Virulence factors and mechanisms of antimicrobial resistance in Shigella strains from periurban areas of Lima (Peru)

Prevalence of plasmid-mediated quinolone resistance genes and biofilm formation in different species of quinolone-resistant clinical Shigella isolates: a cross-sectional study

BACKGROUND

The purpose of this study was to look into the presence of plasmid-mediated quinolone resistance (PMQR) genes and biofilm formation in several species of clinical Shigella isolates that were resistant to quinolones.

METHODS

The stool samples of 150 patients (younger than 10 years) with diarrhea were collected in this cross-sectional study (November 2020 to December 2021). After cultivation of samples on Hektoen Enteric agar and xylose lysine deoxycholate agar, standard microbiology tests, VITEK 2 system, and polymerase chain reaction (PCR) were utilized to identify Shigella isolates. The broth microdilution method was used to determine antibiotic susceptibility. PMQR genes including qnrA, qnrB, qnrC, qnrD, qnrE, qnrS, qnrVC, qepA, oqxAB, aac(6')-Ib-cr, and crpP and biofilm formation were investigated in quinolone-resistant isolates by PCR and microtiter plate method, respectively. An enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique was used to determine the clonal relatedness of quinolone-resistant isolates.

RESULTS

A total of 95 Shigella isolates including S. sonnei (53, 55.8%), S. flexneri (39, 41.1%), and S. boydii (3, 3.2%) were identified. The highest resistance rates of the isolates were against ampicillin (92.6%, n = 88/95). Overall, 42 of 95 (44.2%) isolates were simultaneously resistant against two or more quinolones including 26 (61.9%) S. sonnei and 16 (38.1%) S. flexneri. All isolates were multidrug-resistant (resistance to more than 3 antibiotics). The occurrence of PMQR genes was as follows: qnrS (52.4%), qnrA and aac(6')-Ib-cr (33.3%), and qnrB (19.0%). The prevalence in species was as follows: 61.5% and 37.5% (qnrS), 19.2% and 56.3% (qnrA), 38.5% and 25.0 (aac(6')-Ib-cr), and 19.2% and 18.8% (qnrB) for S. sonnei and S. flexneri, respectively. The other PMQR genes were not detected. In total, 52.8% (28/53) of quinolone-susceptible and 64.3% (27/42) of quinolone-resistant isolates were biofilm producers. Biofilm formation was not significantly different between quinolone-resistant and quinolone-susceptible isolates (P-value = 0.299). Quinolone-resistant isolates showed a high genetic diversity according to the ERIC-PCR.

CONCLUSION

It seems that qnrS, qnrA, and aac(6')-Ib-cr play a significant role in the quinolone resistance among Shigella isolates in our region. Also the quinolone-resistant S. flexneri and S. sonnei isolates had a high genetic diversity. Hence, antibiotic therapy needs to be routinely revised based on the surveillance findings.

The relationship between integrons, antibiotic resistance genes and SXT resistance in Shigella flexneri strains

OBJECTIVE

To investigate the correlation between sulfamethoxazole-trimethoprim (SXT) resistance in Shigella flexneri (S.flexneri) and the presence of integrons and relevant antibiotic resistance genes.

METHODS

We collected 115 strains of Shigella flexneri isolated from feces of children with diarrhea in Jinan from 2012 to 2020 and determined the minimum inhibitory concentration (MIC) of SXT by Etest method. The presence of class 1, class 2, and class 3 integron genes, variable region antibiotic resistance gene cassettes, and sul1, sul2, sul3, and SXT elements were detected using polymerase chain reaction (PCR). Positive results were further analyzed by DNA sequencing and BLAST comparison.

RESULTS

In total, the resistance rate to SXT was 60.9% among the 115 S.flexneri strains. The prevalence of class 1 and class 2 integrons were 88.7% and 87.0%, respectively, with no class 3 integrons detected. Among the strains, 13.0% carried typical class 1 integrons with variable region antibiotic resistance gene cassettes dfrA17-aadA5 and dfrV, while 85.2% carried atypical class 1 integrons with variable region antibiotic resistance gene cassette blaoxa-30-aadA1. The variable region antibiotic resistance gene cassettes of class 2 integrons were all dfrA1+sat1+aadA1. There was a statistical difference between the presence of class 1 integrons and class 2 integrons between the SXT-sensitive and resistant S.flexneri strains (χ2=22.800, χ2=16.365, P<0.01, P<0.01). Integrons carrying dfrV and dfrA1 by integrons also showed a statistical difference in SXT resistance (χ2=9.422, χ2=16.365, P<0.01, P<0.01). PCR revealed the presence of sul1 and sul2 in 13.0% and 47.0% of strains, respectively, with neither sul3 nor SXT elements detected. There was a significant difference between the presence of sul1, sul2 between the SXT-sensitive and resistant S.flexneri strains (χ2=9.588, χ2=65.445, P<0.01, P<0.01).

CONCLUSION

In summary, integrons are involved in SXT resistance of S.flexneri, and dfrV, dfrA1, sul1, sul2 are closely related to SXT resistance of S.flexneri.

The Enterics for Global Health (EFGH) Shigella Surveillance Study in Peru

Background

The Enterics for Global Health (EFGH) Peru site will enroll subjects in a periurban area of the low Amazon rainforest. The political department of Loreto lags behind most of Peru in access to improved sources of water and sanitation, per capita income, children born <2.5 kg, and infant and child mortality. Chronic undernutrition as manifested by linear growth shortfalls is common, but wasting and acute malnutrition are not.

Methods

The recruitment of children seeking care for acute diarrheal disease takes place at a geographic cluster of government-based primary care centers in an area where most residents are beneficiaries of free primary healthcare.

Results

Rates of diarrheal disease, dysentery, and Shigella are known to be high in the region, with some of the highest rates of disease documented in the literature and little evidence in improvement over the last 2 decades. This study will update estimates of shigellosis by measuring the prevalence of Shigella by polymerase chain reaction and culture in children seeking care and deriving population-based estimates by measuring healthcare seeking at the community level.

Conclusions

Immunization has been offered universally against rotavirus in the region since 2009, and in a context where adequate water and sanitation are unlikely to obtain high standards in the near future, control of principal enteropathogens through immunization may be the most feasible way to decrease the high burden of disease in the area in the near future.

Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli

This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum β-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.

Ethnopharmacological Survey, Phytochemical Screening and Antimicrobial Activities of Medicinal Plants Used in the Treatment of Diarrhea in Southeastern Gabon

Diarrhea is a condition that particularly affects children under five the age of years old in developing countries. The aim of this study was to evaluate the efficacy of medicinal extracts plants used in treatment and to characterize their inhibitory capacity in the growth of bacteria isolates in childhood diarrhea in the southeast region of Gabon. An ethnobotanical survey on the plants used in the treatment of diarrhea in southeastern Gabon was carried out and a phytochemical screening of the collected plants was performed. The antimicrobial activity of aqueous extracts was evaluated; 33 plant species were identified, representing 28 genera and 19 families. Bark (39.5%) was the most commonly used plant part, followed by powder formulations (28.9%). The preferred method of preparation and chewing (44.7%), together with drinking (36.8%), were the most prevalent modes of administration. Phytochemical screening showed a plethora of secondary metabolites (terpenoids, alkaloids and phenolic compounds), and a marked level of anti-diarrheal activity was found with Sida acuta and Santiria. ebo against Shigella spp. (16.22 ± 0.7 mm and 14.05 ± 1.4 mm) and Yersinia pestis (16.35 ± 0.5 mm and 15.51 ± 0.5 mm). The high diversity of secondary plant metabolites and their inhibitory ability against enteric pathogens would justify their use at the local level to treat diarrheal infections.

Trends in antimicrobial resistance of Shigella species in Peru, 2011-2020

Objective

To describe the frequency of antimicrobial resistance rates and spatial-temporal distribution of Shigella species from the last 10 years in Peru.

Methods

A cross-sectional descriptive study was carried out. A total of 1668 Shigella strains, remitted as part of the national enteric pathogen surveillance from 2011 to 2020, were analysed. The strains were confirmed by conventional tests and serotyped with polyvalent and monovalent antibodies. Also, antimicrobial susceptibility was performed according to the Kirby-Bauer method.

Results

The most frequent Shigella species was S. sonnei (49.2%), followed by S. flexneri (42.2%), S. boydii (7.9%) and S. dysenteriae (0.7%). Phase II (46.29%) was the most frequent serotype in S. sonnei, serotype 2a (43.61%) in S. flexneri, serotype 2 in S. boydii and serotype 4 in S. dysenteriae. High rates of resistance were detected for trimethoprim/sulfamethoxazole (91.0%), tetracycline (88.4%), ampicillin (73.9%) and chloramphenicol (64.9%), moderate rates for amoxicillin/clavulanic acid (25.1%), ciprofloxacin (16.7%) and nalidixic acid (14.8%), and low rates for cefotaxime (1.74%), nitrofurantoin (0.7%) and ceftazidime (0.6%). Moreover, antimicrobial resistance to fluoroquinolones increased considerably from 2017 to 2020.

Conclusion

S. sonnei was the most frequent species, which have a large proportion of strains resistant to trimethoprim/sulfamethoxazole, and a growing trend of resistance to ciprofloxacin and nalidixic acid. This increase in resistance to commonly used antibiotics in treatments is alarming, threatening the control and management of these currently treatable infections.

The increasing antimicrobial resistance of Shigella species among Iranian pediatrics: a systematic review and meta-analysis

BACKGROUND

Shigellosis remains one of the global causes of morbidity and mortality. However, the global emergence of antibiotic resistance has become the leading cause of treatment failure in shigellosis. This review aimed to provide an updated picture of the antimicrobial resistance rates in Shigella species in Iranian pediatrics.

METHODS

A comprehensive systematic search was performed on PubMed, Scopus, Embase, and Web of Science until 28 July 2021. The meta-analysis was performed by computing the pooled using a random-effects model with Stata/SE software, v.17.1. The discrepancy within articles was surveyed by the forest plot in addition to the I2 statistic. All statistical interpretations were reported on a 95% confidence interval (CI) basis.

RESULTS

Totally, of 28 eligible studies published between 2008 and 2021. The pooled prevalence rate of multidrug-resistant (MDR) was 63% (95% CI 50-76). Regarding suggested antimicrobial agents for Shigella species, the prevalence of resistance for ciprofloxacin, azithromycin, and ceftriaxone as first- and second-line treatments for shigellosis were 3%, 30%, and 28%, respectively. In contrast, resistance to cefotaxime, cefixime, and ceftazidime was 39%, 35%, and 20%. Importantly, subgroup analyses indicated that an increase in resistance rates during the periods (2008-2014, 2015-2021) was recognized for ciprofloxacin (0 % to 6%) and ceftriaxone (6% to 42%).

CONCLUSION

Our findings revealed that ciprofloxacin is an effective drug for shigellosis in Iranian children. The substantially high prevalence estimation proposes that the first- and second-line treatments for shigellosis are the major threat to public health and active antibiotic treatment policies are essential.

Antibiotic resistance trends for common bacterial aetiologies of childhood diarrhoea in low- and middle-income countries: A systematic review

Background

Diarrhoea is the second most common cause of death among children under the age of five worldwide. The World Health Organization (WHO) recommends treating diarrhoea with oral rehydration therapy, intravenous fluids for severe dehydration, and zinc supplements. Antibiotics are only recommended to treat acute, invasive diarrhoea. Rising antibiotic resistance has led to a decrease in the effectiveness of treatments for diarrhoea.

Methods

A systematic literature review in PubMed, Web of Science, and EMBASE was conducted to identify articles relevant to antibiotic-resistant childhood diarrhoea. Articles in English published between 1990 to 2020 that described antibiotic resistance patterns of common pathogens causing childhood diarrhoea in low- and middle-income countries were included. The studies were limited to papers that categorized children as 0-5 years or 0-10 years old. The proportion of isolates with resistance to major classes of antibiotics stratified by major WHO global regions and time was determined.

Results

Quantitative data were extracted from 44 articles that met screening criteria; most focused on children under five years. Escherichia coli isolates had relatively high resistance rates to ampicillin and tetracycline in the African (AFR), American (AMR), and Eastern Mediterranean Regions (EMR). There was moderate to high resistance to ampicillin and third generation cephalosporins among Salmonella spp in the AFR, EMR, and the Western Pacific Region (WPR). Resistance rates for ampicillin, co-trimoxazole, and chloramphenicol for Shigella in the AFR started at an alarmingly high rate ( ~ 90%) in 2006 and fluctuated over time. There were limited antibiotic resistance data for Aeromonas, Yersinia, and V. cholerae. The 161 isolates of Campylobacter analysed showed initially low rates of fluoroquinolone resistance with high rates of resistance in recent years, especially in the Southeast Asian Region.

Conclusions

Resistance to inexpensive antibiotics for treatment of invasive diarrhoea in children under ten years is widespread (although data on 6- to 10-year-old children are limited), and resistance rates to fluoroquinolones and later-generation cephalosporins are increasing. A strong regional surveillance system is needed to carefully monitor trends in antibiotic resistance, future studies should include school-aged children, and interventions are needed to reduce inappropriate use of antibiotics for the treatment of community-acquired, non-invasive diarrhoea.

Registration

This systematic review was registered in Prospero (registration number CRD42020204004) in August 2020.

Class 1 and 2 Integrons in Escherichia coli Strains Isolated from Diarrhea and Bacteremia in Children Less Than 2 Years of Age from Peru

Class 1 and Class 2 integrons are mobilizable elements able to carry a variety of antibiotic resistance determinants. In the present study, Class 1 and 2 integrons present in 355 pathogenic Escherichia coli (285 diarrheagenic, of these 129 were enteropathogenic, 90 enteroaggregative, 66 enterotoxigenic, and 70 bacteremic) isolated from healthy and ill children under age 5 from periurban areas of Lima, Peru, were characterized. The presence of integrase 1 and 2 was established by polymerase chain reaction (PCR), and variable regions were grouped by PCR-restriction fragment length polymorphism and subsequent sequencing. Antimicrobial resistance was established by disk diffusion. Ninety-seven isolates (27.3%) presented integrase 1, and 16 (4.5%) presented integrase 2 (P < 0.0001); in addition, seven (2.0%) isolates, six diarrheagenic and one bacteremic, presented both integrase genes. The presence of integrase 1 was more frequent among bacteremic isolates (P = 0.0004). Variable regions were amplified in 76/120 (63.3%) isolates with up to 14 gene arrangements. The most prevalent gene cassettes were those encoding dihydrofolate reductases as well as aminoglycoside modifying enzymes. Of note, Class 1 integrons tended to be associated with the presence of extended-spectrum β-lactamases (ESBLs). A variety of Class 1 and 2 integrons were detected in diarrheagenic and bacteremic E. coli, demonstrating the heterogeneity of variable regions circulating in the area. The association of integrons with ESBLs is worrisome and has an impact on the development of multidrug resistance.

Molecular detection and characterization of Shigella spp. harboring extended-spectrum β-lactamase genes in children with diarrhea in northwest Iran

Shigellosis is one of the acute bowel infections and remains a serious public health problem in resource-poor countries. The present study aimed to survey the distribution of extended-spectrum β-lactamase (ESBL)-producing Shigella strains isolated from patients with diarrhea in northwest Iran. In the present cross-sectional study, from January 2019 to December 2020, 1280 fecal samples were collected from children with diarrhea in Ardabil, Iran. Multiplex PCR assay was applied for the presence of ipaH, invC, wbgZ, rfpB, and rfc genes to detect Shigella spp., Shigella sonnei, Shigella dysenteriae, Shigella flexneri, and Shigella boydii, respectively. Phenotypic detection of ESBL-producing isolates was carried out using the Double Disc Test (DDT). The frequency of main ESBL encoding genes including bla_CTX-M, bla_SHV, and bla_TEM was detected using multiplex PCR. The genetic similarity of S. sonnei isolates was determined using ERIC PCR. A total of 49 Shigella isolates (3.8%; 49/1280) including 42 (85.7%) S. sonnei, 5 (10.2%) S. flexneri, and 2 (4%) S. dysenteriae were identified. S. boydii was not detected in any fecal samples. ESBLs were produced by 10.2% of Shigella spp. including 3 S. sonnei, 1 S. flexneri, and 1 S. dysenteriae. The ESBL encoding genes include bla_CTX-M and bla_TEM found in 65.3% and 61.2% of isolates, respectively. bla_SHV gene was not detected in any isolates. The ERIC-PCR profiles allowed the differentiation of 42 S. sonnei strains into 6 clusters. Our study revealed a high frequency of ESBL-encoding genes among Shigella spp. in northwest Iran. The high prevalence of S. sonnei harboring ESBL genes, in the present work, is the main challenge for dysentery treatment, and this concern justifies the need for effective and regular monitoring of antibiotic usage among patients.

Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species

The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Burden, Antibiotic Resistance, and Clonality of Shigella spp. Implicated in Community-Acquired Acute Diarrhoea in Lilongwe, Malawi

Although numerous studies have investigated diarrhoea aetiology in many sub-Saharan African countries, recent data on Shigella species’ involvement in community-acquired acute diarrhoea (CA-AD) in Malawi are scarce. This study investigated the incidence, antibiotic susceptibility profile, genotypic characteristics, and clonal relationships of Shigella flexneri among 243 patients presenting with acute diarrhoea at a District Hospital in Lilongwe, Malawi. Shigella spp. were isolated and identified using standard microbiological and serological methods and confirmed by identifying the ipaH gene using real-time polymerase chain reaction. The isolates’ antibiotic susceptibility to 20 antibiotics was determined using the VITEK 2 system according to EUCAST guidelines. Genes conferring resistance to sulfamethoxazole (sul1, sul2 and sul3), trimethoprim (dfrA1, dfrA12 and dfrA17) and ampicillin (oxa-1 and oxa-2), and virulence genes (ipaBCD, sat, ial, virA, sen, set1A and set1B) were detected by real-time PCR. Clonal relatedness was assessed using ERIC-PCR. Thirty-four Shigella flexneri isolates were isolated (an overall incidence of 14.0%). All the isolates were fully resistant to sulfamethoxazole/trimethoprim (100%) and ampicillin (100%) but susceptible to the other antibiotics tested. The sul1 (79%), sul2 (79%), sul3 (47%), dfrA12 (71%) and dfrA17 (56%) sulfonamide and trimethoprim resistance genes were identified; Oxa-1, oxa-2 and dfrA1 were not detected. The virulence genes ipaBCD (85%), sat (85%), ial (82%), virA (76%), sen (71%), stx (71%), set1A (26%) and set1B (18%) were detected. ERIC-PCR profiling revealed that the Shigella isolates were genetically distinct and clonally unrelated, indicating the potential involvement of genetically distinct S. flexneri in CA-AD in Malawi. The high percentage resistance to ampicillin and sulfamethoxazole/trimethoprim and the presence of several virulence determinants in these isolates emphasises a need for continuous molecular surveillance studies to inform preventive measures and management of Shigella-associated diarrhoeal infections in Malawi.

Correlation between the sulfamethoxazole-trimethoprim resistance of Shigella flexneri and the sul genes

The aim of this study was to discuss the correlation between the sulfamethoxazole-trimethoprim resistance of Shigella flexneri (S. flexneri) and the antibiotic resistance genes sul1, sul2, and sul3 and SXT element.From May 2013 to October 2018, 102 isolates of S. flexneri were collected from the clinical samples in Jinan. The Kirby-Bauer (K-B) test was employed to determine the antibiotic susceptibility of the S. flexneri isolates. The antibiotic resistance rate was analyzed with the WHONET5.4 software. The isolates were subject to the PCR amplification of the sul genes (sul1, sul2, and sul3) and the SXT element. On the basis of the sequencing results, the correlation between the sulfamethoxazole-trimethoprim resistance of the S. flexneri isolates and the sul genes was analyzed.The antibiotic resistance rates of the 102 S. flexneri isolates to ampicillin, streptomycin, chloramphenicol, tetracycline, and sulfamethoxazole-trimethoprim were 90.2%, 90.2%, 88.2%, 88.2%, and 62.7%, respectively. The antibiotic resistance rates of these isolates to cefotaxime, ceftazidime, and ciprofloxacin varied between 20% and 35%. However, these isolates were 100% susceptible to cefoxitin. Positive fragments were amplified from 59.8% (61/102) of the 102 S. flexneri isolates, the sizes of the sul1 and sul2 genes being 338 bp and 286 bp, respectively. The sequence alignment revealed the presence of the sul1 and sul2 genes encoding for dihydrofolate synthase. The carrying rate of the sul1 gene was 13.7% (14/102), and that of the sul2 gene was 48.0% (49/102). No target gene fragments were amplified from the 3 isolates resistant to sulfamethoxazole-trimethoprim. The sul3 gene and SXT element were not amplified from any of the isolates. The testing and statistical analysis showed that the resistance of the S. flexneri isolates to sulfamethoxazole-trimethoprim correlated to the sul1 and sul2 genes.The acquired antibiotic resistance genes sul1 and sul2 were closely associated with the resistance of the 102 S. flexneri isolates to sulfamethoxazole-trimethoprim.

Effect of Psidium guajava (guava) L. Leaf Decoction on Antibiotic-resistant Clinical Diarrhoeagenic Isolates of Shigella spp

Background: Although shigellosis is self-limiting, antibiotics are recommended to minimize the severity of symptoms and reduce mortality rates. However, due to the increasing reports of antibiotic resistance, alternative approaches are needed to combat shigellosis. Interest for research on medicinal plants has increased in recent years, and hence, they can be explored to treat this infectious diarrhoea. Objective: To study the effect of Psidium guajava L. (guava) leaf decoction (GLD) on the antibiotic-resistant clinical isolates of Shigella spp. Materials and Methods: A total of 43 isolated Shigella spp. from diarrhoeal patients were used in this study. The effect of GLD on the bacterial viability was initially assessed. The isolates were divided into two categories: sensitive and resistant to GLD. For sensitive isolates, antibacterial activity of GLD was evaluated while for resistant strains, the ability of GLD for reducing the bacterial invasion of the HEp-2 cell line underwent an investigation. Results: Among the 43 Shigella isolates, GLD affected the growth of 23 strains. The invasion of 9 strains from the 20 remaining resistant isolates was unaffected. Although the number of isolates was less, the data suggested that isolates belonging to S. flexneri serogroup were more sensitive to GLD in comparison with other spp (i.e., sonnei, boydii, and dysenteriae). Conclusion: The results of this study revealed the efficacy of GLD against drug-resistant Shigella spp. and thus could be considered for the treatment of diarrhoea. GLD can be a cost-effective alternative to antibiotics.

Virulence-Related Gene Distribution Among Shigella Isolates in Anhui, China: The Association with Antimicrobial Resistance

Objective

The aim of this study was to investigate the antimicrobial resistance profiles and distribution of virulence-related genes (VRGs) among Shigella isolates in Anhui, China, and to identify the correlation between the VRGs and antimicrobial resistance.

Materials and Methods

A total of 525 non-duplicate Shigella isolates (449 S. flexneri, 68 S. sonnei, 3 S. boydii, and 5 S. dysenteriae) were collected in Anhui Province, China between September 2011 and September 2015. The antimicrobial resistance of the strains was determined by the agar dilution method according to CLSI guidelines. The presence of 16 VRGs, including ipaH, ipaA-D, ial, virB, virF, set, sen, icsA, icsB, sigA, sat, pic, and sepA, was evaluated using PCR amplification and sequencing.

Results

Shigella flexneri was the most abundant (85.5%), followed by S. sonnei (13.0%). The proportion of males with S. flexneri was higher than that of females (57% vs 43%; P<0.0001). The most common resistance pattern was the combination of ampicillin, nalidixic acid, and tetracycline for S. flexneri (90.2%) and S. sonnei (94.1%). Resistance to ciprofloxacin and levofloxacin was more common among S. flexneri than among S. sonnei (49.7% vs.19.1%, P<0.0001; 30.5% vs 10.3%, P=0.001, respectively). All the isolates were positive for the ipaH gene, while the set, sat, pic, and sepA genes were not detected among the S. sonnei isolates. Except for sigA and sen, resistance to chloramphenicol and ciprofloxacin was more common among VRG-positive S. flexneri than among VRG-negative S. flexneri (P<0.05). Furthermore, resistance to ceftriaxone and ceftazidime was more frequently detected among sat- and set-positive S. flexneri than among sat- and set-negative S. flexneri (P<0.05). However, gentamicin resistance was more prevalent among VRG-negative (ial, virF, set, sat, pic, and sepA) S. flexneri than among VRG-positive S. flexneri (P<0.05).

Conclusion

Shigella flexneri remains the predominant species in Anhui, China, and the resistance to fluoroquinolones was more widespread among S. flexneri than among S. sonnei. Shigella flexneri strains harboring specific VRGs were associated with antimicrobial resistance. To the best of our knowledge, this is the first report of the correlation between the VRGs and antimicrobial resistance in Anhui, China.

Emergence of multidrug-resistant Shigella species harboring extended-spectrum beta-lactamase genes in pediatric patients with diarrhea from southwest of Iran

Owing to the scarce evidence about the multidrug-resistant (MDR) beta-lactamase-producing Shigella isolates in Iran, this study aimed to evaluate the occurrence of extended-spectrum beta-lactamases (ESBL) and AmpC β-lactamases in Shigella species collected in the southwest of Iran. This study was conducted on Shigella species isolated from stool samples of pediatric patients aged less than 15 years suffering from diarrhea. These isolates were identified by bacteriology tests, serotyping, and polymerase chain reaction (PCR). The antibiotic resistance was determined by disc diffusion. The production of ESBLs and AmpC was investigated by phenotypic confirmatory tests and PCR. In total, 79 Shigella isolates, including 46.8% (n = 37) of S. flexneri and 53.2% (n = 42) of S. sonnei, were isolated, respectively. The most effective antibiotic was imipenem with 93.7% of susceptibility followed by ampicillin (29.1%), and cotrimoxazole (30.4%).The resistance rates of ceftriaxone, ceftazidime, and cefotaxime were 41.8%, 34.2%, and 41.8%, respectively. Also, a total of 57 (72.2%) isolates showed MDR profiles. The phenotypic tests showed that 43.0% (34/79) of isolates can produce ESBLs, and no one was positive for ApmC. The frequency of bla_TEM and bla_CTX-M were 30.4% and 32.9%, respectively, while the bla_PER, bla_SHV, and AmpC genes were not detected. The ESBL-producing isolates had a significant (p-value ˂ 0.05) resistance rate against ceftriaxone, ceftazidime, cefotaxime, cefepime, erythromycin, and amikacin. The significant prevalence of MDR Shigella isolates harboring ESBL genes highlights the need for effective surveillance measures to prevent the more spread of drug resistance among species.

A high number of multidrug-resistant and predominant genetically related cluster of Shigella flexneri strains isolated over 34 years in Brazil

Shigella flexneri has been a major public health problem in developing countries. This work analyzed the frequency of 16 virulence genes, the genotypic diversity, and the antimicrobial resistance profiles of 130 S. flexneri strains isolated in Brazil. The ipaH gene was found in all the 130 strains. The frequencies of the other genes were variable ial (88.5%), sigA (82.3%), iuc (74.6%), virA (73%), pic (72.3%), virF (57.7%), sat (48.5%), ipaBCD (37%), sen (36%), set1A (35.4%), sepA (30%), set1B (30%), virB (14%), icsA (10%), and ipgD (5.4%). A total of 57 (43.8%) strains were multidrug-resistant. ERIC-PCR grouped 96 of the strains into a single cluster with ≥ 70.4% of similarity, 75 of these strains presented a similarity ≥ 80.9%. PFGE grouped 120 of the strains into a single cluster with 57.4% of similarity and 82 of these strains presented a similarity ≥ 70.6%. In conclusion, the high frequency of some virulence genes reinforces the pathogenic potential of the strains studied. The high rates of MDR strains are alarming once it may lead to failure when antimicrobial treatment is necessary. Genotype techniques reveled a major cluster with high genetic similarity including S. flexneri strains from the different Brazilian states and distinct years of isolation, showing that they probably emerged from a common ancestor.

Molecular characterization of Shigella species isolated from diarrheal patients in Tehran, Iran: phylogenetic typing and its association with virulence gene profiles and a novel description of Shigella invasion associated locus

The present study aims to employ a multiplex PCR-based method for phylogenetic typing of Shigella and determine the frequency of several virulence genes among Shigella phylogenetic clades and species. Species identification, phylogenetic typing of 44 previously diagnosed Shigella isolates, and frequency of virulence genes and loci, virA, virB, virF, ipaBCD, ial, sen, and set1A were investigated through performing several PCR assays. Distribution of virulence genes among Shigella phylogenetic clades and species was determined by the statistical analysis. The identities of 40 isolates out of 44 were confirmed as Shigella, and these isolates were classified in four phylogenetic clades, S1 (7.5%), S2 (52.5%), S3 (20%), and S5 (20%) and 4 species, S. sonnei (52.5%), S. flexneri (22.5%), S. dysenteriae (20%), and S. boydii (5%). The prevalence of virA, virB, virF, ipaBCD, ial, sen, and set1A was determined as 67.5%, 72.5%, 72.5%, 65%, 75%, 40%, and 5%, respectively. The presence of sen, uidA, or set1A was found to be statistically correlated with either of Shigella phylogenetic clades or species. A significant statistically association was also determined between set1A and Shigella phylogenetic clades. Furthermore, the nucleotide sequence of invasion-associated locus (ial) was determined and mapped on Shigella genome through in silico analysis. The current study shows the distribution of Shigella isolates and its key virulence genes within the five recently described phylogenetic clades for the first time in the Asia. This is also the first description of ial nucleotide sequence and its exact location on Shigella genome after its initial identification.

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.

Shigella flexneri: an emerging pathogen

Shigella flexneri is a leading etiologic agent of diarrhea in low socioeconomic countries. Notably, various serotypes in S. flexneri are reported from different regions of the world. The precise approximations of illness and death owing to shigellosis are missing in low socioeconomic countries, although it is widespread in different regions. The inadequate statistics available reveal S. flexneri to be a significant food and waterborne pathogen. All over the world, different antibiotic-resistant strains of S. flexneri serotypes have been emerged especially multidrug-resistant strains. Recently, increased resistance was observed in cephalosporins (3rd generation), azithromycin, and fluoroquinolones. There is a need for a continuous surveillance study on antibiotic resistance that will be helpful in the update of the antibiogram. The shigellosis burden can be reduced by adopting preventive measures like delivery of safe drinking water, suitable sanitation, and development of an effective and inexpensive multivalent vaccine. This review attempts to provide the recent findings of S. flexneri related to epidemiology and the emergence of multidrug resistance.

Antibiotic-Resistant Escherichia coli in Drinking Water Samples from Rural Andean Households in Cajamarca, Peru

Antibiotic resistance in pathogenic bacteria is a serious public health issue. The growing threat is a cause for concern and action to prevent the emergence of new resistant strains and the spread of existing ones to humans via the environment. This study aimed at identifying fecal pathogens in drinking water obtained from rural Andean households from Cajamarca, Peru, and measuring the antibiotic resistance profile of Escherichia coli. The study was embedded within a community-randomized controlled trial among 102 communities in the northern highlands of the Cajamarca region, Peru. Of 314 samples, 55.4% (95% CI [49.7, 61.0], n = 174) were identified as thermotolerant coliforms. Among the samples positive for thermotolerant coliform, E. coli was isolated in 37.3% (n = 117), Klebsiella spp. in 8.0% (n = 25), Enterobacter spp. in 5.1% (n = 16), and Citrobacter spp. in 2.5% (n = 8). Of the 117 E. coli samples, 48.7% (95% CI [39.4, 58.1], n = 57) showed resistance to any antibiotic. The E. coli antibiotic resistance profile showed highest resistance against tetracycline (37.6%), ampicillin (34.2%), sulfamethoxazole-trimethoprim (21.4%), and nalidixic acid (13%). Some 19.7% (95% CI [12.9, 28.0], n = 23) of the E. coli isolates displayed multidrug resistance, defined as resistance to at least three classes of antibiotics. The CTX-M-3 gene, which encodes extended-spectrum resistance to beta-lactamase antibiotics, was found in one isolate. The high prevalence of fecal contamination in drinking water highlights the importance of household water treatment methods. Likewise, the high levels of antibiotic resistance found indicate a need for further research to identify the origins of potential environmental contamination, misuse, or inadequate disposal of antibiotics.

Characterizing Shigella species distribution and antimicrobial susceptibility to ciprofloxacin and nalidixic acid in Latin America between 2000-2015

BACKGROUND

Shigellosis is the second leading cause of diarrheal death globally. The global burden has been complicated by the emergence of Shigella strains resistant to first line antibiotic treatments such as ciprofloxacin. This study aims to describe the epidemiologic distribution of the most common Shigella species, and their antimicrobial susceptibility patterns to ciprofloxacin and nalidixic acid (NA) in Latin America.

METHODS

Laboratory data from 19 countries were obtained through the Latin American Network for Antimicrobial Resistance Surveillance (ReLAVRA) from 2000-2015. The Clinical Laboratory Standards Institute reduced susceptibility breakpoints for Enterobacteriaceae was used to interpret the disc diffusion tests for Shigella susceptibility to ciprofloxacin and NA. Negative binominal regression was used to analyze longitudinal trends of Shigella isolates antimicrobial susceptibility.

RESULTS

79,548 Shigella isolates were tested and reported between 2000-2015. The most common isolated species were S. flexneri (49%), and S. sonnei (28%). There was a steady increase in the proportion of S. sonnei isolates within the region(p<0.001). The average annual percentage increase (AAPI) in nonsusceptibility was 18.4% (p<0.001) for ciprofloxacin (baseline = 0.3); and 13.2%(p<0.001) for NA (baseline = 3). AAPI nonsusceptibility to ciprofloxacin was 13.3% for S. flexneri (p<0.04); and 39.9% for S. sonnei (p<0.001). Honduras, Dominican Republic, Venezuela, and Chile reported the highest increase in nonsusceptibility to ciprofloxacin among all Shigella isolates.

CONCLUSION

There is an increasing trend in Shigella nonsusceptibility to ciprofloxacin and NA, including among the most common shigella species, in Latin America. This rise of nonsusceptibility among Shigella species to commonly used treatments such as ciprofloxacin is alarming and threatens the control and management of this currently treatable infection. Improved data quality, collection and reporting is needed in Latin America to respond effectively to the rising trends observed. This includes the need for quality isolate level epidemiological data; molecular data, and data on antibiotic consumption and use.

Virulence gene profiles of Shigella species isolated from stool specimens in India: its association with clinical manifestation and antimicrobial resistance

Shigella is the major cause of bacillary dysentery worldwide, especially in developing countries. There are several virulence factors essential for the organism to be virulent which are generally present in the virulence plasmid and on chromosomal pathogenicity islands. The present study was undertaken to determine the virulence gene profile of Shigella spp isolated from a clinical specimen and to study their significant association with common clinical symptoms and antimicrobial resistance. Sixty Shigella whole genome sequences, including 22 S. flexneri, 14 S. sonnei, 17 S. boydii and 7 S. dysenteriae were analyzed for the presence of virulence genes. The gene found predominantly in this study were ipaH (90%) followed by sigA (83%), and lpfA (78%) respectively. The virulence genes were significantly higher in S. flexneri, particularly in serotype 2 compared to S. sonnei. Interestingly, a significant association was observed between sigA gene and fever whereas sepA and sigA were found to be associated with diarrhea. Among the studied Shigella isolates, the presence of virulence genes was found higher in isolates resistant to more than three antibiotic classes. The present work revealed the varying incidence of virulence determinants among different Shigella serogroups and shows their contribution to disease severity.

Azithromycin resistance levels and mechanisms in Escherichia coli

Despite azithromycin being used in some countries to treat infections caused by Gram-negative pathogens, no resistance breakpoint for Escherichia coli exists. The aim of this study was to analyse the levels and mechanisms of azithromycin resistance in E. coli. The presence of chromosomal (rplD, rplV and 23S rRNA) mutations, 10 macrolide resistance genes (MRGs) and efflux pump overexpression was determined in 343 E. coli isolates. Overall, 89 (25.9%) isolates had MICs ≥ 32 mg/L to azithromycin, decreasing to 42 (12.2%) when assayed in the presence of Phe-Arg-β-Napthylamide, with 35 of these 42 possessing at least one MRG. Efflux pumps played a role in azithromycin resistance affecting the Minimal Inhibitory Concentration (MIC) levels of 91.2% isolates whereas chromosomal alterations seem to have a minimal role. At least one MRG was found in 22.7% of the isolates with mph(A) being the most commonly found gene. The mph(A) gene plays the main role in the development of azithromycin resistance and 93% of the mph(A)-carrying isolates showed a MIC of 32 mg/L. In the absence of a specific resistance breakpoint our results suggest a MIC of 32 mg/L to be considered in order to detect isolates carrying mechanisms able to confer azithromycin resistance.

Use of quantitative molecular diagnostic methods to assess the aetiology, burden, and clinical characteristics of diarrhoea in children in low-resource settings: a reanalysis of the MAL-ED cohort study

Background

Optimum management of childhood diarrhoea in low-resource settings has been hampered by insufficient data on aetiology, burden, and associated clinical characteristics. We used quantitative diagnostic methods to reassess and refine estimates of diarrhoea aetiology from the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) cohort study.

Methods

We re-analysed stool specimens from the multisite MAL-ED cohort study of children aged 0–2 years done at eight locations (Dhaka, Bangladesh; Vellore, India; Bhaktapur, Nepal; Naushero Feroze, Pakistan; Venda, South Africa; Haydom, Tanzania; Fortaleza, Brazil; and Loreto, Peru), which included active surveillance for diarrhoea and routine non-diarrhoeal stool collection. We used quantitative PCR to test for 29 enteropathogens, calculated population-level pathogen-specific attributable burdens, derived stringent quantitative cutoffs to identify aetiology for individual episodes, and created aetiology prediction scores using clinical characteristics.

Findings

We analysed 6625 diarrhoeal and 30 968 non-diarrhoeal surveillance stools from 1715 children. Overall, 64·9% of diarrhoea episodes (95% CI 62·6–71·2) could be attributed to an aetiology by quantitative PCR compared with 32·8% (30·8–38·7) using the original study microbiology. Viral diarrhoea (36·4% of overall incidence, 95% CI 33·6–39·5) was more common than bacterial (25·0%, 23·4–28·4) and parasitic diarrhoea (3·5%, 3·0–5·2). Ten pathogens accounted for 95·7% of attributable diarrhoea: Shigella (26·1 attributable episodes per 100 child-years, 95% CI 23·8–29·9), sapovirus (22·8, 18·9–27·5), rotavirus (20·7, 18·8–23·0), adenovirus 40/41 (19·0, 16·8–23·0), enterotoxigenic Escherichia coli (18·8, 16·5–23·8), norovirus (15·4, 13·5–20·1), astrovirus (15·0, 12·0–19·5), Campylobacter jejuni or C coli (12·1, 8·5–17·2), Cryptosporidium (5·8, 4·3–8·3), and typical enteropathogenic E coli (5·4, 2·8–9·3). 86·2% of the attributable incidence for Shigella was non-dysenteric. A prediction score for shigellosis was more accurate (sensitivity 50·4% [95% CI 46·7–54·1], specificity 84·0% [83·0–84·9]) than current guidelines, which recommend treatment only of bloody diarrhoea to cover Shigella (sensitivity 14·5% [95% CI 12·1–17·3], specificity 96·5% [96·0–97·0]).

Interpretation

Quantitative molecular diagnostics improved estimates of pathogen-specific burdens of childhood diarrhoea in the community setting. Viral causes predominated, including a substantial burden of sapovirus; however, Shigella had the highest overall burden with a high incidence in the second year of life. These data could improve the management of diarrhoea in these low-resource settings.

Funding

Bill & Melinda Gates Foundation.

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.

Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales, 2015

Objectives

Phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in Shigella sonnei in England and Wales were compared and evaluated.

Methods

WGS data from 341 isolates of S. sonnei isolated between June 2015 and January 2016 were mapped to genes known to be associated with phenotypic AMR. Antimicrobial susceptibility testing was performed on all viable isolates (n = 335).

Results

Fifteen of 335 isolates had a discrepancy between phenotypic and genotypic testing for 1 of the 10 antimicrobial classes tested, equating to 15 (0.45%) discordant results out of a possible 3350 isolate/antimicrobial combinations. All 15 mismatched results were genotypically resistant but phenotypically susceptible. Eleven of the 15 discrepancies were observed in streptomycin resistance profiles. The most common resistance profile was trimethoprim, sulphonamides, tetracyclines and streptomycin, occurring in 97 (28.4%) isolates. Resistances to ciprofloxacin and the third-generation cephalosporins, not detected in England and Wales prior to 2002, were identified in 18.2% and 12% of isolates, respectively. Three hundred and four (89.1%) isolates were MDR. There was no significant association between any of the AMR determinants tested and recent foreign travel in male or female cases. The number of isolates of S. sonnei harbouring blaTEM-1 and ermB/mphA was significantly higher in men who reported no recent travel outside the UK.

Conclusions

The use of WGS for routine public health surveillance is a reliable method for rapid detection of emerging AMR in isolates of S. sonnei.

Differences in tetracycline resistance determinant carriage among Shigella flexneri and Shigella sonnei are not related to different plasmid Inc-type carriage

OBJECTIVES

The aim of this study was to establish the prevalence of the most common molecular mechanisms involved in tetracycline resistance as well as their relationship with plasmid incompatibility (Inc) groups in a collection of Shigella spp. causing traveller's diarrhoea.

METHODS

Tetracycline susceptibility was established in 187 Shigella spp. (74 Shigella flexneri and 113 Shigella sonnei), of which 153 isolates were recovered as a confirmed cause of traveller's diarrhoea. The prevalence of the tet(A), tet(B) and tet(G) genes was analysed by PCR. Eighteen plasmid Inc groups was determined in a subset of 59 isolates.

RESULTS

Among 154 tetracycline-resistant isolates, 122 (79.2%) harboured at least tet(A) or tet(B). The tet(B) gene was the most frequently detected, being present in 70 isolates (45.5%), whilst tet(A) was detected in 57 isolates (37.0%). The tet(G) gene was present in only 11 (7.2%) isolates. Moreover, the tet(A) gene was more frequent in S. sonnei (P=0.0007), whilst the tet(B) gene was more frequent in S. flexneri (P<0.0001). Plasmids belonging to Inc group B (P<0.05) were significantly more frequent among S. flexneri, whilst those belonging to groups K, FIC and FIIA (P<0.05) were preferentially detected among S. sonnei.

CONCLUSION

The prevalence of the tet(A) and tet(B) genes differed between S. sonnei and S. flexneri. Moreover, the prevalence of plasmid Inc groups in S. flexneri and S. sonnei differed. However, no relationship was found between the two phenomena.

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

Background

The ability of Shigella to invade, colonize, and eventually kill host cells is influenced by many virulence factors. However, there is no analysis of related genes in Jiangsu Province of China so far. Shigella flexneri was collected from 13 cities of Jiangsu Province through the provincial Centers for Disease Control (CDC) for analysis of distribution of major virulence genes (ipaH, ipaBCD, ial, virF, virB, sigA, set1A, sepA, sat, pic, set1B and sen) detected by PCR technology.

Results

A total of 545 isolates received were confirmed as S. flexneri which belongs to 11 serotypes of S. flexneri, among which serotype 2a was the most predominant (n = 223, 40.9%). All isolates were positive for ipaH gene, followed by sat (94.1%), sigA (78.9%), set1B (78.0%), pic (77.6%), set1A (74.5%), virF (64.8%), sepA (63.5%), sen (56.9%), ipaBCD (50.5%), ial (47.0%) and virB (47.0%). The presence of virulence genes in different serotypes was distinct. The existence of virulence genes of serotype 1b was generally lower than other serotype-the positive rate for virulence genes was between 0.0 and 14.1% except for ipaH and sat. In addition, virulence genes also fluctuated in different regions and at different times in Jiangsu province. The result of analysis on the relationship between virulence genes of S. flexneri showed that the existence of virulence genes of Shigella could be well represented by multiplex PCR combination ipaH + ial + set1A, which had a high clinical value.

Conclusions

The present study was designed to explore the prevalence of 12 S. flexneri-associated virulence genes. The data showed high diversity of virulence genes with regard to periods, regions and serotypes in Jiangsu Province of China.

Electronic supplementary material

The online version of this article (10.1186/s13099-017-0222-9) contains supplementary material, which is available to authorized users.

Molecular characterization of virulence and antimicrobial resistance profile of Shigella species isolated from children with moderate to severe diarrhea in northeastern Brazil

Molecular characterization of virulence and antimicrobial resistance profiles were determined for Shigella species isolated from children with diarrhea in Fortaleza, Brazil. Fecal specimens were collected along with socioeconomic and clinical data from children with moderate to severe diarrhea requiring emergency care. Shigella spp. were isolated by standard microbiological techniques, and we developed 4 multiplex polymerase chain reaction assays to detect 16 virulence-related genes (VRGs). Antimicrobial susceptibility tests were performed using disk diffusion assays. S. flexneri and S. sonnei were the predominant serogroups. S. flexneri was associated with low monthly incomes; more severe disease; higher number of VRGs; and presence of pic, set, and sepA genes. The SepA gene was associated with more intense abdominal pain. S. flexneri was correlated with resistance to ampicillin and chloramphenicol, whereas S. sonnei was associated with resistance to azithromycin. Strains harboring higher numbers of VRGs were associated with resistance to more antimicrobials. We highlight the correlation between presence of S. flexneri and sepA, and increased virulence and suggest a link to socioeconomic change in northeastern Brazil. Additionally, antimicrobial resistance was associated with serogroup specificity in Shigella spp. and increased bacterial VRGs.

A Study of prevalence of Shigella species and antimicrobial resistance patterns in paediatric medical center, Ahvaz, Iran

BACKGROUND AND OBJECTIVES

Shigella infections are one of the major causes of diarrhea worldwide, and especially in developing countries. Antimicrobial resistance has complicated the empirical treatment. The aim of this study was to define the clinical and antibiotic resistance patterns of Shigella gastroenteritis cases.

MATERIALS AND METHODS

Stool samples of patients with diarrhea and fever diagnosed with shigellosis were collected, from June 2013 to May 2014 at Abuzar Hospital, Iran. All samples were cultured for Shigella spp on selective and differential media. Shigella isolates were evaluated for antimicrobial resistance.

RESULTS

Among 193 Shigella isolates, S. flexneri (64.8%) was the predominant species followed by S. sonnei (32.6%). The most frequent antibiotic resistance observed, was towards co-trimoxazole (89%), ampicillin (77%) and ceftriaxone (51%) and the lowest resistance were seen in ciprofloxacin (1.5%), azithromycin (7%).

CONCLUSION

Due to the high resistance to ceftriaxone, this drug is not recommended as an empirical therapy for shigellosis. However, azithromycin should be used as the first-line treatment for paediatric patients, suffering from shigellosis and ciprofloxacin can be used as an alternative.

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R² = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

In vitro antibacterial activity of poly (amidoamine)-G7 dendrimer

BACKGROUND

Nano-scale dendrimers are synthetic macromolecules that frequently used in medical and health field. Traditional anibiotics are induce bacterial resistence so there is an urgent need for novel antibacterial drug invention. In the present study seventh generation poly (amidoamine) (PAMAM-G7) dendrimer was synthesized and its antibacterial activities were evaluated against representative Gram- negative and Gram-positive bacteria.

METHODS

PAMAM-G7 was synthesized with divergent growth method. The structural and surface of PAMAM-G7 were investigated by transmission electron microscopy, scanning electron microscope and fourier transform infrared. Pseudomonas. aeruginosa (n = 15), E. coli (n = 15), Acinetobacter baumanni (n = 15), Shigella dysenteriae (n = 15), Klebsiella pneumoniae (n = 10), Proteus mirabilis (n = 15), Staphylococcus aureus (n = 15) and Bacillus subtilis (n = 10) have been used for antibacterial activity assay. Additionally, representative standard strains for each bacterium were included. Minimum Inhibitory Concentration (MIC) was determined using microdilution method. Subsequently, Minimum Bactericidal Concentration (MBC) was determined by sub-culturing each of the no growth wells onto Mueller Hinton agar medium. The cytotoxicity of PAMAM-G7 dendrimer were evaluated in HCT116 and NIH 3 T3 cells by MTT assay.

RESULTS

The average size of each particle was approximately 20 nm. PAMAM-G7 was potentially to inhibit both Gram positive and gram negative growth. The MIC50 and MIC90 values were determined to be 2-4 μg/ml and 4-8 μg/ml, respectively. The MBC50 and MBC90 values were found to be 64-256 μg/ml and 128-256 μg/ml, respectively. The cytotoxity effect of dendrimer on HCT116 and NIH 3 T3 cells is dependent upon exposure time to and concentration of dendrimers. The most reduction (44.63 and 43%) in cell viability for HCT116 and NIH 3 T3 cells was observed at the highest concentration, 0.85 μM after 72 h treatmentm, respectively.

CONCLUSIONS

This study we conclude that PAMAM-G7 dendrimer could be a potential candidate as a novel antibacterial agent.

Escherichia coli pathotypes and Shigella sero-groups in diarrheic children in Nairobi city, Kenya

AIM

In the present study, we investigated the prevalence of E. coli pathotypes and Shigella sero-groups and their antimicrobial profiles among diarrheic children in Nairobi city, Kenya.

BACKGROUND

Although diarrheagenic E. coli pathotypes and Shigella sero-groups are leading causes of diarrhea in children under five years in developing countries, their distribution and antimicrobial resistance vary from place to place and over time in a given region.

METHODS

In a cross-sectional study, we enrolled diarrheic children (n=354) under five years seeking treatment at Mbagathi Hospital, Nairobi city, Kenya,. Stool samples were collected from all children for bacterial culture. Bacterial isolation and identification was performed by conventional microbiological methods. Polymerase chain amplification was used to detect aspU, aggR, andpcvd432 for EAEC, est and elt for ETEC, eae for EPEC, stx for EHEC, and ipaH for EIEC and Shigella species. Antimicrobial profile was determined by disk diffusion method.

RESULTS

The prevalence of EAEC, ETEC, EPEC (eae), EIEC (ipaH) was 21.2%, 10.5%, 4.5%, and 0.6%, respectively, while that of mixed infection was 0.6%for ETEC/EAEC and 0.3%for EAEC/EPEC/ETEC. No EHEC strain was isolated. Pathogenetic analysis for EAEC showed that5.9% carried aspU,8.2% possessed both aspU and aggR and 7.1% had a combination of aspU, aggR andpcvd432 while that of ETEC was 2.3% for elt, 6.5% for both elt and est and 1.7% for est. The combination of aspU with aggR, elt and est, and pcvd432 with aggR, aspU and est was 0.3% for each case of ETEC/EAEC mixed infection. The aspU gene co-existed with aggR, pcvd432, eae and elt in the EAEC/EPEC/ETEC mixed infection. The prevalence of S. boydii, S. dysenteriae, S. flexneriand,S. sonnei was 0.8%, 0.6%, 1.7%, and 0.8%, respectively. No E. coli pathotype and shigella co-infection was detected. In addition, both E. coli pathotypes and Shigella species were resistant to ampicillin, trimethoprim/sulfamethoxazole, streptomycin, chloramphenicol and tetracycline while gentamycin and kanamycin resistance occurred in diarrheagenic E. coli.

CONCLUSION

E. coli pathotypes and Shigella sero-groups harboring virulent genes are important causes of diarrhea in children in Kenya. The increasing spectrum of antibiotic resistance in diarrheagenic E. coli and Shigella species necessitates the development of antimicrobial stewardship education-programs to influence prescribing behavior as well as optimizing the use of effective antimicrobials in Kenya.

Decreased Susceptibility to Azithromycin Among Clinical Shigella Isolates from China

The aim of this study was to detect the decreased susceptibility to azithromycin (DSA) and associated mechanisms in Shigella from China. Three hundred and ninety-two Shigella isolates, including 134 Shigella flexneri and 258 Shigella sonnei isolates, were examined for minimum inhibitory concentrations (MICs) and zone sizes to azithromycin by broth microdilution and disk diffusion methods, respectively. The MICs were compared with corresponding zone diameters to find whether there was uniformity between both tests. Twelve macrolide-resistant genes located on mobile elements were determined for the DSA isolates by PCR, and chromosomal efflux pump activity was analyzed using Phe-Arg-β-naphthylamide inhibition test and quantitative real-time PCR. Shigella isolates displayed MICs of 0.125-512 μg/ml and zone sizes of 6-26 mm against azithromycin. There were 80 (20.4%) isolates to be DSA. No significant difference was found between the DSA rates of S. flexneri and S. sonnei isolates (p = 0.052). There was an intimate relativity between MICs and zone diameters (p < 0.001). Only the plasmid-borne mphA conferring high-level DSA was detected in 55.0% (44/80) DSA-Shigella isolates. This study highlighted the prevalence of DSA-Shigella and mphA in the region studied. Clinical laboratories and clinicians should pay attention to the elevated azithromycin MICs in Shigella spp.

The importance of integrons for development and propagation of resistance in Shigella: the case of Latin America

In Latin America, the disease burden of shigellosis is found to coexist with the rapid and rampant spread of resistance to commonly used antibiotics. The molecular basis of antibiotic resistance lies within genetic elements such as plasmids, transposons, integrons, genomic islands, etc., which are found in the bacterial genome. Integrons are known to acquire, exchange, and express genes within gene cassettes and it is hypothesized that they play a significant role in the transmission of multidrug resistance genes in several Gram-negative bacteria including Shigella. A few studies have described antibiotic resistance genes and integrons among multidrug resistant Shigella isolates found in Latin America. For example, in Brazil, Bolivia, Chile, Costa Rica and Peru, class 1 and class 2 integrons have been detected among multidrug resistant strains of Shigella; this phenomenon is more frequently observed in S. flexneri isolates that are resistant to trimethoprim, sulfamethoxazole, streptomycin, ampicillin, chloramphenicol, and tetracycline. The gene cassette sul2, which is frequently detected in Shigella strains resistant to the sulfonamides, suggests that the sulfonamide-resistant phenotype can be explained by the presence of the sul2 genes independent of the integron class detected. It is to be noted that sul3 was negative in all isolates analyzed in these studies. The high frequency of sulfonamide (as encoded by sul2) and trimethoprim resistance is likely to be a result of the recurrent use of trimethoprim sulfamethoxazole as a popular regimen for the treatment of shigellosis. The observed resistance profiles of Shigella strains confirm that ampicillin and trimethoprim-sulfamethoxazole are ineffective as therapeutic options. In-depth information regarding antibiotic resistance mechanism in this pathogen is needed in order to develop suitable intervention strategies. There is a pressing need for regional and local antimicrobial resistance profiling of Shigella to be included as a part of the public health strategy.

Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei

The most common mechanism of trimethoprim (TMP)-resistance is the acquisition of dihydrofolate reductase enzyme resistant to this drug. Previous molecular characterization of TMP-genes resistance in Chilean isolates of Shigella sonnei searching for dfrA1 and dfrA8, showed solely the presence of dfrA8 (formerly dhfrIIIc). However, these genetic markers were absent in S. sonnei strains further isolated during an outbreak in 2009. To identify the TMP-resistance gene in these strains, a genomic DNA library from a TMP-resistant (TMP^R) S. sonnei representative strain for the outbreak was used to clone, select and identify a TMP-resistance marker. The TMP^R clone was sequenced by primer walking, identifying the presence of the dfrA14 gene in the sul2-strA'-dfrA14-‘strA-strB gene arrangement, harbored in a native 6779-bp plasmid. The same plasmid was isolated by transforming with a ~4.2 MDa plasmid extracted from several TMP^RS. sonnei strains into Escherichia coli. This plasmid, named pABC-3, was present only in dfrA14-positive strains and was homologous to a previously described pCERC-1, but different due to the absence of an 11-bp repetitive unit. The distribution of dfrA1, dfrA8, and dfrA14 TMP-resistance genes was determined in 126 TMP^RS. sonnei isolates. Most of the strains (96%) carried only one of the three TMP-resistance genes assessed. Thus, all strains obtained during the 2009-outbreak harbored only dfrA14, whereas, dfrA8 was the most abundant gene marker before outbreak and, after the outbreak dfrA1 seems have appeared in circulating strains. According to PFGE, dfrA14-positive strains were clustered in a genetically related group including some dfrA1- and dfrA8-positive strains; meanwhile other genetic group included most of the dfrA8-positive strains. This distribution also correlated with the isolation period, showing a dynamics of trimethoprim genetic markers prevalent in Chilean S. sonnei strains. To our knowledge, dfrA14 gene associated to a small non-conjugative plasmid was detected for the first time in Shigella. Apparently, the strain causing the outbreak must have been introduced, changing drastically the genetic distribution of trimethoprim resistance in Chilean S. sonnei strains.

pic gene of enteroaggregative Escherichia coli and its association with diarrhea in Peruvian children

Enteroaggregative Escherichia coli (EAEC) causes acute and persistent diarrhea among children, HIV-infected patients, and travelers to developing countries. We have searched for 18 genes-encoding virulence factors associated with aggregative adherence, dispersion, biofilm, toxins, serine protease autotransporters of Enterobacteriaceae (SPATEs) and siderophores, analyzed in 172 well-characterized EAEC strains (aggR(+)) isolated from stool samples of 97 children with diarrhea and 75 healthy controls from a passive surveillance diarrhea cohort study in Peru. Eighty-one different genetic profiles were identified, 37 were found only associated with diarrhea and 25 with control samples. The most frequent genetic profile was aggC(+)aatA(+)aap(+)shf(+)fyuA(+), present in 19 strains, including diarrhea and controls. The profile set1A(+)set1B(+)pic(+) was associated with diarrhea (P < 0.05). Of all genes evaluated, the most frequent were aatA (CVD 342) present in 159 strains (92.4%) and fyuA in 157 (91.3%). When EAEC strains were analyzed as a single pathogen (excluding co-infections), only pic was associated with diarrhea (P < 0.05) and with prolonged diarrhea (diarrhea ≥ 7 days) (P < 0.05). In summary, this is the first report on the prevalence of a large set of EAEC virulence genes and its association with diarrhea in Peruvian children. More studies are needed to elucidate the exact role of each virulence factor.

Virulence factors profiles and ESBL production in Escherichia coli causing bacteremia in Peruvian children

The presence of 25 virulence genes (VGs), genetic phylogroups, quinolone-resistance and Extended Spectrum β-lactamase (ESBL)-production was assessed in 65 Escherichia coli isolates from blood cultures in children <5 years in Peru. The most frequent VGs were fimA (89.2%), iutA (83.1%), agn43 (72.3%), iucA (67.7%), and fyuA (49.2%). The isolates belonged to D (47.7%), A (26.1%), B1 (21.5%), and B2 (4.6%) phylogroups. D + B2 isolates presented a high number of fimA, hly, papC, sat, and fyuA genes. Quinolone-susceptible (22 isolates - 33.8%) and ESBL-negative (31 isolates - 47.7%) isolates carried more VGs that their respective counterparts (5.7 vs. 4.7 and 5.3 vs. 4.4 respectively); the frequency of the fyuA, aat, aap, and hly genes significantly differed between quinolone-resistant and quinolone-susceptible isolates. Neonatal sepsis isolates tended to be more quinolone-resistant (P = 0.0697) and ESBL-producers (P = 0.0776). Early-onset neonatal sepsis isolates possessed a high number of VGs (5.2 VGs), especially in neonates of ≤1 day (5.9 VGs).