Clinical features of patients with novel Yersinia species

Insights into the genomic traits of Yersinia frederiksenii, Yersinia intermedia and Yersinia kristensenii isolated from diverse sources in Brazil

Yersinia is an important genus comprising foodborne, zoonotic and pathogenic bacteria. On the other hand, species of the so-called group Yersinia enterocolitica-like are understudied and mostly characterized as non-pathogenic, despite of some reports of human infections. The present study aimed to provide genomic insights of Yersinia frederiksenii (YF), Yersinia intermedia (YI) and Yersinia kristensenii (YK) isolated worldwide. A total of 22 YF, 20 YI and 14 YK genomes were searched for antimicrobial resistance genes, plasmids, prophages, and virulence factors. Their phylogenomic relatedness was analyzed by Gegenees and core-genome multi-locus sequence typing. Beta-lactam resistance gene blaTEM-116 and five plasmids replicons (pYE854, ColRNAI, ColE10, Col(pHAD28) and IncN3) were detected in less than five genomes. A total of 59 prophages, 106 virulence markers of the Yersinia genus, associated to adherence, antiphagocytosis, exoenzymes, invasion, iron uptake, proteases, secretion systems and the O-antigen, and virulence factors associated to other 20 bacterial genera were detected. Phylogenomic analysis revealed high inter-species distinction and four highly diverse YF clusters. In conclusion, the results obtained through the analyses of YF, YI and YK genomes suggest the virulence potential of these strains due to the broad diversity and high frequency of prophages and virulence factors found. Phylogenetic analyses were able to correctly distinguish these closely related species and show the presence of different genetic subgroups. These data contributed for a better understanding of YF, YI and YK virulence-associated features and global genetic diversity, and reinforced the need for better characterization of these Y. enterocolitica-like species considered non-pathogenic.

Brief report of complicated Yersinia enterocolitica infection in an immunocompetent host: Review of the literature and pathogenicity mechanisms

Background

We report a case of a 47-year-old male presenting with Yersinia enterocolitica septicemia with no known risk factors for invasive infection, found to have multiloculated liver and splenic abscesses with an antecedent history of mild enterocolitis.

Case presentation

Our patient presented with septic shock in the setting of gastroenteritis with abdominal pain and fever. On work-up, he was found to have multiloculated hepatic and splenic abscesses secondary to Y. enterocolitica. No identifiable risk factors (ie, iron-overload syndrome or immunosuppression) for Y. enterocolitica septicemia were identified in our patient. Our patient was treated with a prolonged course of antibiotics until imaging resolution of his liver and splenic abscesses.

Conclusion

Invasive Y. enterocolitica in an immunocompetent host is rare. Our case highlights the pathogenicity of Y. enterocolitica, and important treatment and management considerations.

Hematochezia in children with acute diarrhea seeking emergency department care - a prospective cohort study

OBJECTIVES

Although the passage of blood in stools in children represents a medical emergency, children seeking emergency department (ED) care remain poorly characterized. Our primary objective was to compare clinical characteristics and etiologic pathogens in children with acute diarrhea with and without caregiver-reported hematochezia. Secondary objectives were to characterize interventions and resource utilization.

METHODS

We conducted a secondary analysis of the Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE) database. Children <18 years presenting to two pediatric EDs within a 24-hour period and <7 days of symptoms were consecutively recruited.

RESULTS

Of 1,061 participants, 115 (10.8%) reported hematochezia at the enrollment visit at which time those with hematochezia, compared to those without, had more diarrheal episodes/24-hour period (9 vs. 6; difference: 2; 95% confidence interval [CI]: 2.0, 4.0; p < 0.001), and were less likely to have experienced vomiting (54.8% vs. 80.2%; difference: -25.4; 95% CI: -34.9, -16.0; p < 0.001). They were more likely to receive intravenous fluids (33.0% vs. 17.9%; difference: 15.2; 95% CI: 6.2, 24.1; p < 0.001) and require repeat health care visits (45.5% vs. 34.7%; difference: 10.7; 95% CI: 0.9, 20.6; p = 0.03). A bacterial pathogen was identified in 33.0% of children with hematochezia versus 7.9% without (difference: 25.1; 95% CI: 16.3, 33.9; p < 0.001); viruses were detected in 31.3% of children with hematochezia compared to 72.3% in those without (difference: -41.0%, 95% CI: -49.9, -32.1; p < 0.001).

CONCLUSION

In children with acute diarrhea, caregiver report of hematochezia, compared to the absence of hematochezia, was associated with more diarrheal but fewer vomiting episodes, and greater resource consumption. The former group of children was also more likely to have bacteria detected in their stool.

Performance of four commercial real-time PCR assays for the detection of bacterial enteric pathogens in clinical samples

OBJECTIVES

Many laboratories use culture-independent diagnostic tests for bacterial gastroenteritis (ie. real-time polymerase chain reaction [RT-PCR]) instead of culture because of better sensitivity, automation, and faster turnaround times. To address some gaps in initial evaluations and lack of intraassay comparisons for many commercial RT-PCRs we compared the ability of four commercially available RT-PCR tests (Ridagene, Fast Track Diagnostics, BD Max, and Prodesse Progastro) to detect five major bacterial enteric pathogens: Campylobacter, Salmonella, Shiga-toxin producing E. coli (STEC), Shigella and Yersinia.

METHODS

Clinical stool specimens and contrived samples comprising commonly circulating species, serotypes, biovars and/or toxin subtypes were used for the comparison.

RESULTS

Concordance rates for RT-PCR and culture using culture positive and negative clinical stools were greater than 90% for Campylobacter (97.5-100%), Salmonella (97.5-100%), Shigella (100%) and STEC (90-100%). However, the agreement between RT-PCR and culture for Y. enteroccolitica ranged from 70-90%. For the contrived sample set, stx_2f was detected by only 1 of 4 assays. Of note, no assay could detect Yersinia non-enterocolitica and C. upsaliensis.

CONCLUSIONS

Depending on the prevalence of certain stx sub-types, Yersinia and Campylobacter species in a laboratory's jurisdiction, culture methods remain critical for the detection of these pathogens without further improvement in PCR assays.

A Case Series of Diarrheal Diseases Associated with Yersinia frederiksenii

To date, Yersinia pestis, Yersinia enterocolitica, and Yersinia pseudotuberculosis are the three Yersinia species generally agreed to be pathogenic in humans. However, there are a limited number of studies that suggest some of the “non-pathogenic” Yersinia species may also cause infections. For instance, Yersinia frederiksenii used to be known as an atypical Y. enterocolitica strain until rhamnose biochemical testing was found to distinguish between these two species in the 1980s. From our regional microbiology laboratory records of 18 hospitals in Eastern Ontario, Canada from 1 May 2018 to 1 May 2021, we identified two patients with Y. frederiksenii isolates in their stool cultures, along with their clinical presentation and antimicrobial management. Both patients presented with diarrhea, abdominal pain, and vomiting for 5 days before presentation to hospital. One patient received a 10-day course of sulfamethoxazole-trimethoprim; his Y. frederiksenii isolate was shown to be susceptible to amoxicillin-clavulanate, ceftriaxone, ciprofloxacin, and sulfamethoxazole-trimethoprim, but resistant to ampicillin. The other patient was sent home from the emergency department and did not require antimicrobials and additional medical attention. This case series illustrated that diarrheal disease could be associated with Y. frederiksenii; the need for antimicrobial treatment should be determined on a case-by-case basis.

Systemic Yersinia pseudotuberculosis as a Cause of Osteomyelitis in a Captive Ring-tailed Lemur (Lemur catta)

Yersinia pseudotuberculosis and Yersinia enterocolitica are ubiquitous pathogens with wildlife and domestic animal reservoirs. Outbreaks of 'non-plague' yersiniosis in man and non-human primates are reported frequently (including zoological specimens and research breeding colonies) and are usually characterized by enteritis, mesenteric lymphadenitis and occasionally organ abscessation. In people, non-septic reactive arthritis is a common sequela to yersiniosis. However, there have been rare reports in people of septic arthritis and osteomyelitis because of active systemic infection with Y. pseudotuberculosis. Osteomyelitis has also been reported rarely in historical yersiniosis outbreaks in farmed turkeys in England and the USA. This paper reports the first case of osteomyelitis caused by systemic infection with Y. pseudotuberculosis O:1 in a non-human primate, a captive ring-tailed lemur (Lemur catta). The lemur had a short clinical history of hyporexia and weight loss with reduction in mobility, especially of the left hindlimb. On post-mortem examination there was evidence of multi-organ abscessation. In addition, severe necrosis, inflammation and large bacterial colonies were present in the musculature, periosteum and bone marrow in the hip, ribs and a vertebra at the cervicothoracic junction. Osteomyelitis should be considered as a rare clinical presentation in non-human primates with systemic Y. pseudotuberculosis infection.

Multilocular Hepatic Abscess Formation and Sepsis due to Yersinia enterocolitica in a Patient with Hereditary Hemochromatosis and Type 2 Diabetes Mellitus

Infection with Yersinia enterocolitica (YE) typically presents with mild gastroenteritis without systemic infection. However, systemic YE infection has been described in states of iron overload. We present the case of a patient with sepsis with hepatic abscesses due to YE infection. Workup revealed a past diagnosis of diabetes mellitus and hemochromatosis which had been untreated for the previous 5 years due to patient refusal. This case highlights risk factors for systemic infection with YE. A high degree of suspicion for YE infection is warranted in patients with iron overload, diabetes mellitus, or immunosuppression.

Presence of foodborne pathogens, extended-spectrum β-lactamase -producing Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus in slaughtered reindeer in northern Finland and Norway

BACKGROUND

Various food-producing animals were recognized in recent years as healthy carriers of bacterial pathogens causing human illness. In northern Fennoscandia, the husbandry of semi-domesticated reindeer (Rangifer tarandus tarandus) is a traditional livelihood and meat is the main product. This study determined the presence of selected foodborne pathogens, methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in healthy semi-domesticated reindeer at slaughter in northern Finland and Norway.

RESULTS

All 470 reindeer fecal samples tested negative for Salmonella spp., whereas L. monocytogenes was detected in 3%, Yersinia spp. in 10%, and Shiga toxins genes (stx1 and/or stx2) in 33% of the samples. Listeria monocytogenes isolates belonged to the serotype 1/2a (14/15) and 4b, Yersinia spp. were identified mainly as Y. kristensenii (30/46) and Y. enterocolitica (8/46), and stx2 predominated among the Shiga toxin genes (stx2 alone or in combination with stx1 was found in 25% of the samples). With regard to the frequency and distribution of stx1/stx2, striking differences were evident among the 10 different areas of origin. Hence, reindeer could constitute a reservoir for Shiga toxin-producing E. coli (STEC), but strain isolation and characterization is required for verification purposes and to assess the potential human pathogenicity of strains. On the other hand, the favorable antibiotic resistance profiles (only 5% of 95 E. coli isolates were resistant to one or more of the tested antibiotics) and the absence of MRSA and ESBL-producing Enterobacteriaceae (when applying selective methods) suggest only a limited risk of transmission to humans.

CONCLUSIONS

Healthy semi-domesticated reindeer in northern Finland and Norway can be carriers of certain bacterial foodborne pathogens. Strict compliance with good hygiene practices during any step of slaughter (in particular during dehiding and evisceration) is therefore of central importance to avoid carcass contamination and to prevent foodborne pathogens from entering the food chain.

Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC)

The genus Yersinia includes species with a wide range of eukaryotic hosts (from fish, insects, and plants to mammals and humans). One of the major outer membrane proteins, the porin OmpC, is preferentially expressed in the host gut, where osmotic pressure, temperature, and the concentrations of nutrients and toxic products are relatively high. We consider here the molecular evolution and phylogeny of Yersinia ompC. The maximum likelihood gene tree reflects the macroevolution processes occurring within the genus Yersinia. Positive selection and horizontal gene transfer are the key factors of ompC diversification, and intraspecies recombination was revealed in two Yersinia species. The impact of recombination on ompC evolution was different from that of another major porin gene, ompF, possibly due to the emergence of additional functions and conservation of the basic transport function. The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.

Trends of the major porin gene (ompF) evolution: insight from the genus Yersinia

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species.

Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture

Campylobacter jejuni and Salmonella, Shigella, and Yersinia species (along with Shiga toxin-producing Escherichia coli) are the most common causes of acute bacterial diarrheal disease in the United States. Current detection techniques are time-consuming, limiting usefulness for patient care. We developed and validated a panel of rapid PCR assays for the detection and identification of C. jejuni, C. coli, Salmonella, and Yersinia species and Shigella and enteroinvasive E. coli in stool samples. A total of 392 archived stool specimens, previously cultured for enteric pathogens, were evaluated by PCR. Overall, 104 stool specimens had been culture positive (C. jejuni/coli [n = 51], Salmonella species [n = 42], Shigella species [n = 6], and Yersinia species [n = 5]). Compared to culture, the overall sensitivity and specificity of PCR detection of these organisms were 92 and 98% (96/104 and 283/288), respectively, from fresh or Cary Blair stool (P = 0.41); 87 and 98% (41/47 and 242/246), respectively, from fresh stool (P = 0.53); and 96 and 98% (55/57 and 41/42), respectively, from Cary Blair stool (P = 0.56). For individual genera, PCR was as sensitive as the culture method, with the exception of Salmonella culture using selenite enrichment for which PCR was less sensitive than culture from fresh, but not Cary Blair (P = 0.03 and 1.00, respectively) stools. This PCR assay panel for the rapid diagnosis of acute infectious bacterial diarrheal pathogens has a sensitivity and specificity equivalent to that of culture for stools in Cary Blair transport medium. Paired with reflexive culture of stools testing positive, this should provide an improvement in care for patients with acute infectious diarrheal disease.

Characteristics of beta-lactamases and their genes (blaA and blaB) in Yersinia intermedia and Y. frederiksenii

Background

The presence of β-lactamases in Y. enterocolitica has been reported to vary with serovars, biovars and geographical origin of the isolates. An understanding of the β-lactamases in other related species is important for an overall perception of antibiotic resistance in yersiniae. The objective of this work was to study the characteristics of β-lactamases and their genes in strains of Y. intermedia and Y. frederiksenii, isolated from clinical and non-clinical sources in India.

Results

The enzymes, Bla-A (a constitutive class A penicillinase) and Bla-B (an inducible class C cephalosporinase) were found to be present in all the clinical and non-clinical strains of Y. intermedia and Y. frederiksenii by double disc diffusion method. The results showed differential expression of Bla-A as indicated by presence/absence of synergy whereas expression of Bla-B was quite consistent. The presence of these enzymes was also reflected in the high minimum inhibitory concentrations, MIC₅₀ (126–1024 mg/L) and MIC₉₀ (256–1024 mg/L) of β-lactam antibiotics against these species. Restriction fragment length polymorphism (RFLP) revealed heterogeneity in both blaA and blaB genes of Y. intermedia and Y. frederiksenii. The blaA gene of Y. intermedia shared significant sequence identity (87–96%) with blaA of Y. enterocolitica biovars 1A, 1B and 4. The sequence identity of blaA of Y. frederiksenii with these biovars was 77–79%. The sequence identity of blaB gene of Y. intermedia and Y. frederiksenii was more (85%) with that of Y. enterocolitica biovars 1A, 1B and 2 compared to other species viz., Y. bercovieri, Y. aldovae and Y. ruckeri. Isoelectric focusing data further revealed that both Y. intermedia and Y. frederiksenii produced Bla-A (pI 8.7) and "Bla-B like" (pI 5.5–7.1) enzymes.

Conclusion

Both Y. intermedia and Y. frederiksenii showed presence of blaA and blaB genes and unequivocal expression of the two β-lactamases. Limited heterogeneity was detected in blaA and blaB genes as judged by PCR-RFLP. Phylogenetic relationships showed that the two species shared a high degree of identity in their bla genes. This is the first study reporting characteristics of β-lactamases and their genes in strains of Y. intermedia and Y. frederiksenii isolated from Asian region.

Biochemical and genetic characterization of the β-lactamases of Y. aldovae, Y. bercovieri, Y. frederiksenii and ‘Y. ruckeri’ strains

The beta-lactamases of five strains each of Y. aldovae and "Y. ruckeri", and 10 strains each of Y. bercovieri and Y. frederiksenii were examined phenotypically and genetically. Beta-lactamase activity and induction assays and SDS-PAGE were applied for phenotypic characterization of these enzymes. Genotypically, PCR experiments applying degenerated primer pairs for the detection of AmpC beta-lactamase genes were performed. All yersiniae yielded specific amplification products for ampC and all these strains expressed beta-lactamases. Each species produced its own, species-specific AmpC beta-lactamase. Inducibility of these enzymes was shown for Y. bercovieri, but not for the low-level enzyme producing species Y. aldovae and "Y. ruckeri". In contrast to these species, induction tests for Y. frederiksenii revealed heterogeneous results. Whereas the beta-lactamases of 6 of 10 strains were inducible, the enzyme activities after induction in the remaining four were similar to those measured without an inducer. In addition to the AmpC enzyme, all Y. frederiksenii strains expressed a second beta-lactamase belonging to Ambler class A. The present study enlarges the knowledge about the beta-lactamases of four novel Yersinia species that are likely to be involved in human disease. Beta-lactamases of Y. aldovae and "Y. ruckeri" have been characterized for the first time.

Natural antimicrobial susceptibilities and biochemical profiles of Yersinia enterocolitica-like strains: Y. frederiksenii, Y. intermedia, Y. kristensenii and Y. rohdei

The natural susceptibility of 131 Yersinia strains of Y. frederiksenii (n=38), Y. intermedia (n=48), Y. kristensenii (n=26) and Y. rohdei (n=19) to 70 antibiotics was tested. Minimum inhibitory concentration (MIC) values were determined with a microdilution procedure in IsoSensitest broth (all strains) and cation-adjusted Mueller Hinton broth (some strains). All species were naturally sensitive or sensitive and of intermediate susceptibility to tetracyclines, aminoglycosides, acylureidopenicillins, numerous cephalosporins, carbapenems, aztreonam, quinolones, chloramphenicol, folate-pathway inhibitors, nitrofurantoin, and fosfomycin. Uniform natural resistance was found with penicillin G, oxacillin, several macrolides, lincosamides, streptogramins, glycopeptides, rifampicin and fusidic acid. Species-specific differences in susceptibility affecting clinical assessment criteria were seen with aminopenicillins (in the presence and absence of beta-lactamase inhibitors), ticarcillin and some cephalosporins. Major medium-dependent susceptibilities were found with fosfomycin. beta-Lactam MIC susceptibility patterns suggested that most strains of the species tested produce both class A and class C (AmpC) beta-lactamases that are characteristic for the species. The present study describes a database concerning the natural susceptibility of some Y. enterocolitica-like species to a wide range of antibiotics, which can be applied to validate forthcoming antibiotic susceptibility tests of these strains and might contribute to their identification. An evaluation of 30 biochemical tests that secured phenotypic identification to the Yersinia species level is presented.