Prevalence and genetic properties of Salmonella enterica serovar typhimurium definitive phage type 104 isolated from Rattus norvegicus and Rattus rattus house rats in Yokohama City, Japan

Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo

BACKGROUND

Invasive non-typhoidal Salmonella (iNTS-mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans.

METHODOLOGY/PRINCIPAL FINDINGS

From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans-obtained from blood cultures at Kisangani University Hospital-was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible.

CONCLUSION

The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa.

Emergence of Salmonella enterica subsp. enterica serovar Chester in a rural area of Japan

In Japan, only one outbreak of Salmonella enterica subsp. enterica serovar Chester (S. Chester) has been confirmed in 1999. We performed a single-center retrospective case review of S. Chester infections that occurred in a rural area of Japan in 2016 (n=8). Case 5 and 6 occurred in twin infants who had contact with a pet dog. The dog's stool culture was positive for S. Chester. Pulsed-field gel electrophoresis and cluster analysis of S. Chester strains revealed that all the isolates appeared to be derived from the same genetic clone. Emergence of Salmonella infection can be overlooked if cases are not reported to health authorities; therefore, core hospitals should play a role to alert the occurrence of public health issue.

Genetic characteristics of emerging Salmonella enterica serovar Agona strains isolated from humans in the prior period to occurrence of the serovar shift in broilers

Our previous studies found that a dominant serovar of Salmonella enterica isolates from three farms raising broilers in 2014 and 2015 was serovar Agona and the number of Infantis isolates decreased (the serovar shift). In this study, 52 S. Agona strains which isolated between 1993 and 2008, were compared to the serovar shift clone by molecular epidemiology and phylogenetic analyses, using pulsed field gel electrophoresis and whole genome sequence analyses. Of the 52 strains, one strain isolated from a human case in 1995 was genetically identical to the serovar shift clone, even though it was isolated prior to the serovar shift. These results suggested that the S. Agona serovar shift clone had existed in a source other than chicken penetrated chicken population.

Antimicrobial Resistance of Salmonella spp. Isolates and Heavy Metal Traces from Rodent Meat Purchased from Roadside Markets, Central Thailand

Although game meat consumption is widespread across the globe, involving a great diversity of species in very different ecological and sociocultural environments, the safety of wild meat products is rarely assessed routinely. We conducted a survey to evaluate the safety of two rodents products (Rattus tanezumi and Bandicota indica) purchased from roadside markets in central Thailand. Total aerobic bacteria and Escherichia coli counts measured were above Thai poultry product standards for 83.3% and 100% of the samples, respectively (n = 108), although there was no difference between rat species (analysis of variance [ANOVA], p > 0.05). Salmonella spp. were isolated from 32% of the swabs collected (67/208), including 19 different serovars. All strains were resistant or partially resistant to at least 2 of the 16 antibiotics tested, with levels of resistance varying greatly among antibiotics (e.g., 97% of strains sensitive to ciprofloxacin and 98.5% of strains resistant to cloxacillin). Detectable traces of Cd and Pb were found in 98% and 46% of the samples analyzed, respectively (n = 61). Pb and Cd concentrations measured in the kidneys of R. tanezumi were significantly higher than in the liver and muscles and significantly higher than B. indica muscles and kidneys but not liver (ANOVA, p < 0.05). These results highlight potential health hazards that may be associated with rodent-meat consumption, including contamination by coliform bacteria, multiresistant Salmonella spp. strains, and heavy metals. The significance of these results for public health cannot be determined precisely in the absence of appropriate standards, and information gaps remain regarding the frequency of rodent-meat consumption and the origin of bacterial and heavy metal contaminations (i.e., capture environment or during carcass handling and processing). We suggest that appropriate information and training on best hygienic practices for preparing, cooking, and preserving rodent meat should be provided to the producers and to the consumers.

Isolation of Salmonella enterica serovar Agona strains and their similarities to strains derived from a clone caused a serovar shift in broilers

Salmonella enterica serovar Agona strains isolated from human cases were compared to strains that were derived from a clone caused a serovar shift in broilers. Pulsed field gel electrophoresis (PFGE) analysis with XbaI or BlnI digestion showed that three of seven strains from human case strains and most of the 81 strains from broilers were clustered in single complex in a minimum spanning tree (MST) reconstructed from the PFGE data. All the strains from human cases and 22 randomly selected strains from broilers were also analyzed by whole genome sequencing (WGS). Analysis of single nucleotide polymorphism (SNP) in the S. Agona core genes showed that four strains from human cases and all the strains from broilers were clustered in a maximum likelihood phylogenetic tree (ML tree) and an MST. These results indicated that the strains derived from the clone caused the serovar shift had already spread to humans. PFGE analysis with XbaI showed that four strains from broilers did not cluster with the other strains in an MST, though all those strains clustered in an ML tree and an MST reconstructed from SNP data. Moreover, three strains from broilers did not cluster in an MST reconstructed from PFGE with BlnI digestion, though those strains clustered in an ML tree and an MST reconstructed from SNP data. Therefore, it was suggested that S. Agona strains derived from a particular clone could not be traced by PFGE analysis but can be investigated by WGS analysis.

Environmental Factors Associated with the Carriage of Bacterial Pathogens in Norway Rats

Worldwide, Norway rats (Rattus norvegicus) carry a number of zoonotic pathogens. Many studies have identified rat-level risk factors for pathogen carriage. The objective of this study was to examine associations between abundance, microenvironmental and weather features and Clostridium difficile, antimicrobial-resistant (AMR) Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA) carriage in urban rats. We assessed city blocks for rat abundance and 48 microenvironmental variables during a trap-removal study, then constructed 32 time-lagged temperature and precipitation variables and fitted multivariable logistic regression models. The odds of C. difficile positivity were significantly lower when mean maximum temperatures were high (≥ 12.89°C) approximately 3 months before rat capture. Alley pavement condition was significantly associated with AMR E. coli. Rats captured when precipitation was low (< 49.40 mm) in the 15 days before capture and those from blocks that contained food gardens and institutions had increased odds of testing positive for MRSA. Different factors were associated with each pathogen, which may reflect varying pathogen ecology including exposure and environmental survival. This study adds to the understanding of how the microenvironment and weather impacts the epidemiology and ecology of zoonotic pathogens in urban ecosystems, which may be useful for surveillance and control activities.

Environmental Factors and Zoonotic Pathogen Ecology in Urban Exploiter Species

Knowledge of pathogen ecology, including the impacts of environmental factors on pathogen and host dynamics, is essential for determining the risk that zoonotic pathogens pose to people. This review synthesizes the scientific literature on environmental factors that influence the ecology and epidemiology of zoonotic microparasites (bacteria, viruses and protozoa) in globally invasive urban exploiter wildlife species (i.e., rock doves [Columba livia domestica], European starlings [Sturnus vulgaris], house sparrows [Passer domesticus], Norway rats [Rattus norvegicus], black rats [R. rattus] and house mice [Mus musculus]). Pathogen ecology, including prevalence and pathogen characteristics, is influenced by geographical location, habitat, season and weather. The prevalence of zoonotic pathogens in mice and rats varies markedly over short geographical distances, but tends to be highest in ports, disadvantaged (e.g., low income) and residential areas. Future research should use epidemiological approaches, including random sampling and robust statistical analyses, to evaluate a range of biotic and abiotic environmental factors at spatial scales suitable for host home range sizes. Moving beyond descriptive studies to uncover the causal factors contributing to uneven pathogen distribution among wildlife hosts in urban environments may lead to targeted surveillance and intervention strategies. Application of this knowledge to urban maintenance and planning may reduce the potential impacts of urban wildlife-associated zoonotic diseases on people.

Animal-related factors associated with moderate-to-severe diarrhea in children younger than five years in western Kenya: A matched case-control study

BACKGROUND

Diarrheal disease remains among the leading causes of global mortality in children younger than 5 years. Exposure to domestic animals may be a risk factor for diarrheal disease. The objectives of this study were to identify animal-related exposures associated with cases of moderate-to-severe diarrhea (MSD) in children in rural western Kenya, and to identify the major zoonotic enteric pathogens present in domestic animals residing in the homesteads of case and control children.

METHODOLOGY/PRINCIPAL FINDINGS

We characterized animal-related exposures in a subset of case and control children (n = 73 pairs matched on age, sex and location) with reported animal presence at home enrolled in the Global Enteric Multicenter Study in western Kenya, and analysed these for an association with MSD. We identified potentially zoonotic enteric pathogens in pooled fecal specimens collected from domestic animals resident at children's homesteads. Variables that were associated with decreased risk of MSD were washing hands after animal contact (matched odds ratio [MOR] = 0.2; 95% CI 0.08-0.7), and presence of adult sheep that were not confined in a pen overnight (MOR = 0.1; 0.02-0.5). Variables that were associated with increased risk of MSD were increasing number of sheep owned (MOR = 1.2; 1.0-1.5), frequent observation of fresh rodent excreta (feces/urine) outside the house (MOR = 7.5; 1.5-37.2), and participation of the child in providing water to chickens (MOR = 3.8; 1.2-12.2). Of 691 pooled specimens collected from 2,174 domestic animals, 159 pools (23%) tested positive for one or more potentially zoonotic enteric pathogens (Campylobacter jejuni, C. coli, non-typhoidal Salmonella, diarrheagenic E. coli, Giardia, Cryptosporidium, or rotavirus). We did not find any association between the presence of particular pathogens in household animals, and MSD in children.

CONCLUSIONS AND SIGNIFICANCE

Public health agencies should continue to promote frequent hand washing, including after animal contact, to reduce the risk of MSD. Future studies should address specific causal relations of MSD with sheep and chicken husbandry practices, and with the presence of rodents.

Rodents as a Source of Salmonella Contamination in Wet Markets in Thailand

BACKGROUND

Few studies have been conducted on the presence of Salmonella in the rodents that inhabit the wet markets that play an important role in daily life in Southeast Asia. The results of studies of rodents as carriers of Salmonella vary greatly, ranging from an absence of Salmonella to high prevalences. Previous studies investigated habitats such as farms and urban and wild areas where there is less rodent-human interaction than in wet markets. Consequently, the potential role of rodents as reservoirs and transmitters of Salmonella in wet markets is of great interest.

METHODS

Rodents were trapped in eight traditional wet markets in Thailand and identified to species level. Subsequently, they were screened for Salmonella and isolates were serotyped.

RESULTS

A total of 110 rats (Rattus norvegicus and Rattus exulans) were examined. Overall, the prevalence of Salmonella in rats was 49.10%, but varied between 0% and 73.3% among markets. Three serovars were identified: Salmonella Typhimurium (30%), S. Weltevreden (12.7%), and S. 4,[5],12:i:- (6.4%).

CONCLUSIONS

Our results show that rodents in wet markets are a potential reservoir of Salmonella due to the close contact they have with humans and food. The three isolated serovars, of which serovar S. 4,[5],12:i:- is reported for the first time in rodents, are among the 10 commonest serovars isolated from humans in Thailand. Thus, more attention should be paid to rodents as potential reservoirs of Salmonella.

Aboriginal and invasive rats of genus Rattus as hosts of infectious agents

From the perspective of ecology of zoonotic pathogens, the role of the Old World rats of the genus Rattus is exceptional. The review analyzes specific characteristics of rats that contribute to their important role in hosting pathogens, such as host-pathogen relations and rates of rat-borne infections, taxonomy, ecology, and essential factors. Specifically the review addresses recent taxonomic revisions within the genus Rattus that resulted from applications of new genetic tools in understanding relationships between the Old World rats and the infectious agents that they carry. Among the numerous species within the genus Rattus, only three species-the Norway rat (R. norvegicus), the black or roof rat (R. rattus), and the Asian black rat (R. tanezumi)-have colonized urban ecosystems globally for a historically long period of time. The fourth invasive species, R. exulans, is limited to tropical Asia-Pacific areas. One of the points highlighted in this review is the necessity to discriminate the roles played by rats as pathogen reservoirs within the land of their original diversification and in regions where only one or few rat species were introduced during the recent human history.

PREVALENCE AND CHARACTERISTICS OF ESCHERICHIA COLI AND SALMONELLA SPP. IN THE FECES OF WILD URBAN NORWAY AND BLACK RATS (RATTUS NORVEGICUS AND RATTUS RATTUS) FROM AN INNER-CITY NEIGHBORHOOD OF VANCOUVER, CANADA

Although rat feces are widely suspected to be a source of pathogenic bacteria, few investigators have studied fecal pathogens in rats. We investigated the prevalence and characteristics of Escherichia coli and Salmonella spp. in Norway and black rats (Rattus norvegicus and Rattus rattus, respectively) from an urban neighborhood of Vancouver, Canada, collected September 2011-August 2012. Colon content was cultured for E. coli and Salmonella spp. and screened for the seven most-common enteropathogenic Shiga toxin-producing E. coli (STEC) serotypes by PCR. Isolates were tested for antimicrobial resistance and Salmonella isolates were serotyped. We detected E. coli in 397/633 (62.7%) urban rats. Forty-one of 397 (6.5%) E. coli isolates were resistant to ≥ 1 antimicrobial while 17 (4.3%) were multidrug resistant (including two isolates demonstrating extended-spectrum β-lactamase resistance). Ten of 633 (1.6%) urban rats were carrying STEC serotypes including O145, O103, O26, and O45. Norway rats were more likely to be carrying E. coli compared to black rats, and there was geographic clustering of specific resistance patterns and STEC serotypes. Salmonella spp. were detected in 3/633 (0.5%) rats including serotypes Derby, Indiana, and Enteritidis. In contrast to zoonotic pathogens for which rats are the natural reservoir (e.g., Leptospira interrogans, Rickettsia typhi, Seoul virus), rats likely acquired E. coli and Salmonella spp. from their environment. The ability of rats to be a 'sponge' for environmental pathogens has received little consideration, and the ecology and public health significance of these organisms in rats requires further investigation.

Rat sightings in New York City are associated with neighborhood sociodemographics, housing characteristics, and proximity to open public space

Rats are ubiquitous in urban environments and, as established reservoirs for infectious pathogens, present a control priority for public health agencies. New York City (NYC) harbors one of the largest rat populations in the United States, but surprising little study has been undertaken to define rat ecology across varied features of this urban landscape. More importantly, factors that may contribute to increased encounters between rats and humans have rarely been explored. Using city-wide records of rat sightings reported to the NYC Department of Health and Mental Hygiene, this investigation sought to identify sociodemographic, housing, and physical landscape characteristics that are associated with increased rat sightings across NYC census tracts. A hierarchical Bayesian conditional autoregressive Poisson model was used to assess these associations while accounting for spatial heterogeneity in the variance. Closer proximity to both subway lines and recreational public spaces was associated with a higher concentration of rat sightings, as was a greater presence of older housing, vacant housing units, and low education among the population. Moreover, these aspects of the physical and social landscape accurately predicted rat sightings across the city. These findings have identified specific features of the NYC urban environment that may help to provide direct control targets for reducing human–rat encounters.

Prevalence of zoonotic Bartonella species among rodents and shrews in Thailand

We investigated the prevalence of Bartonella species in 10 rodent and one shrew species in Thailand. From February 2008 to May 2010, a total of 375 small animals were captured in 9 provinces in Thailand. Bartonella strains were isolated from 57 rodents (54 from Rattus species and 3 from Bandicota indica) and one shrew (Suncus murinus) in 7 of the 9 provinces, and identified to the species level. Sequence analysis of the citrate synthase and RNA polymerase β subunit genes identified the 58 isolates from each Bartonella-positive animal as B. tribocorum in 27 (46.6%) animals, B. rattimassiliensis in 17 (29.3%) animals, B. elizabethae in 10 (17.2%) animals and B. queenslandensis in 4 (6.9%) animals. R. norvegicus, R. rattus, and Suncus murinus carried B. elizabethae, which causes endocarditis in humans. The prevalence of Bartonella bacteremic animals by province was 42.9% of the animals collected in Phang Nga, 26.8% in Chiang Rai, 20.4% in Sa Kaeo, 16.7% in Nakhon Si Thammarat, 12.0% in Surat Thani, 9.1% in Mae Hong Son and Loei Provinces. These results indicate that Bartonella organisms are widely distributed in small mammals in Thailand and some animal species may serve as important reservoirs of zoonotic Bartonella species in the country.

Genomic comparison of Salmonella typhimurium DT104 with non-DT104 strains

DT104 emerged as a new branch of Salmonella typhimurium with resistance to multiple antimicrobials. To reveal some general genomic features of DT104 for clues of evolutionary events possibly associated with the emergence of this relatively new type of this pathogen, we mapped 11 independent DT104 strains and compared them with non-DT104 S. typhimurium strains. We found that all 11 DT104 strains contained three insertions absent in non-DT104 strains, i.e., the previously reported ST104, ST104B and ST64B. However, SGI-1, a genomic island known to be responsible for DT104 multidrug resistance, was not present in all DT104 strains examined in this study: one DT104 strain did not contain SGI-1 but carried a 144 kb plasmid, suggesting possible evolutionary relationships between the two DNA elements in the development of antimicrobial resistance.

Animal contact as a source of human non-typhoidal salmonellosis

Non-typhoidal Salmonella represents an important human and animal pathogen world-wide. Most human salmonellosis cases are foodborne, but each year infections are also acquired through direct or indirect animal contact in homes, veterinary clinics, zoological gardens, farm environments or other public, professional or private settings. Clinically affected animals may exhibit a higher prevalence of shedding than apparently healthy animals, but both can shed Salmonella over long periods of time. In addition, environmental contamination and indirect transmission through contaminated food and water may complicate control efforts. The public health risk varies by animal species, age group, husbandry practice and health status, and certain human subpopulations are at a heightened risk of infection due to biological or behavioral risk factors. Some serotypes such as Salmonella Dublin are adapted to individual host species, while others, for instance Salmonella Typhimurium, readily infect a broad range of host species, but the potential implications for human health are currently unclear. Basic hygiene practices and the implementation of scientifically based management strategies can efficiently mitigate the risks associated with animal contacts. However, the general public is frequently unaware of the specific disease risks involved, and high-risk behaviors are common. Here we describe the epidemiology and serotype distribution of Salmonella in a variety of host species. In addition, we review our current understanding of the public health risks associated with different types of contacts between humans and animals in public, professional or private settings, and, where appropriate, discuss potential risk mitigation strategies.

The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium

Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.

Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.