Development of ceftriaxone resistance in Salmonella enterica serotype Oranienburg during therapy for bacteremia

Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, whole-genome sequencing (WGS) was used to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement among susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50-60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring bla CMY- and bla CTX-M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.

The contribution of nano-based strategies in overcoming ceftriaxone resistance: a literature review

Antimicrobial drug resistance, including resistance to multiple antibiotics, is continuously increasing. According to research findings, many bacteria resistant to other antibiotics were susceptible to ceftriaxone. However, over the last few years, ceftriaxone resistance has become growing and extremely worrisome challenge to the global healthcare system and several strategies have been initiated to contain the spread of antimicrobial drug resistance. Its extended use for therapeutic or preventative measures in humans and farm animals resulted in the development and spread of resistance. Recent advances in nanotechnology also offer novel formulations based on distinct types of nanostructure particles with different sizes and shapes, and flexible antimicrobial properties. For ceftriaxone, several nanostructured formulations through conjugation, intercalation, encapsulation with lipid carrier, and polymeric films have been investigated by different groups with promising results in combating the development of resistance. This review addressed the existing knowledge and practice on the contribution of nano-based delivery approaches in overcoming ceftriaxone resistance. Evidences have been generated from published research articles using major search electronic databases such as PubMed, Medline, Google Scholar, and Science Direct.

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State

Salmonella enterica serotype Typhimurium (S. Typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using New York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using whole-genome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. The two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. Typhimurium to the twentieth century, largely within the era of antibiotic usage.

Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a global public health concern due to increasing antimicrobial resistance (AMR). Characterization of S Typhi genomes for AMR and the evolution of different lineages, especially in countries where typhoid fever is endemic such as Bangladesh, will help public health professionals to better design and implement appropriate preventive measures. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh during 1999 to 2013 and compared those sequences with data from a recent outbreak in Pakistan reported previously by E. J. Klemm, S. Shakoor, A. J. Page, F. N. Qamar, et al. (mBio 9:e00105-18, 2018, https://doi.org/10.1128/mBio.00105-18), and a laboratory surveillance in Nepal reported previously by C. D. Britto, Z. A. Dyson, S. Duchene, M. J. Carter, et al. [PLoS Negl. Trop. Dis. 12(4):e0006408, 2018, https://doi.org/10.1371/journal.pntd.0006408]. WGS had high sensitivity and specificity for prediction of ampicillin, chloramphenicol, co-trimoxazole, and ceftriaxone AMR phenotypes but needs further improvement for prediction of ciprofloxacin resistance. We detected a new local lineage of genotype 4.3.1 (named lineage Bd) which recently diverged into a sublineage (named Bdq) containing qnr genes associated with high-level ciprofloxacin resistance. We found a ceftriaxone-resistant isolate with the bla _CTX-M-15 gene and a genotype distinct from the genotypes of extensively drug-resistant (XDR) isolates from Pakistan. This result suggests a different source and geographical origin of AMR. Genotype 4.3.1 was dominant in all three countries but formed country-specific clusters in the maximum likelihood phylogenetic tree. Thus, multiple independent genetic events leading to ciprofloxacin and ceftriaxone resistance took place in these neighboring regions of Pakistan, Nepal, and Bangladesh. These independent mutational events may enhance the risk of global spread of these highly resistant clones. A short-term global intervention plan is urgently needed.IMPORTANCE Typhoid fever, caused by Salmonella enterica serovar Typhi, is responsible for an estimated burden of approximately 17 million new episodes per year worldwide. Adequate and timely antimicrobial treatment invariably cures typhoid fever. The increasing antimicrobial resistance (AMR) of S Typhi severely limits the treatment options. We studied whole-genome sequences (WGS) of 536 S Typhi isolates collected in Bangladesh between 1999 and 2013 and compared those sequences with data from a recent outbreak in Pakistan and a laboratory surveillance in Nepal. The analysis suggests that multiple ancestral origins of resistance against ciprofloxacin and ceftriaxone are present in three countries. Such independent genetic events and subsequent dissemination could enhance the risk of a rapid global spread of these highly resistant clones. Given the current treatment challenges, vaccination seems to be the most appropriate short-term intervention to reduce the disease burden of typhoid fever at a time of increasing AMR.

Molecular epidemiology of the emerging ceftriaxone resistant non-typhoidal Salmonella in southern Taiwan

BACKGROUND/PURPOSE

The increasing trend of ceftriaxone resistant non-typhoidal Salmonella (NTS) worldwide is of serious concern, however, data is lacked in southern Taiwan.

METHODS

Salmonella isolates were collected at a regional hospital in Kaohsiung during 2004-2013. Ceftriaxone resistant NTS isolates were further characterized for beta-lactamases, typed by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and their plasmids were analyzed by PCR replicon typing and plasmid mutilocus sequence typing.

RESULTS

Among 528 NTS isolates, the most common serogroup is serogroup B (44.9%), followed by serogroup D, and serogroup C. Eleven (2.1%) isolates were resistant to ceftriaxone and were distributed in three peak periods (2010, 2011, and 2013). PFGE and MLST revealed the ten serogroup B isolates were of two clones. Beta-lactamase genes were detected in 10 of the 11 isolates, including CMY-2 (5 isolates), TEM-1 (2), CTX-M-14 (1), and 2 isolates carried both TEM-1 and CMY-2. Plasmid incompatibility types were identified in 9 (81.8%) isolates; three were IncI1, three was IncHI2, one was IncFIB and two had both replicons of IncI1 and IncHI2. The only ESBL gene bla_CTM-X-14 was found in an isolate with plasmid belonged to IncHI2, which has not been reported in NTS in Taiwan before. Most MLST types and plasmid MLST types of NTS isolates in this study are different from those in northern Taiwan.

CONCLUSION

Though clonal spread of ceftriaxone resistant NTS was suggested by PFGE and MLST, plasmid characterization and beta-lactamase detection revealed their plasmid types and beta-lactamase types were different.

Changes in epidemiology and antimicrobial susceptibility of nontyphoid Salmonella in children in southern Taiwan, 1997-2016

BACKGROUND

This study aimed to investigate the changing trends in serogroup distribution and antimicrobial susceptibility of nontyphoid Salmonella (NTS) isolated from children in the past two decades in Taiwan.

METHODS

This retrospective study enrolled patients aged younger than 18 years with culture-proven NTS infection in a tertiary medical center from 1997 to 2016. Data on age, Salmonella serogroup, culture sample, and antimicrobial susceptibility were obtained from medical records. The rates of Salmonella serogroups and antimicrobial resistance were compared between period 1 (1997-2006) and period 2 (2007-2016).

RESULTS

A total of 2075 NTS isolates were identified from 1997 to 2016 (1036 in period 1, 1039 in period 2). The major isolates were from feces (89.1%) and blood (10.4%). The most common serogroup was serogroup B (54.8%), followed by serogroup D (18.8%). There was a significant decline in the proportion of serogroup B with a concomitant rise in serogroup D in the past two decades. In period 2, resistance to cefotaxime and cefixime increased remarkably among serogroup B, whereas resistance to ampicillin increased notably among serogroup D. Furthermore, the incidence of multidrug-resistant (≥3 antibiotics) NTS significantly decreased in both serogroup B and serogroup D in period 2.

CONCLUSION

This study revealed a significant rise in serogroup D with a concomitant decline in serogroup B NTS infection in Taiwanese children. Moreover, antimicrobial resistance to third-generation cephalosporins increased in serogroup B. Continuous surveillance of NTS serogroup distribution and antimicrobial susceptibility is mandatory to formulate therapeutic strategies for NTS infections.

Whole-Genome Sequencing Identifies In Vivo Acquisition of a blaCTX-M-27-Carrying IncFII Transmissible Plasmid as the Cause of Ceftriaxone Treatment Failure for an Invasive Salmonella enterica Serovar Typhimurium Infection

We report a case of ceftriaxone treatment failure for bacteremia caused by Salmonella enterica subsp. enterica serovar Typhimurium, due to the in vivo acquisition of a bla_CTX-M-27-encoding IncFII group transmissible plasmid. The original β-lactamase-susceptible isolate ST882S was replaced by the resistant isolate ST931R during ceftriaxone treatment. After relapse, treatment was changed to ciprofloxacin, and the patient recovered. Isolate ST931R could transfer resistance to Escherichia coli at 37°C. We used whole-genome sequencing of ST882S and ST931R, the E. coli transconjugant, and isolated plasmid DNA to unequivocally show that ST882S and ST931R had identical chromosomes, both having 206 identical single-nucleotide polymorphisms (SNPs) versus S Typhimurium 14028s. We assembled a complete circular genome for ST931R, to which ST882S reads mapped with no SNPs. ST882S and ST931R were isogenic except for the presence of three additional plasmids in ST931R. ST931R and the E. coli transconjugant were ceftriaxone resistant due to the presence of a 60.5-kb IS26-flanked, bla_CTX-M-27-encoding IncFII plasmid. Compared to 14082s, ST931R has almost identical Gifsy-1, Gifsy-2, and ST64B prophages, lacks Gifsy-3, and instead carries a unique Fels-2 prophage related to that found in LT2. ST882S and ST931R both had a 94-kb virulence plasmid showing >99% identity with pSLT14028s and a cryptic 3,904-bp replicon; ST931R also has cryptic 93-kb IncI1 and 62-kb IncI2 group plasmids. To the best of our knowledge, in vivo acquisition of extended-spectrum β-lactamase resistance by S Typhimurium and bla_CTX-M-27 genes in U.S. isolates of Salmonella have not previously been reported.