Predominance and high antibiotic resistance of the emerging Clostridium difficile genotypes NAP _CR1 and NAP9 in a Costa Rican hospital over a 2-year period without outbreaks

Abstract

Clostridium difficile is the major causative agent of nosocomial antibiotic-associated diarrhea. In a 2009 outbreak of C. difficile-associated diarrhea that was recorded in a major Costa Rican hospital, the hypervirulent NAP1 strain (45%) predominated together with a local genotype variant (NAPCR1, 31%). Both strains were fluoroquinolone-resistant and the NAPCR1 genotype, in addition, was resistant to clindamycin and rifampicin. We now report on the genotypes and antibiotic susceptibilities of 68 C. difficile isolates from a major Costa Rican hospital over a 2-year period without outbreaks. In contrast to our previous findings, no NAP1 strains were detected, and for the first time in a Costa Rican hospital, a significant fraction of the isolates were NAP9 strains (n=14, 21%). The local NAPCR1 genotype remained prevalent (n=18, 26%) and coexisted with 14 strains (21%) of classic hospital NAP types (NAP2, NAP4, and NAP6), eight new genotypes (12%), four environmental strains classified as NAP10 or NAP11 (6%), three strains without NAP designation (4%) and seven non-toxigenic strains (10%). All 68 strains were resistant to ciprofloxacin, 88% were resistant to clindamycin and 50% were resistant to moxifloxacin and rifampicin. Metronidazole and vancomycin susceptibilities were universal. The NAPCR1 and NAP9 strains, which have been associated with more severe clinical infections, were more resistant to antibiotics than the other strains. Altogether, our results confirm that the epidemiology of C. difficile infection is dynamic and that A−B+ strains from the NAP9 type are on the rise not only in the developed world. Moreover, our results reveal that the local NAPCR1 strains still circulate in the country without causing outbreaks but with equally high antibiotic-resistance rates and levels.

The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile

“…C. difficile NAP CR1 /RT012/ST-54 isolates caused an epidemic in Costa Rica and are now widely distributed in hospitals from this country (López-Ureña et al, 2016 ). Genome sequence analysis of several of these isolates in an earlier study revealed the presence of prophages that were novel, particularly in genome size and composition compared to other C. difficile phage genomes (Ramírez-Vargas et al, 2017 ).…”

“…However, the epidemiology of CDI changes over time in groups at risk of infection and in dominant strains (Goudarzi et al, 2014 ), such that now community-acquired CDI is more prevalent and the “hypervirulent” epidemic NAP1/RT027 strains are no longer predominant. Instead, the NAP7/RT078 or NAP9/RT017 strains are emerging among humans and animals from Asia, Australia, Costa Rica (López-Ureña et al, 2016 ) and other regions of the world (Janoir, 2016 ). Although reasons for this change are unclear, phage and other mobile genetic elements (MGE) are thought to contribute to the evolution of C. difficile , as it has been demonstrated for other human pathogens (Davies et al, 2016 ).…”

“…A group of C. difficile strains classified as NAP CR1 /RT012/ST-54 caused a serious outbreak of CDI in a large Costa Rican hospital in 2009 (Quesada-Gómez et al, 2010 ). These isolates belong to the MLST Clade 1, show increased virulence in cell and animal models (Quesada-Gómez et al, 2015 ), and are now endemic in Costa Rica hospitals (López-Ureña et al, 2016 ). Their genomes were found to be extremely diverse, as indicated by their distribution in at least 10 Sma I macrorestriction patterns, the small size of their core genome (74%), and the large number of MGE-associated genes in their genomes (Ramírez-Vargas et al, 2017 ).…”

Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

“…The NAP CR1 /ST54 strains show high virulence in animal models despite their close phylogenetic relationship to nonepidemic ST54 isolates such as the C. difficile reference strain 630 (CD630) ( Quesada-Gómez et al. 2015 ; López-Ureña et al. 2016 ).…”

A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements

“…NAP CR1 isolates induced a severe clinical presentation, were associated with mortality and recurrence rates comparable to those of NAP1/RT027 strains, and produced a strong inflammatory reaction in animal models (12). These strains continue to circulate in several hospitals of this Central American country (13), and their closest known relative is the multidrug-resistant (MDR) strain CD630, which is also classified as RT012/ST-54 and has been claimed to carry bona fide determinants for tetracycline, erythromycin, daunorubicin, bacitracin, nogalamycin, beta-lactam, tellurite, streptogramin, and lantibiotic resistance (14).…”