Low distribution of genes encoding virulence factors in Shigella flexneri serotypes 1b clinical isolates from eastern Chinese populations

Prevalence and changing antimicrobial resistance profiles of Shigella spp. isolated from diarrheal patients in Kolkata during 2011-2019

BACKGROUND

The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serogroups isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011-2019.

PRINCIPAL FINDINGS

During the study period, Shigella isolates were tested for their serogroups, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to β-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70-80% clonal similarity among each Shigella serotype.

CONCLUSION

This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region.

CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella

Introduction. Virulence factors (VFs) are the most potent weapon in the molecular armoury of Shigella . In bacteria, the mobile genetic elements (MGEs) are contributors to the evolution of different types of clustered regularly interspaced short palindromic repeats-CRISPR associated genes (CRISPR-cas) variants and plasmid incompatibility types. The present study explored the virulence potential of Shigella in relation to the CRISPR-cas pattern and incompatibility types among the isolates.

Hypothesis/Gap Statement. The profile of the CRISPR-cas systems among clinical isolates of Shigella in India has not been reported earlier. Limited knowledge is available on the pattern of plasmid incompatibility groups among clinical isolates Shigella . The bias is always towards studying the genetic elements associated with AMR, but the present study highlights CRISPR-cas and incompatibility types among Shigella in association with virulence.

Aim. We aimed to investigate the distribution of virulence factors, CRISPR-cas pattern followed by plasmid incompatibility types among Shigella isolates.

Methodology. Between 2012–2017, a total of 187 isolates of Shigella were included in the study. The virulence genes' distribution was carried out. CRISPR-cas profiling followed by analysis of the repeats and spacers was carried out. PCR-based replicon typing was used to determine the incompatibility types. The interplay was statistically determined using STATA.

Results. The distribution of virulence genes showed varied pattern with ipaH present in all the isolates followed by ompA (93.6 %), virF (66.8 %), ial and sen (60.4 %), set1A (39.6 %) and set1B (39 %). CRISPR 1, CRISPR 3 and Cas6-Cas5 region were dominantly conserved. Twenty-two types of spacers were identified. The CRISPR3 repeat appeared to have a highly conserved sequence. CRISPR2 being the least common CRISPR type showed a strong association with an array of virulence genes (ial-set1A-set1B-virF) while CRISPR1 being the most dominant showed the least association with virulence genes (sen-virF). The dominant plasmids were found to be belonging to the inc FII group. The incompatibility groups FII, IncIγ, U, FIIS, FIIK, K, A/C, I1alpha was found to be associated with a greater number of virulence genes.

Conclusion. The isolates showed increasing diversity in their gene content that contributes to increasing heterogeneity among the isolates, which is a known virulence strategy among pathogens.

High frequency of antimicrobial resistance and virulence gene in Shigella species isolated from pediatric patients in an Iranian Referral Hospital

BACKGROUND

Shigella is a main cause of gastroenteritis and it is responsible for 5 to 10 % of diarrhea through the world. The aims of this study were to assess the antibiotic susceptibility pattern and the presence of 3 common virulence genes (sigA, virF, invE) of Shigella strains isolated from patients with gastroenteritis in Children's Medical Center Hospital, Tehran, Iran.

METHODS

Over a period of 15 months, all Shigella species collected from the patients with gastroenteritis were entered to the study. Susceptibility testing of all isolates towards different antibiotics was performed using the disk diffusion method and the prevalence of virulence genes was detected by polymerase chain reaction (PCR) technology.

RESULTS

Among a total of 183 Shigella strains, 128 Shigella sonnei (70%) and 55 S. flexneri (30%) were isolated. The resistance rate to the antibiotics in S. sonnei strains was higher than S. flexneri. The most sensitive antibiotics for S. flexneri strains were gentamicin (98%), amikacin (85%) and ciprofloxacin (82%), while high resistance rate to trimethoprim-sulfamethoxazole (96%), ampicillin (96%), nalidixic acid (64%) and cefotaxime (60%) was observed. The frequency of invE, virF and sigA gene in S. flexneri strains was 89 %, 93 % and 56 %, respectively; whereas they found in 93 %, 96 %, and 100 % of S. sonnei strains, respectively. SigA gene was identified significantly higher in the S. sonnei strains (100%). There was no significant difference between the presence of virF and invE genes among Shigella strains.

CONCLUSION

The high presence of sigA gene in S. sonnei strains plays an important role in its pathogenesis, and the high frequency of invE and virF genes showed that this classical pathway regulating the expression of Shigella virulence factor genes could play a key role in the pathogenesis of this bacterium.

Virulence profiling of Shigella flexneri and emergence of serotype 2b as a highly virulent shigellosis causing strain in Pakistan

Bacillary diarrhea caused by Shigella flexneri is mediated by various virulence factors which make it the leading agent of diarrhea in developing countries. Previously, a high prevalence of S. flexneri, associated with diarrhea has been reported in Pakistan but no data is available on their virulence profile. The present study reports for the first time analysis of various virulence factors among S. flexneri serotypes isolated from clinical (diarrheal stool) and non-clinical (retail raw foods and drinking water) sources. A total of 199 S. flexneri (clinical: 155, raw foods: 22, water: 22) belonging to various serotypes were subjected to virulence genes detection and virulence profiling. The most frequent virulence gene was found to be ipaH (100%), followed by sat (98%), ial (71.3%), set1B (65.8%) and set1A (38.7%). A high level of virulence was detected in serotype 2b as compared to other serotypes as 32.3% of all serotype 2b have the entire set of five virulence genes including ipaH (100%), ial (100%), sat (37.7%), set1A (89.3%), and set1B (100%). Seven different virulence gene profiles (V1 - V7) were detected and the most frequently observed to be V1 (ipaH+, ial+, sat+, set1A+, set1B+) followed by V3 (ipaH+, ial+, sat+, set1B+). The predominant virulence gene pattern in serotype 2b isolated from clinical and non-clinical samples were V1 and V3. Furthermore, about 32% strains belonging to serotype 2b contain the complete set of five virulence genes isolated from patients with high disease severity. In conclusion, the current finding revealed for the first times that serotype 2b was the most virulent strains in both clinical and non-clinical samples in Pakistan. In addition, the virulence of serotype 2b was well correlated with high disease severity.

Distribution of genes encoding virulence factors of Shigella strains isolated from children with diarrhea in southwest Iran

This study aimed to investigate the distribution of virulence factor genes in Shigella strains isolated from children with diarrhea in the southwest, Iran. In this cross-sectional study, 1530 diarrheal stool specimens were collected from children aged under 15 years. The Shigella strains were identified by biochemical methods and polymerase chain reaction (PCR). Subsequently, all Shigella isolates were evaluated by PCR for the presence of nine virulence genes ipaH (responsible for dissemination from cell to cell), ial (responsible for epithelial cell penetration), sat (displays cytopathic activity in several intestinal cell lines), sigA (toxic to epithelial cells), pic (associated with colonization), pet (cytotoxic for epithelial cells), sepA (contribute to intestinal inflammation and colonization), virF and invE (regulatory proteins). A total of 91 isolates including 47 S. flexneri, 36 S. sonnei, and 8 S. boydii were identified. All isolates were positive for the ipaH gene. The other genes include ial, virF, invE, sigA, sat, sepA, pic and pet found in 84.6%, 72.5%, 68.1%, 62.6%, 51.6%, 39.5%, 37.3% and 28.5% of the isolates, respectively. The results showed a high distribution of virulence genes among Shigella strains in our region. It seems that for different Shigella spp. different virulence factors contribute to pathogenesis. The current study provided insights into some baseline information about the distribution of some virulence genes of Shigella isolates in Southwest Iran.

Case report on a swift shift in uropathogens from Shigella flexneri to Escherichia coli: a thin line between bacterial persistence and reinfection

Background

Urinary tract infections (UTI) are mostly caused by bacteria. Urine cultures are usually a definitive measure to select the appropriate antibiotics for the elimination of a uropathogen and subsequent recovery from the infection. However, the preferred antibiotics as determined by urine culture and sensitivity may still not eliminate the infection and would require further examination to ascertain the cause of treatment failure which could be unresolved bacteriuria, bacterial persistence, immediate reinfection with a different uropathogen or misdiagnosis.

Case presentation

A 2-years 7 months-old female was admitted in the Regional hospital of Buea following persistent fever. An auto medication with amoxicillin was reported. Urinalysis was done on the first day and the sediment of the cloudy urine revealed many bacteria and few pus cells. Ceftriaxone was prescribed as empirical treatment and a request for urine and blood culture was made. Three days after admission, the temperature and CRP were 39.0 °C and 96 mg/l, respectively. The urine culture results (> 10⁵ CFU/ml of Shigella flexneri sensitive to ofloxacin) were presented to the doctor on the 4th day of admission. Patient was put on ofloxacin. Three days after, the temperature (38.5 °C) and CRP (24 mg/l) were still elevated. The blood culture result came out negative. A second urine culture was requested which came back positive (> 10⁵ CFU/ml of Escherichia coli resistant to ofloxacin and sensitive to meropenem and amikacin). Ofloxacin was discontinued and the patient put on meropenem and amikacin. The third urine culture recorded no significant growth after 48 h of incubation. The patient was discharged looking healthy once more with a normal body temperature.

Conclusion

Antibiotics tailored towards the elimination of a particular bacterial species may as well provide a favorable environment for other bacterial species that are resistant to it in the course of treating a UTI episode. This apparent treatment failure may first of all require a second urine culture for confirmation rather than considering the possibilities of a misdiagnosis.

High Rates of Antimicrobial Resistance and Virulence Gene Distribution Among Shigella spp. Isolated from Pediatric Patients in Tehran, Iran

Background

Shigella continues to be important causes of acute pediatric diarrhea worldwide. Shigella produces numerous virulence factors involved in colonization and invasion into epithelial cells which eventually result in the disease. The present study was conducted to evaluate the prevalence of virulence genes and to investigate antibiotic resistance profiles among Shigella isolates obtained from pediatric patients in Iran.

Methods

A total of 141 Shigella isolates were collected between March 2017 and September 2018 from stool of children under 14 who were suspected to have shigellosis. Shigella isolates were identified using standard microbiological and serological tests and antimicrobial susceptibility testing was carried out via Kirby–Bauer disk diffusion method. In addition, the presence of seven virulence determinants including ipaH, ipaB, ipaC, ipaD, ipgD, sen, and virA were evaluated using PCR.

Results

S. sonnei (78.7%) was the most prevalent shigella spp. among children with shigellosis followed by S. flexneri (19.9%) and S. boydii (1.4%). Antimicrobial susceptibility testing revealed that most of the isolates were considered as multidrug-resistant (MDR) strains. Our findings also showed a high resistance rate against trimethoprim-sulfamethoxazole in Shigella isolates. The prevalence of ipaH, ipaC, sen, ipaD, virA, ipaB, and ipgD were 100%, 95.7%, 95.7%, 94.3%, 93.6%, 92.9%, and 80.8%, respectively.

Conclusion

The current study revealed that S. sonnei was the predominant species isolated from children with shigellosis in Iran. Our results also indicated a high distribution of type III secretion system effector protein-encoding genes and high multidrug-resistance among shigella spp. in Iran. Therefore, it is suggested that antimicrobial susceptibility testing be performed prior to antibiotic prescription.

Molecular epidemiology of Shigella flexneri isolated from pediatrics in a diarrhea-endemic area of Khyber Pakhtunkhwa, Pakistan

Shigella flexneri is considered as an important causative agent of Shigellosis causing diarrhea in the countries with a low socioeconomic status. No study has been carried out on the molecular prevalence of S. flexneri in Khyber Pakhtunkhwa, Pakistan. So this study was designed to evaluate the molecular prevalence of S. flexneri and their associated risk factors. A total of 2014 diarrheal stool samples were collected from January 2016 to May 2017 from pediatrics patients of Khyber Pakhtunkhwa followed by identification of S. flexneri through biochemical, serological, and molecular methods. The overall prevalence of Shigella species was found to be 7.9% (n = 160). The predominant Shigella specie was S. flexneri (n = 155, 96.8%) followed by S. boydii (n = 5, 3.1%). Interestingly, no sample was found positive for S. sonnei and S. dysenteriae. The majority of Shigellosis cases occurred from June to September. Potential risk factors related with Shigellosis were unhygienic latrine usage, bad hand washing, and consumption of unhygienic food and water, and pipe leakage in the sewage system. In this study, we have observed a high number of Shigellosis cases especially those caused by S. flexneri. It is suggested that effective health awareness programs should be organized by the regional health authorities to minimize the magnitude of pediatrics Shigellosis.

Distribution of Genes Encoding Virulence Factors and the Genetic Diversity of Enteroinvasive Escherichia coli (EIEC) Isolates from Patients with Diarrhea in Ahvaz, Iran

BACKGROUND

Entero-invasive E. coli (EIEC) is one of the causes of bacillary dysentery in adults and children. The ability of EIEC to invade and colonize the surface of epithelial cells is influenced by many virulence factors. This study aimed to investigate the distribution of virulence factor genes in EIEC strains isolated from patients with diarrhea in Ahvaz, Iran, as well as the genetic diversity between these isolates by Multilocus variable-number tandem repeat analysis (MLVA).

MATERIALS AND METHODS

A total of 581 diarrheic stool samples were collected from patients with diarrhea attending two hospitals, in Ahvaz, Iran. The E. coli strains were identified by biochemical methods. Subsequently, all E. coli isolates were identified as EIEC by polymerase chain reaction (PCR) for the ipaH gene. The EIEC isolates evaluated by PCR for the presence of 8 virulence genes (ial, sen, virF, invE, sat, sigA, pic, and sepA). All EIEC strains were genotyped by the MLVA typing method.

RESULTS

A total of 13 EIEC isolates were identified. The presence of ial, virF, invE, sen, sigA, pic, and sat genes was confirmed among 92.3%, 84.6%, 84.6%, 76.9%, 69.2%, and 15.3% of EIEC isolates, respectively. On the other hand, none of the isolates were positive for the sepA gene. The EIEC isolates were divided into 11 MLVA types.

CONCLUSION

Our results showed a high distribution of virulence genes among EIEC isolates in our region. This study showed that MLVA is a promising typing technique for epidemiological studies. MLVA can supply data in the form of codes that can be saved in the database and easily shared among laboratories, research institutes, and even hospitals.

Extensive inter-strain diversity among clinical isolates of Shigella flexneri with reference to its serotype, virulence traits and plasmid incompatibility types, a study from south India over a 6-year period

Background

Shigella has evolved as a result of acquiring extragenetic material through horizontal gene exchange. These aid in the rapid emergence of bacterial inter-strain diversity in virulence factors and serotype variants through O-antigenic switching. Plasmid incompatibility typing of isolates is insightful in understanding local expansion of virulence plasmids, as whether virulence dissemination involves diverse plasmids or one dominant ‘epidemic’ type. The broad question underlying this study was that of how inter-strain genetic, serotype and plasmid incompatibility type variations can help understand the emergence of Shigella as a highly virulent pathogen.

Results

A total of 101 confirmed isolates of S. flexneri were included in this study. The distribution of the subtypes were variable, type 2a (48/101, 47.5%), type 6 (15/101, 14.9%), type 1b (8/101, 7.9%), type 1 variant (7/101, 6.9%), type 3b (12/101, 11.9% 0, type 4 (6/101, 6.0%), variant Y (2/101, 1.9%) and variant X (1/101, 1%). All had the ipaH gene (101/101, 100%) followed by ompA (92/101, 91.1%), ial (84/101, 83.4%), sen (82/101, 81.2%), virF (84/101, 83.2%), set1A and set1B (59/101, 58.4%). Out of the total of 49 isolates that showed all the virulence related genes studied here the IncIγ plasmid was detected in all isolates studied followed by FII (33/49, 67.3%), FIIS (20/49, 40.8%). Inc K was positive in two isolates (2/49, 4%) studied. The inc groups IncI1-α, Inc T were detected in 1 isolate each and Inc L and Inc P formed part of the multireplicon in the same isolate.

Conclusions

In order to estimate the burden of the disease caused by the new serotypes, it is important to have knowledge of the locally prevalent serotype. This will prove helpful in developing strategies for prevention of same especially since, the immunity in such diseases is serotype specific. Thus, the emergence of non-typable atypical serotypes of S. flexneri from natural infections needs to be investigated further. This study highlights the emergence of genetic variants exhibiting resistance to many antibiotics which needs to be studied for understanding the ever-changing landscape of this pathogen.

Electronic supplementary material

The online version of this article (10.1186/s13099-019-0314-9) contains supplementary material, which is available to authorized users.

Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh

AIMS

This study conducted bacterial community, virulence and antibiogram profiling inside the hindgut and skin of freshly caught hilsa fish and those sold at markets.

METHODS AND RESULTS

The results of 16S rRNA-based high-throughput sequencing showed a higher number of bacterial genera in marketed fish samples than in fresh fish samples. The total operational taxonomic units, genus counts and diversity index were significantly higher (P > 0·05) in marketed fish, which also had abundant pathogenic bacterial groups. Skin samples had a lower profusion of pathogenic bacteria than gut samples. A total of 52 bacterial isolates from nine species were identified in this study, of which 25 were from a Chittagong market and 22 were from a Dhaka market, whereas only five were from fresh hilsa. The polymerase chain reaction amplification of 12 species-specific virulence genes in the 52 isolates, namely, aer, hly, chxA, toxB, rtxC, sfa, uge, norB, trx, toxA, ipaH, sigA and coa, indicated a high number of positive samples containing Vibrio cholerae, Aeromonas spp., Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus. Antibiogram profiling of these bacteria against 10 commercial antibiotics showed high-resistance patterns of the isolates against sulfamethoxazole, kanamycin, neomycin, ampicillin and tetracycline.

CONCLUSION

The results reveal the spread of multidrug-resistant bacteria in hilsa fish marketed for human consumption in Bangladesh.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the risk of spreading environmentally and clinically pathogenic bacteria in fish sold for human consumption in Bangladesh. Such bacteria come from aquatic pollution and poor handling, storage and transportation practices that may predispose fish to major outbreaks of infectious and waterborne diseases.

First investigation of the presence of SPATE genes in Shigella species isolated from children with diarrhea infection in Ahvaz, southwest Iran

Background:SPATE (serine protease autotransporters of enterobacteriaceae) genes are considered as a group of the main virulence factors of Shigella species This study aimed to investigate for the first time the distribution of SPATE genes among Shigella spp. isolated from children with diarrhea infection in Ahvaz, Iran.

Methodology: In this study, a total of 74 Shigella isolates were collected between August 2016 and June 2017 from feces of children with diarrhea and identified by biochemical and molecular methods for Shigella species. The frequency distribution of the SPATE genes, including pic, pet, sat, sigA and sepA, was evaluated using PCR. The genetic relationship of all isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR.

Results: The most common species of Shigella was S. flexneri, followed by S. sonnei and S. boydii. In total, 95.94% of Shigella isolates had at least one of the SPATE genes. The presence of pic, pet, sat, sigA and sepA genes was confirmed among 35.13%, 27%, 47.29%, 58.1% and 39.18% of Shigella isolates, respectively. Of these SPATE genes, the sat and sigA genes were recognized as the most common autotransporters among S. flexneri and S. sonnei isolates, respectively. Also, either S. flexneri or S. sonnei isolates belonging to a same clone type had similar SPATE genes profile.

Conclusion: Our results revealed that the high distribution of SPATE genes among Shigella isolates in our region. Hence, this study highlights a need for epidemiological programs to monitor the distribution of SPATE genes locally for prevention from further dissemination of the Shigella isolates harboring them.

Virulence-related genes are associated with clinical and nutritional outcomes of Shigella/Enteroinvasive Escherichia coli pathotype infection in children from Brazilian semiarid region: A community case-control study

Shigella/Enteroinvasive Escherichia coli (EIEC) pathotype is a major enteropathogen associated with diarrhea and malnutrition in children from developing countries. This study aimed to correlate Shigella/EIEC virulence-related genes (VRGs) with clinical symptoms, nutritional status and coenteropathogens in children from the Brazilian semiarid region. We designed a case-control study of community diarrhea in six cities of the Brazil semiarid region with 1200 children aging 2-36 months. Standardized questionnaire was applied for collecting sociodemographic, nutritional status and clinical information of the children. DNA samples were extracted from stools and diagnosed for Shigella/EIEC using PCR-based approaches. Positive samples were tested for 28 VRGs using four multiplex PCRs. Intestinal inflammation was determined by measuring fecal myeloperoxidase (MPO). Shigella/EIEC pathotype was detected in 5% of the children and was significantly associated with diarrhea. The genes sen (encoding Shigella enterotoxin 2), ipgB2, ipgB1 (both encoding type 3 secretion system-T3SS effectors that modulate actin filament), and ospF (encoding a T3SS effector involved in suppression of host responses) were further associated with diarrhea in Shigella/EIEC positive children. Among children presenting diarrhea, virA gene (encoding a T3SS effector that promotes microtubule destabilization) was associated with fever, while virB (encoding a major transcriptional activator) was associated with low height-for-age z-score. In addition, these VRGs were associated with increased fecal MPO, and coinfection with Salmonella spp. was associated with increased abdominal pain. These data reinforce the impact of Shigella/EIEC on diarrhea in children from Brazilian semiarid region and highlighted the contributions of specific virulence genes for its pathobiology.

Antimicrobial sensitivity trends and virulence genes in Shigella spp. from the Oceania region

Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2-4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns.