Molecular, microbiological and clinical characterization of Clostridium difficile isolates from tertiary care hospitals in Colombia

Regional and temporal genotype profiling of Clostridioides difficile in a multi-institutional study in Japan

Clostridioides difficile, a cause of healthcare-associated infections, poses a significant global health threat. This multi-institutional retrospective study focuses on epidemic dynamics, emphasizing minor and toxin-negative clinical isolates through high-resolution genotyping. The genotype of the C. difficile clinical isolates during 2005 to 2022 was gathered from 14 hospitals across Japan (N = 982). The total number of unique genotypes was 294. Some genotypes were identified in every hospital (cross-regional genotypes), while others were unique to a specific hospital or those in close geographic proximity (region-specific genotypes). Notably, a hospital located in a sparsely populated prefecture exhibited the highest prevalence of region-specific genotypes. The isolation rate of cross-regional genotypes positively correlated with the human mobility flow. A 6-month interval analysis at a university hospital from 2019 to 2021 revealed a temporal transition of the genotype dominance. The frequent isolation of identical genotypes over a brief timeframe did not always align with the current criteria for defining nosocomial outbreaks. This study highlights the presence of diverse indigenous C. difficile strains in regional environments. The cross-regional strains may have a higher competency to spread in the human community. The longitudinal analysis underscores the need for further investigation into potential nosocomial spread.

Best Practices in the Management of Clostridioides difficile Infection in Developing Nations

Clostridioides difficile infection (CDI) is a well-known cause of hospital-acquired infectious diarrhea in developed countries, though it has not been a top priority in the healthcare policies of developing countries. In the last decade, several studies have reported a wide range of CDI rates between 1.3% and 96% in developing nations, raising the concern that this could represent a healthcare threat for these nations. This review defines developing countries as those with a human development index (HDI) below 0.8. We aim to report the available literature on CDI epidemiology, diagnostics, management, and prevention in developing countries. We identify limitations for CDI diagnosis and management, such as limited access to CDI tests and unavailable oral vancomycin formulation, and identify opportunities to enhance CDI care, such as increased molecular test capabilities and creative solutions for CDI. We also discuss infection prevention strategies, including antimicrobial stewardship programs and opportunities emerging from the COVID-19 pandemic, which could impact CDI care.

Clostridioides Difficile in Latin America: An Epidemiological Overview

Clostridioides difficile infection is one of the most significant causes of nosocomial diarrhea associated with antibiotic use worldwide. In recent years, the incidence of Clostridioides difficile infection in Latin American countries has increased due to the emergence and spread of epidemic Clostridioides difficile strains, such as RT027/NAP1/ST1, RT078/ST11, and RT017/ST37; additionally, endemic multi-drug-resistant strains have recently appeared due to the lack of heterogeneous diagnostic algorithms and guidelines for antibiotic use in each country. The aim of this review is to present the latest information regarding Clostridioides difficile and emphasize the importance of epidemiological surveillance of this pathogen in Latin American countries.

Clostridioides difficile in Latin America: A comprehensive review of literature (1984-2021)

This narrative review summarizes literature on C. difficile and C. difficile infections (CDI) that emerged from Latin America (LA) between 1984 and 2021. The revised information includes papers in English, Spanish, or Portuguese that were retrieved from the databases Pubmed, Scopus, Web of Science, Google Scholar, Scielo, and Lilacs. Information is presented chronologically and segregated in subregions, focusing on clinical presentation, risk factors, detection and typing methods, prevalence and incidence rates, circulating strains, and, when available, phenotypic traits, such as antimicrobial susceptibility patterns. Studies dealing with cases, clinical aspects of CDI, and performance evaluations of diagnostic methods predominated. However, they showed substantial differences in case definitions, measuring units, populations, and experimental designs. Although a handful of autochthonous strains were identified, predominantly in Brazil and Costa Rica, the presentation and epidemiology of CDI in LA were highly comparable to what has been reported in other regions of the world. Few laboratories isolate and type this bacterium and even less generate whole genome sequences or perform basic science on C. difficile. Less than ten countries lead academic productivity on C. difficile or CDI-related topics, and information from various countries in Central America and the Caribbean is still lacking. The review ends with a global interpretation of the data and recommendations to further develop and consolidate this discipline in LA.

Predictive factors, outcomes, and molecular epidemiology of Clostridioides difficile diarrhea in Brazilian hospitals

Little is known about the role of lineage of strains of Clostridioides difficile (CD) on the clinical presentation of CD infection (CDI) in Latin America, especially regarding the treatment response. We conducted a multicenter, prospective study to investigate the predictive factors and treatment outcomes of CDI in hospitalized patients and to performed phenotypical and molecular characterization of CD strains. A total of 361 diarrheic patients at 5 hospitals from different regions of the country were enrolled. All stool samples were tested for glutamate dehydrogenase (GDH), toxins A and B, and toxin genes using a nucleic acid amplification test (NAAT). Specimens were cultured and susceptibility profile and whole-genome sequencing (WGS) were performed. CDI positivity was 15% (56/377). Predictive factors for CDI were prior use of meropenem (OR 4.09, 95% CI 2.097-7.095; p<0.001), mucus in stools (OR 3.29; 95% CI 1.406-7.722; p=0.006) and neutrophil left-shift with >20% of bands (OR 3.77; 95% IC 1.280-11.120; p=0.016). Overall mortality was 19%, with no deaths attributed to CDI. Oral metronidazole was used in 74% of cases, with 85% of cure and 14% of recurrence. A total of 35 CD isolates were recovered, all of them susceptible to metronidazole and vancomycin. The WGS revealed 17 different STs, six of which were novel. ST42 was the most common ST and hypervirulent strains were not found. Severe CDI were caused by ST42, ST5, ST8, ST48, ST33 and a novel ST667. The ermB gene was more frequently found in isolates of ST42 (p=0.004).

Unique Clindamycin-Resistant Clostridioides difficile Strain Related to Fluoroquinolone-Resistant Epidemic BI/RT027 Strain

During a surveillance study of patients in a long-term care facility and the affiliated acute care hospital in the United States, we identified a Clostridioides difficile strain related to the epidemic PCR ribotype (RT) 027 strain associated with hospital outbreaks of severe disease. Fifteen patients were infected with this strain, characterized as restriction endonuclease analysis group DQ and RT591. Like RT027, DQ/RT591 contained genes for toxin B and binary toxin CDT and a tcdC gene of identical sequence. Whole-genome sequencing and multilocus sequence typing showed that DQ/RT591 is a member of the same multilocus sequence typing clade 2 as RT027 but in a separate cluster. DQ/RT591 produced a similar cytopathic effect as RT027 but showed delayed toxin production in vitro. DQ/RT591 was susceptible to moxifloxacin but highly resistant to clindamycin. Continued surveillance is warranted for this clindamycin-resistant strain that is related to the fluoroquinolone-resistant epidemic RT027 strain.

Assessing risk factors, mortality, and healthcare utilization associated with Clostridioides difficile infection in four Latin American countries

Background

Clostridioides difficile infection (CDI) is the most common cause of healthcare-associated infections in Western countries. Risk factors, mortality, and healthcare utilization for CDI in Latin America are poorly understood. This study assessed risk factors and burden associated with nosocomial CDI in four Latin American countries.

Methods

This retrospective, case-control study used databases and medical records from 8 hospitals in Argentina, Brazil, Chile, and Mexico to identify nosocomial CDI cases from 2014 − 2017. Cases were patients aged ≥18 years with diarrhea and a positive CDI test ≥72 h after hospital admission. Two controls (without diarrhea; length of hospital stay [LOS] ≥3 days; admitted ±14 days from case patient; shared same ward) were matched to each case. CDI-associated risk factors were assessed by univariate and multivariable analyses. CDI burden (LOS, in-hospital mortality) was compared between cases and controls.

Results

The study included 481 cases and 962 controls. Mean age and sex were similar between cases and controls, but mean Charlson comorbidity index (4.3 vs 3.6; p < 0.001) and recent hospital admission (35.3% vs 18.8%; p < 0.001) were higher among cases. By multivariable analyses, CDI risk was associated with prior hospital admission within 3 months (odds ratio [OR], 2.08; 95% CI: 1.45, 2.97), recent antibiotic use (ie, carbapenem; OR, 2.85; 95% CI: 1.75, 4.64), acid suppressive therapy use (OR, 1.71; 95% CI: 1.14, 2.58), and medical conditions (ie, renal disease; OR, 1.48; 95% CI: 1.19, 1.85). In-hospital mortality rate (18.7% vs 6.9%; p < 0.001) and mean overall LOS (33.5 vs 18.8 days; p < 0.001) were higher and longer, respectively, in cases versus controls.

Conclusion

Antibiotic exposure, preexisting medical conditions, and recent hospital admission were major risk factors for CDI in Argentina, Brazil, Chile, and Mexico. CDI was associated with increased in-hospital risk of death and longer LOS. These findings are consistent with published literature in Western countries.

Prevention of Clostridioides difficile in hospitals: A position paper of the International Society for Infectious Diseases

Clostridioides difficile infection is an increasing presence worldwide. Prevention is multipronged, reflecting a complex and evolving epidemiology. Multiple guidelines exist regarding the prevention of C. difficile infection in healthcare settings; however, existing guidelines do not address C. difficile in low- and middle-income countries (LMIC). Nevertheless, the prevalence of C. difficile in LMIC likely parallels, if not exceeds, that of high-income countries, and LMIC may experience additional challenges in C. difficile diagnosis and control. A panel of experts was convened by the International Society for Infectious Diseases (ISID) to review the current state of C. difficile infections globally and make evidence-based recommendations for infection prevention that are broadly applicable.

Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes

There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.

AM, Álvarez-Lobos M, Quesada-Gómez C, Paredes-Sabja D, Rodríguez C. Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico

Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.

Clostridioides difficile ribotype 106: A systematic review of the antimicrobial susceptibility, genetics, and clinical outcomes of this common worldwide strain

Clostridioides difficile typing is invaluable for the investigation of both institution-specific outbreaks as well as national surveillance. While the epidemic ribotype 027 (RT027) has received a significant amount of resources and attention, ribotype 106 (RT106) has become more prevalent throughout the past decade. The purpose of this systematic review was to comprehensively summarize the genetic determinants, antimicrobial susceptibility, epidemiology, and clinical outcomes of infection caused by RT106. A total of 68 articles published between 1999 and 2019 were identified as relevant to this review. Although initially identified in the United Kingdom in 1999, RT106 is now found worldwide and became the most prevalent strain in the United States in 2016. Current data indicate that RT106 harbors the tcdA and tcdB genes, lacks binary toxin genes, and does not contain any deletions in the tcdC gene, which differentiates it from other epidemic strains, including ribotypes 027 and 078. Interestingly, RT106 produces more spores than other strains, including RT027. Overall, RT106 is highly resistant to erythromycin, clindamycin, fluoroquinolones, and third-generation cephalosporins. However, the MIC90 in most studies are one to two fold dilutions below the epidemiologic cut-off values of metronidazole and vancomycin, suggesting both are acceptable treatment options from an in vitro perspective. The few clinical outcomes studies available concluded that RT106 causes less severe disease than RT027, but patients were significantly more likely to experience multiple CDI relapses when infected with a RT106 strain. Specific areas warranting future study include potential survival advantages provided by genetic elements as well as a more robust investigation of clinical outcomes associated with RT106.

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Background

Clostridium difficile infection (CDI) is an emerging healthcare problem in the world. The purpose of this study was to perform a systematic epidemiological research of CDI in Tongji hospital, the central of China.

Methods

Stool samples from hospitalized adults suspected of CDI were enrolled. The diagnosis of CDI were based on the combination of clinical symptoms and laboratory results. Clinical features of CDI and non-CDI patients were compared by appropriate statistical tests to determine the risk factors of CDI. Multilocus sequence typing (MLST) was employed for molecular epidemiological analysis. Susceptibility testing and relevant antimicrobial agent resistance genes were performed as well.

Results

From June 2016 to September 2017, 839 hospitalized adults were enrolled. Among them, 107 (12.8%, 107/839) patients were C. difficile culture positive, and 73 (8.7%, 73/839) were infected with toxigenic C. difficile (TCD), with tcdA + tcdB+ strains accounting for 90.4% (66/73) and tcdA-tcdB+ for 9.6% (7/73). Meanwhile, two TCD strains were binary toxin positive and one of them was finally identified as CD027. Severe symptoms were observed in these two cases. Multivariate analysis indicated antibiotic exposure (p = 0.001, OR = 5.035) and kidney disease (p = 0.015, OR = 8.329) significantly increased the risk of CDI. Phylogenetic tree analysis demonstrated 21 different STs, including one new ST (ST467); and the most dominant type was ST54 (35.6%, 26/73). Multidrug-resistant (MDR) TCD were 53.4% (39/73); resistance to ciprofloxacin, erythromycin, and clindamycin were > 50%. Other antibiotics showed relative efficiency and all strains were susceptible to metronidazole and vancomycin. All moxifloxacin-resistant isolates carried a mutation in GyrA (Thr82 → Ile), with one both having mutation in GyrB (Ser366 → Ala).

Conclusions

Knowledge of epidemiological information for CDI is limited in China. Our finding indicated tcdA + tcdB+ C. difficile strains were the dominant for CDI in our hospital. Significant risk factors for CDI in our setting appeared to be antibiotic exposure and kidney disease. Metronidazole and vancomycin were still effective for CDI. Although no outbreak was observed, the first isolation of CD027 in center China implied the potential spread of this hypervirulent clone. Further studies are needed to enhance our understanding of the epidemiology of CDI in China.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3841-6) contains supplementary material, which is available to authorized users.

Clostridium difficile-associated Diarrhea in Developing Countries: A Systematic Review and Meta-Analysis

INTRODUCTION

The prevalence of Clostridium difficile infection is rapidly increasing worldwide, but prevalence is difficult to estimate in developing countries where awareness, diagnostic resources, and surveillance protocols are limited. As diarrhea is the hallmark symptom, we conducted a systematic review and meta-analysis to determine the prevalence and incidence of C. difficile infection in patients in these regions who presented with diarrhea.

METHODS

We conducted a systematic literature search of MEDLINE/PubMed, Scopus, and Latin-American and Caribbean Health Sciences Literature databases to identify and analyze data from recent studies providing prevalence or incidence rates of C. difficile-associated diarrhea in developing countries within four regions: Africa-Middle East, developing Asia, Latin America, and China. Our objectives were to determine the current prevalence and incidence density rates of first episodes of C. difficile-associated diarrhea in developing countries.

RESULTS

Within the regions included in our analysis, prevalence of C. difficile infection in patients with diarrhea was 15% (95% CI 13-17%) (including community and hospitalized patients), with no significant difference across regions. The incidence of C. difficile infection in 17 studies including this information was 8.5 per 10,000 patient-days (95% CI 5.83-12.46). Prevalence was significantly higher in hospitalized patients versus community patients (p  = 0.0227).

CONCLUSION

Our prevalence estimate of 15% is concerning; however, low awareness and inconsistent diagnostic and surveillance protocols suggest this is markedly underestimated. Enhanced awareness and management of C. difficile infection in patients with diarrhea, along with improvements in infection control and surveillance practices, should be implemented to reduce prevalence of C. difficile-associated diarrhea in developing countries.

FUNDING

Pfizer Inc.

Molecular epidemiology of Clostridioides difficile and risk factors for the detection of toxin gene-positive strains

In this study, we investigated all Clostridioides difficile strains isolated from stool samples in Nagasaki University Hospital between January 2012 and December 2014. Toxin genes (tcdA, tcdB and cdtA/cdtB) were analyzed for multiplex PCR in a total of 213 strains. In the toxin gene-positive strain, PCR ribotyping was conducted using capillary gel electrophoresis-based PCR and the Webribo database. Patients' backgrounds were analyzed by departments, disorders, antimicrobials, and clinical dates. The positive rates of tcdA, tcdB, and cdtA/cdtB genes were 62.9%, 63.4%, and 2.8%, respectively. The most frequent PCR ribotype was 047 (14.1%), followed by 014/0 (11.1%) and 002/0 (8.2%). In univariate analysis, the risk factors for the detection of toxin gene-positive strains in patients were older age (p = 0.0036), over ≥ 65 years old (p = 0.0175), the patients hospitalized at Department of Digestive Surgery (P = 0.0059), higher CRP level (P = 0.0395), and lower albumin level (p = 0.0014). In the multivariate analysis, the risk factor for detection of toxin gene-positive strains was the patients hospitalized at Department of Digestive Surgery (OR; 4.62, 95% CI; 1.18-18.0, p = 0.0274). In this study, the percentage of toxin gene-positive and cdtA/cdtB gene-positive strains was almost the same as that reported in previous studies, but the ribotype was different. In addition, we revealed that the risk factor associated with the detection of toxin gene-positive strains was the patients hospitalized at Department of digestive surgery.

Subtyping of Clostridium difficile PCR ribotypes 591, 106 and 002, the dominant strain types circulating in Medellin, Colombia

We aimed to achieve a higher typing resolution within the three dominant Clostridium difficile ribotypes (591,106 and 002) circulating in Colombia. A total of 50 C. difficile isolates we had previously typed by PCR-ribotyping, representing the major three ribotypes circulating in Colombia, were analyzed. Twenty-seven isolates of ribotype 591, 12 of ribotype 106 and 11 of ribotype 002 were subtyped by multiple locus variable-number tandem-repeat analysis (MLVA). The presence of the PaLoc genes (tcdA/tcdB), toxin production in culture and antimicrobial susceptibility were also determined. From the total C. difficile ribotypes analyzed, 20 isolates (74%) of ribotype 591, nine (75%) of ribotype 106 and five (45.5%) of ribotype 002 were recovered from patients with Clostridium difficile infection (CDI). MLVA allowed us to recognize four and two different clonal complexes for ribotypes 591 and 002, respectively, having a summed tandem-repeat difference (STRD) <2, whereas none of the ribotype 106 isolates were grouped in a cluster or clonal complex having a STRD >10. Six ribotype 591 and three ribotype 002 isolates belonging to a defined clonal complex were isolated on the same week in two different hospitals. All ribotypes harbored either tcdA⁺/tcdB⁺ or tcdA^-/tcdB⁺ PaLoc genes. Moreover, 94% of the isolates were positive for toxin in culture. All isolates were susceptible to vancomycin and metronidazole, while 75% to 100% of the isolates were resistant to clindamycin, and less than 14.8% of ribotype 591 isolates were resistant to moxifloxacina. No significant differences were found among ribotypes with respect to demographic and clinical patients’ data; however, our results demonstrated a high molecular heterogeneity of C. difficile strains circulating in Colombia.

Assessing the Burden of Clostridium difficile Infection in Low- and Middle-Income Countries

In contrast to the significant resources invested in the diagnosis and prevention of Clostridium difficile infection (CDI) in resource-rich settings, in resource-limited settings patients with community- and hospital-acquired diarrhea may not routinely be tested for CDI. Is CDI actually less frequent or severe in resource-limited settings, or might we be missing an important opportunity to prevent CDI-related morbidity and mortality (and to promote antibiotic stewardship) in these settings? Here, we review the literature to assess the overall burden of CDI in low- and middle-income countries.

Community-acquired infection with hypervirulent Clostridium difficile isolates that carry different toxin and antibiotic resistance loci: a case report

Background

Clostridium difficile infection (CDI) leads to the onset of antibiotic-associated diarrhea (AAD) and a wide range of gastrointestinal pathologies. Currently, CDI is one of the most important opportunistic infections at the intrahospital level and an exponential increase in community-acquired infections has been reported. Herein, we evaluated the relationships (at phylogenetic and genetic population structure levels), as well as the molecular toxigenic and antibiotic resistance profiles of a set of isolates established from a case of community acquired-CDI.

Case presentation

A 30-year-old woman with no history of hospitalization who was exposed to antibiotics (ampicillin/sulbactam and metronidazole) after a cat-bite wound was presented. The patient had a continuous episode of diarrhea; a stool sample was then collected and community acquired-CDI was confirmed by molecular tests and in vitro culture. Seven isolates were established and subsequently subjected to: (i) Multilocus sequence typing, all isolates belonging to ST-1 (associated with hypervirulent strain (027/BI/NAP1); (ii) description of their toxigenic profile: two of the isolates (Gcol.49 and Gcol.91) were positive for the genes coding for the major toxins (tcdA and tcdB) and their negative regulator (tcdC). All isolates were positive for the cdtB gene encoding one of the binary toxin subunits, while only two (Gcol.51 and Gcol.52) were positive for cdtA; and (iii) identification of antibiotic resistance molecular markers, where there was no difference in gyrA or gyrB gene polymorphisms (related to quinolone resistance), but rather at loci presence/absence, being just one isolate negative, whereas the others showed a differential presence of the tet, ermB and Tn916 regions. The former was associated with resistance to tetracycline and the other two for erythromycin/clindamycin.

Conclusions

This case represents the first report of community acquired-CDI in Colombia associated with hypervirulent strains and shows that isolates obtained from a single patient can carry different toxin and antibiotic resistance loci.

Electronic supplementary material

The online version of this article (10.1186/s13099-017-0212-y) contains supplementary material, which is available to authorized users.