial ELISA tests, at baseline, 1 month after maternal vaccination, at delivery, and in infants from cord blood and before and after the primary series (EPI: month 2-3-4) of a pertussis containing vaccine. Significantly higher geometric mean concentrations (GMC) were observed for all 3 measured pertussis antigens in the offspring of the Tdap group, up to 2 months of age. One month after completion of the primary infant vaccination schedule, anti-Prn GMC, but not anti-PT and anti-FHA GMCs, was significantly (p=0.006) higher in the control group. Maternal antibodies induced by vaccination during pregnancy close the susceptibility gap for pertussis in young infants. Limited interference with the infant vaccine responses was observed. Whether this interference effect disappears with the administration of a fourth vaccine dose is further studied.