Staphylococcus aureus and Methicillin Resistant S. aureus in Nepalese Primates: Resistance to Antimicrobials, Virulence, and Genetic Lineages.
1. IntroductionStaphylococcus aureus is a ubiquitous pathogen and colonizer in humans and in a variety of wild and domestic animals [1,2]. However, there are only a few studies on its presence, and molecular epidemiology, in monkeys and apes. In earlier studies, we characterized methicillin-resistant S. aureus (MRSA) isolates from nasal samples in a United States Primate Center [2], Three species of macaques [Macaca mulatta, M. fascicularis, and M. nemestrim] were identified with an MRSA as well as a few methicillin-susceptible S. aureus (MSSA) isolates [2,3]. Two different MRSA clones were identified as having a previously uncharacterized sequence type (ST3268) and ST188, which is a rare ST in the United States but more common among humans from Southeast Asia [2,3] and wild animals [1]. Both clones have been identified in other United States primate facilities as well as commercial facilities [1,3 and unpublished observations]. The isolates were characterized by PCR, multilocus sequence typing (MLST), whole genome sequencing, single -nucleotide polymorphism [SNP] analysis, pulsed-field gel electrophoresis (PFGE) and microarray-based assays [2-4], The data suggested an importation of the MRSA strains together with the primates from outside rather than an introduction by local staff members [2,3].
Therefore, it was of interest to look at wild Macaca spp. to determine if either ST188 or ST3268 were carried by these primates as well. We did two studies in Nepal characterizing MRSA isolates cultured from wild rhesus macaques (Macaca mulatta) saliva samples [4,5]. The animals were living in and around temple areas of the Kathmandu valley in Nepal, where human-macaque interaction is common. In this first study, we found four MRSA belonging to two sequence types (ST), 22 SCCmec type IV and CC239 SCC mec type III. Both lineages are known pandemic MRSA lineages. ST239-MRSA-III is a hospital-associated strain that spread globally for the last five decades. CC22-MRSA-IV comprises several related strains with different SCC mec IV subtypes and toxin genes profiles [4-6]. This includes EMRSA-15, which is a common and widespread strain in hospital and community settings especially in Western Europe. It also includes a strain that harbors PVL and tst1 genes emerging in Arabian Gulf countries that appear to be identical by microarray with regard to a rare combination of Panton-Valentine Leukocidin (PVL) and the toxic shock (tst-1) gene and by SCC mec IV subtype to the Nepalese isolates. CC22-MRSA were first identified in Nepal from hospitalized patients in 2012 [7], although other studies did not identify CC22 in hospital samples [8]. The data from the previous work led us to hypothesize that humans were a likely source of the CC22-MRSA and CC239-MRSA isolates in the wild Nepalese macaques. In the second study, we collected saliva samples from Macaca mulatta as well as environmental samples from five surrounding areas, including the Bajrayogini temple site outside the Kathmandu valley [4] (Figure 1). Thirteen MRSA were isolated from primates, 19 were isolated from the environment, and 5 were taken, for comparison, from humans. Four (31%) of the primate isolates, 14 (74%) of the environmental, and the five human MRSA isolates were all CC22 SCC mec IV, as found in the first study [5]. Sixteen (89%) carried both the PVL and the tst-1 gene, which is an unusual combination that according to the microarray profiles is the same as in the previously characterized strains from both Nepalese macaques and pigs [5]. Most of the strains from both the primates and environment are known from earlier studies to be associated with humans [4,5].
In the current study, we wanted to focus on MSSA isolates from these primates in order to elucidate if their native MSSA population also was directly related to those in humans. This has been previously the case of MSSA isolated from great apes and lemurs in a wildlife sanctuary in Africa, where human interaction was significant compared to that found typically in the US Primate Centers and zoos [1,9]. We also wanted to look at a primate population with limited human interaction and a different host species than has previously been sampled and thus, we chose to sample Assam macaques (Macaca assamensis). This would allow us to determine if MSSA and MRSA isolates are most likely acquired from humans in the Assam macaque's population or if there is a potential to have primate-specific MSSA and/or MRSA. We included a few MRSA from areas previously sampled to verify that the clones had not changed over the years, since our first and second set of isolates were taken as well as new areas not previously sampled.
2. Results
2.1. CC for MSSA Typing and CC and SCCmec Typing for MRSA Ancestral Lineage
The sampling locations, the primate host species, and the SCCmec typing data are provided for the seven MRSA, which includes one MRSA from an Assam macaque sample and six isolates from rhesus macaque samples. The same information without the SCCmec typing data are provided for the 33 MSSA isolates, including five MSSA sampled from the Assam macaques and 28 sampled from the rhesus macaques (Table 1).
There were ten (25%) isolates that could be assigned to known lineages (Table 1). This includes all seven MRSA isolates including one isolated from the Assam macaque and three MSSA isolates [2 rhesus and 1 Assam] (Table 1). The other 30 MSSA isolates were not able to be clonally characterized using the StaphyType DNA microarrays and the underlaying database, although experiments were valid. This indicated affiliation to previously unknown lineages (Supplementary Table S1 MLST Sequences). The presence of genes of the Staphyloxanthin operon (crtM, crtN, crtO, crtP, as established by a second array-based assay for one isolate of each strain) ruled out an identification as Staphylococcus argenteus. Strong positive reactivity with probes for coA, nucl, and sbi ruled out Staphylococcus schweitzeri.
2.2. Antibiotic Resistance Genes
Antibiotic resistance gene carriage, based on the microarray, is shown in Table 2 for all 40 isolates. The antibiotic susceptibility patterns are shown in Table 3 with the actual MIC data in Supplementary Table S2. The microarray detection of specific antibiotic resistance genes and the phenotypic susceptibility patterns are correlated with the MSSA isolates that could not be assigned to known lineage while also being susceptible to all 20 antibiotics tested. Thirty of 33 (91%) MSSA isolates, which includes all of the isolates for which we could not determine their clonal lineage, did not carry any of the 33 detected antibiotic resistance genes often associated with MSSA and MRSA isolates (aacA-aphD, aadD, aphA3, blaZ, cat, cfr, dfrA, erm(A), erm(B), erm(C), farl, fexA, fusC, lnu(A), mecA, mecC, mef(A), msr(A), mph(C), mupR, sat, tet(K), tet(M), qacA, qacC, vga(A), vanA, vanB, vanZ, vga(B), vgb(A), vat(A), and vat(B)), which were detected by the StaphyType DNA microarrays. The remaining three MSSA and all seven MRSA carried a variety of antibiotic resistance genes. All MRSA isolates carried one to six different antibiotic resistance genes besides the mecA gene. The CC722-MRSA-V carried six of the eight antibiotic resistance genes identified in the MRSA and MSSA isolates.
CC06 MRSA-IV isolate carried, besides mecA, only the errii(C) macrolide--lincosamide--streptogramin B resistance gene (Table 2). The CC22-MRSA-IV isolates carried blaZ (beta-lactamase) and the bifunctional aminoglycoside resistance gene aacA-aphD. The dfrA gene coding for co-trimoxazole resistance was present in all five isolates, but it was not always expressed; two isolates were susceptible. The erm(C) gene was found in four out of five isolates; it translated into inducible clindamycin resistance. The MRSA isolate #97 from the Assam macaque had the same antibiotic resistance profile as three of the four other CC22 MRSA-IV [isolates #93, #94, #C] isolated from rhesus macaque samples in areas with more human contact. (Tables 2 and 3).
The CC772-MRSA carried aacA-aphD, the mph(C) macrolide resistance gene, and the msr(A) macrolide and streptogramin B resistance gene. It also harbored both aph3, coding aminoglycoside resistance, and sat, coding for streptothricin resistance, which is a combination that is frequently present in CC772 "Bengal Bay Clone" isolates [10].
Three MSSA isolates [CC15 Rhesus, CC96 Assam, CC2990 Rhesus] carried between one and two different antibiotic resistance genes. The CC15 [#83] carried the blaZ and the errii(C) genes, while CC96 [#89] carried the msr(A) and the CC2990 isolate [H] was positive for the aacA-aphD gene. The remaining 30 MSSA regardless of where they were collected and whether they were from Assam or rhesus macaques carried none of the antibiotic resistance genes covered by the microarray assays, and apart from intermediate resistance to nitrofurantoin, they did not show phenotypic resistance to the compounds tested (Table 3).
2.3. Accessory and Virulence Factors
The presence of important virulence factors is summarized in Table 4. The five CC22 MRSA-IV carried most notably the PVL and tst-1 genes (Tables 1 and 4). Thus, it is the same clone as identified in previous work on MRSA carriage in Nepalese rhesus macaques [4,5]. The CC772-MRSA-V harbored not only PVL but also the egc enterotoxin cluster genes, enterotoxins sea, sec, and sel as well as an enterotoxin homologue ORF CM14. This is in accordance with previous descriptions of that strain [10-12], The CC96 MSSA from the Assam macaque had virulence-associated genes lukD/E, cna, and sasG. The CC15 MSSA carried virulence-associated genes lukD/E, chp, and sen, which is in accordance with previously described human isolates [13]. CC2990 is a poorly known clonal complex. One isolate, from a rhesus, was found to harbor sec+sel, lukD/E, sak, chp, sen, edinB+etD2, cm, and snsG. The other MSSA isolates from both primate species had different sets of virulence-associated genes (Table 4); two of these 17 lineages carried the egc cluster; four harbored edinB (epidermal cell differentiation inhibitor B/ADP-ribosyltransferase; GenBank AB057421.1, 7154 to 7897) and an exfoliative toxin homologue etD2 (GenBank HF563069), which is a rare combination among previously studied strains (see Discussion).
3. Discussion
The S. aureus isolates from free-ranging Nepalese macaques could roughly be divided into three categories. First, there were MRSA strains that frequently have been observed also in humans, in Nepal, the Indian subcontinent, and in the Arabian Gulf states [6,7], The CC6-MRSA-IV and CC22-MRSA-IV (PVL+/fsf+) are human MRSA with strong Middle Eastern connections [6]. CC772-MRSA-V (PVL+), "Bengal Bay Clone", is an epidemic strain emerging from the Indian subcontinent, being common in India, Pakistan, and Bangladesh, as well as in the Gulf States where there are many Indian/Pakistani and Nepalese working migrants [10-13]. It might be speculated that Nepalese expatriates brought these strains from the Arabian Gulf states into Nepal, triggering local outbreaks among humans and, via food and sacrificial offering at temples, among macaque populations [14].
Second, there are MSSA strains that might come from humans or from animals/livestock, although data for some of these lineages are not sufficient to assess their host specificity and geographic distribution. The MSSA CC15 is a common lineage among humans [15]. MSSA CC96 is a rare lineage among humans, with a few reports on MRSA from Malaysia, Central Asia, and Middle East [16]. It has also previously been isolated from rabbits [17], so that it cannot be decided if it was primarily a zoonotic or anthropozoonotic lineage. One isolate was assigned to CC2990 based on both the microarray profile and MLST, matching some Western European isolates of this lineage; however, these were PVL-positive (unpublished observation by the authors).
Third, the remaining 17 lineages comprising 30 MSSA isolates did not match with any known array profile, neither human nor known animal ones; thus, no CC could be assigned (Supplementary Table S1 MLST Sequences) and no information on origin, host specificity, and geographic distribution is available. In contrast to the other lineages, from this as well as from the previous studies [4,5], they did not carry commonly found antibiotic resistance genes and did not display phenotypic resistance. With regard to virulence factors, there was a conspicuous presence of edinB and etD2 in four of the unknown lineages as well as in CC2990. The edinB gene is rare among human isolates, and it is usually linked to an exfoliative toxin homologue, etD (GenBank AB057421.1, 5409 to 6254). For instance, they can be found in the European community-acquired CC80-MRSA-IV clone. The divergent etD2 exfoliative toxin homologue was previously identified in European sheep and hedgehogs (GenBank E1F563069) [18,19]. The role of these virulence factors in macaques is not yet elucidated. These 17 lineages can preliminarily be considered as colonizers native to wild macaque populations. However, since virtually nothing is known on MSSA population structures among humans and livestock in remote Nepalese regions, this cannot currently be assessed. Further investigations on geographic distribution, host specificity, and possible relevance for animal/livestock and human health are warranted.
We found the same strains circulating among Assam macaques and rhesus macaques (Tables 1-4). Sample numbers are too low to detect possible differences in carriage between the two macaque species. However, this suggests that there could be a transmission between macaque species, and it strongly indicates a transmission of "human", anthropozoonotic strains (such as CC22 and CC772-MRSA) from contaminated environments and occasional human or livestock contact to the Assam and rhesus macaques. How the colonization of MRSA impacts the carriage of MSSA in the same host should also be investigated, as well as the impact on the health of the primate hosts. It is not clear whether exposure to such anthropozoonotic MRSA strains might pose a danger to wild monkey populations, especially given the fact that Assam macaques are much more rare than rhesus. Luckily, PVL seems to be less effective as a cytotoxin in macaques (long-tailed macaque, Macaca fascicularis) than in humans [20]. However, there are no data on the ability to cause disease in wild monkeys, neither for these "human" and/or PVL-positive strains nor for the 17 novel macaque lineages. Conversely, it is not known if macaque-specific lineages can be passed to humans and if "human" strains, in Nepal and elsewhere, evolved from macaque strains. This can be elucidated only by genome-wide analysis of less known, local, human strains and those macaque strains. Furthermore, it should be determined if the MSS A lineages identified in the current study are primarily found in primates from Nepal or also in wild primates elsewhere and/or in other wild animals. It would also be of interest to determine if these MSSA isolates are carried with or without causing disease in either primates or humans.
4. Materials and Methods
4.1. Primate Sampling
A total of 11 locations were sampled in the current study (Figure 1). The locations, all of which represent religious/temples sites, included Bajrayogini, Nilbarahi, Pashupati, Swayambhu [21], and Thapathali (these five locations were sampled in 2018 [5] and 2019 [4]). Additionally, six new locations were sampled including, Chitwan, Guheswari, Gokarna, Hetauda, Rupandehi, and Ramdi. All of the locations involved the sampling of rhesus macaques with the exception of Ramdi, where we sampled a resident group of Assam macaques consisting of about 32 individuals living around the Ramdi temple (West-Ramdi) [22], Human dwellings are situated a few hundred meters from the temple. The diet of these macaques consists of food from the forest, but they also are fed fruits and other household scraps by the local people and pilgrims visiting the temple. These macaques are habituated to humans and have been reported to visit and raid human settlements and crop fields in the area [23]. The sampled macaques appeared healthy based on physical appearance and behavior.
The collection technique involved an adaptation of the non-invasive oral sampling method previously described [4,5,14] using SalivaBio Children's Swabs (Salimetrics LLC, State College, PA, USA) [4,24], Swabs were soaked in a sterile glucose solution (10% w/v) and thrown to the macaques. A new pair of disposable gloves was used before taking the swab out of the tube and providing it to the monkey. After chewing for several seconds/minutes, the monkey realized the swab was not food and discarded it. The storage tube contained enrichment broth Bacto[R] m Staphylococcus Broth (Difco Laboratories, Sparks, MD, USA) supplemented with a final concentration of 75 mg/L of polymyxin B, 0.01% potassium tellurite, and either with or without 12.5 mg/L nystatin to prevent fungal growth (Sigma-Aldrich, St Louis, MO, USA). The tubes were returned to the laboratory the same day when possible and incubated at 37 [degrees]C until turbid (24-96 h), as previously described [25]. The broth was streaked for isolation onto mannitol salt agar plates (HiMedia Laboratories, Mumbai, India), and yellow colonies were sub-cultured onto blood agar plates (HiMedia Laboratories, Mumbai, India). Colonies that had [beta]-hemolysis were verified as S. aureus as described below. Forty isolates, including 7 MRSA and 33 MSSA, were randomly selected from a total of 97 isolates (85 MSSA and 13 MRSA). One MRSA was selected from each region that had an MRSA isolate. All five of the MSSA from the Assam were included, while from the other regions, 28 randomly selected MSSA were included in the current study.
4.2. Ethical Statement
The research protocol for the sampling of free-ranging primates in Nepal was approved by the Department of Forest and Soil Conservation under the Ministry of Forest and Environment, Government of Nepal (Reference Letter Number: 075/076/663). This research also complied with the animal use protocol for primates (#3143-04) approved by the Institutional Animal Care and Use Committee at the University of Washington, USA, and the American Society of Primatologists (ASP) Principles for the Ethical Treatment of Nonhuman Primates.
4.3. Identification of S. aureus from Primates
Colonies that had p-hemolysis on blood agar plates were verified as S. aureus by Gram stain and with the Staphaurex test as previously described (Thermo Fisher Scientific Remel Products, Lenexa, KS [25]. MRSA isolates were identified by their ability to grow on Mueller-Hinton agar (HiMedia Laboratories, India) supplemented with 4 mg/L of oxacillin (HiMedia Laboratories, India). The MRSA isolates were confirmed using the Thermo Scientific PBP2' latex agglutination test kit according to the manufacturer's instructions (Thermo Fisher Scientific Remel Products, Lenexa, KS, USA) [25].
4.4. Antibiotic Susceptibility Testing
The antimicrobial testing was done for 20 antibiotics: benzylpenicillin, oxacillin, cefoxitin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, moxifloxacin, erythromycin, clindamycin, linezolid, teicoplanin, vancomycin, tetracycline, fosfomycin, nitrofurantoin, fusidic acid, mupirocin, rifampicin, and trimethoprim/sulfamethoxazole using automated microdilution, VITEK 2 by Biomerieux according to VITEK 2 by Biomerieux using the manufacturer's instructions and utilizing European Committee on Antimicrobial Susceptibility Testing EUCAST breakpoints Table 2 [26].
4.5. DNA Microarray Analysis
The StaphyType (Abbott/Alere Technologies, Jena, Germany) DNA microarray-based assay was used to screen for a presence or absence of a multitude of genes, including antibiotic resistance markers, virulence factors, species-specific controls, and typing markers (Tables 1, 3 and 4). This system has previously been used for a variety of studies on MRSA [3,4,11,19,20,27-29]. The microarray typing includes 334 target sequences and [approximately equal to]170 separate genes and allelic variants including species markers, SCCmec, capsule, and agr group typing markers, which commonly carried staphylococcal antibiotic resistance genes, toxins, and microbial surface components recognizing adhesive matrix molecules [MSCRAMM] genes. Isolates were assigned to clonal complexes (CCs) by an automated comparison of the microarray hybridization profiles to a large database of previously characterized isolates [11]. Then, strains were assigned to clonal complexes when possible. However, 30 of the isolates could not be assigned to a clonal complex and were assumed to be novel (Supplementary Table S1). The detailed protocol as well as the sequences of primers and probes have previously been published [15]. A second array was used on representative isolates for the detection of Staphyloxanthin genes [30].
4.6. Multilocus Sequence Analysis
Genomic DNA was isolated from an overnight culture grown at 37 [degrees]C on Columbia Blood Agar plates (Becton Dickinson GmbH, Heidelberg, Germany) using a Macherey and Nagel NucleoSpin[R] Microbial DNA kit (MACHEREY-NAGEL GmbH & Co. KG, Dueren, Germany). The Oxford Nanopore MinlON platform was used for sequencing the whole genome of twelve isolates. Briefly, size selection and DNA clean-up were performed using Agencourt AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) in a ratio of 1/1 (v/v). The DNA library was generated using the Nanopore native barcoding genomic DNA kit SQK-LSK109 in combination with the native barcoding expansion kit EXP-NBD104 (Oxford Nanopore Technologies, Oxford, UK) according to the manufacturer's instructions. The used flow cell FLO-MIN106 (revD R9.4.1) was primed by the flow cell priming kit EXP-FLP001 (Oxford Nanopore, Oxford, UK). The protocol named "Native barcoding genomic DNA" was used in version NBE_9065_vl09_revV_14Aug2019 (Last update: 21/02/2020).
The Guppy basecaller (version 4.0.14+8d3226e, Oxford Nanopore Technologies, Oxford, UK) translated the MinlON raw reads (FAST5) into quality tagged sequence reads (4000 reads per FASTQ-file) using the barcode trimming option. Flye (v2.8-b1674) was used to assemble the quality tagged sequence reads of each strain to one big circular contig. The polishing of assemblies was split into two steps. At first, racon (v1.4.17) was iteratively used four times with the following parameter: match 8; mismatch 6; gap 8; and windows-lengths 500. Afterwards, medaka (v1.0.3) (https://nanoporetech. github.io/medaka/) ran on the last racon polished assembly using the model r941_min_high_g360. Corrected assemblies were used for further MLST analysis by upload to the S. aureus pubMLST database (https://pubmlst.org/bigsdb?db=pubmlst_saureus_seqdef&page=sequenceQuery).
5. Conclusions
The MRSA isolated from both Assam and rhesus macaques were linked to other countries including India and Middle East as the previous study illustrated for MRSA isolated in 2017-2018 [4,5]. The same cannot be said for the majority of the MSS A. Thirty isolates representing 17 distinct lineages did not belong to previously characterized clonal complexes nor did they carry antibiotic resistance genes commonly found in S. aureus. This suggests that these isolates may not commonly circulate in humans and may be adapted for macaques. We did not find comparable MRSA to these novel MSSA, suggesting that the two may use different transmission routes in the primates. Future studies will need to expand the knowledge of MSSA in primates and determine if these isolates can be identified in domestic or other types of wild animals. The number of isolates from Assam macaques that have limited contact with humans suggest that they carry the same type of MRSA and MSSA as the rhesus. Therefore, it will be of interest to determine if both MRSA and MSSA are transmitted from Assam adults to their infants and how contaminated their environment is with MSSA.
doi: 10.3390/antibiotics9100689
Supplementary Materials: The following are available online at http://www.mdpi.com/2079-6382/9/10/689/s1, Table S1: MLST Sequences. Table S2 MICs of the Isolates.
Author Contributions: M.C.R. and R.C.K. coordinated the study and supervised the original field and data collection. P.R.J. coordinated the in-country collection of the primate samples and writing the mansucript. S.R and M.A. helped with sample collection and processing. S.M., R.E., E.M. and D.G. did data analyses and helped with writing the manuscript along with P.R.J. and L.K., L.K., N.P.K. and M.C. helped with facilitating access to isolates. E.M. and D.G. did array experiments, E.M. did the susceptibility tests, C.D. and S.D.B. did the sequencing. All authors have read and agreed to the published version of the manuscript.
Funding: The project was supported in part by the One Earth Institute and the Office of Research Infrastructure Programs (ORIP) of the National Institutes of Health through Grant Number P510D010425 to the WaNPRC.
Acknowledgments: We would like to thank the Department of Forest and Soil Conservation, Kathmandu, Nepal for permission to conduct sampling. We also thank Nima Singh who helped with the laboratory preparation of the samples.
Conflicts of Interest: The authors declare they have no conflict of interest.
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[21.] Kyes, R.C.; Jones-Engel, L.; Chalise, M.K.; Engel, G.; Heidrich, J.; Grant, R.; Bajimaya, S.S.; McDonough, J.; Smith, D.G.; Ferguson, B. Genetic characterization of rhesus macaques (Macaca mulatto) in Nepal. Am. J. Primatol. 2006, 68, 445M55. [CrossRef]
[22.] Khanal, L.; Chalise, M.K.; He, K.; Acharya, B.K.; Kawamoto, Y.; Jiang, X. Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya. Am. J. Primatol. 2018, 80, e22748. [CrossRef] [PubMed]
[23.] Adhikari, K.P; Khanal, L.; Chalise, M.K. Status and effects of food provisioning on ecology of Assamese monkey (Macaca assamensis) in Ramdi area of Palpa, Nepal. J. Inst. Sci. Technol. 2018, 22,183-190. [CrossRef]
[24.] Evans, T.S.; Barry, P. A.; Gilardi, K.V.; Goldstein, T.; Deere, J.D.; Fike, J.; Yee, J.-A.; Ssebide, B.J.; Karmacharya, D.; Cranfield, M.R.; et al. Optimization of a novel non-invasive oral sampling technique for zoonotic pathogen surveillance in nonhuman primates. PLoS Negl. Prop. Dis. 2015, 9, e0003813. [CrossRef]
[25.] Roberts, M.C.; Soge, O.O.; Horst, J.A.; Ly, K.A.; Milgrom, P. Methicillin-resistant Staphylococcus aureus from dental school clinic surfaces and students. Am. J. Infect. Control. 2011, 39, 628-632. [CrossRef]
[26.] ISO 20776-1 (2006). Clinical Laboratory Testing and In Vitro Diagnostic Test. Systems--Susceptibility Testing of Infectious Agents and Evaluation of Performance of Antimicrobial Susceptibility Test. Devices--Part. 1: Reference Method for Testing the In Vitro Activity of Antimicrobial Agents against Rapidly Growing Aerobic Bacteria Involved in Infectious Diseases. 2006. Available online: http://www.eucast.org/ast_of_bacteria/mic_ determination/ (accessed on 1 September 2020).
[27.] Kinneyvey, P.M.; Shore, A.C.; Brennan, G.I.; Sullivan, D.J.; Ehricht, R.; Monecke, S.; Slickers, P.; Coleman, D.C. Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals. Antimicrob. Agents Chemother. 2012,57,524-531. [CrossRef]
[28.] Monecke, S.; Jatzwauk, L.; Muller, E.; Nitschke, H.; Pfohl, K.; Slickers, P.; Reissig, A.; Ruppelt-Lorz, A.; Ehricht, R. Diversity of SCCmec elements in Staphylococcus aureus as observed in South-Eastern Germany. PLoS ONE 2016,11, e0162654. [CrossRef]
[29.] Monecke, S.; Slickers, P.; Gawilik, D.; Muller, E.; Reissig, A.; Ruppelt-Lorz, A.; Akpaka, P.E.; Bandt, D.; Bes, M.; Boswihi, S.S.; et al. Molecular typing of ST239-MRSA-III from diverse geographic locations and the evolution its SCCmec III element during its intercontinental spread. Front. Microbiol. 2018,9,1436. [CrossRef]
[30.] Monecke, S.; Jatzwauk, L.; Weber, S.; Slickers, P.; Ehricht, R. DNA microarray-based genotyping of methicillin-resistant Staphylococcus aureus strains from eastern saxony. Clin. Microbiol. Infect. 2009, 14, 534-545. [CrossRef]
Marilyn C. Roberts (1), *, Prabhu Raj Joshi (2), Stefan Monecke (3,4,5), Ralf Ehricht (3,4,6), Elke Muller (3,4), Darius Gawlik (7), Celia Diezel (3,4), Sascha D. Braun (3,4), Saroj Paudel (2) [ID], Mahesh Acharya (2), Laxman Khanal (8) [ID], Narayan P. Koju (9,10), Mukesh Chalise (11) and Randall C. Kyes (12)
(1) Department of Environmental and Occupational Health, School of Public Health, University of Washington, Seattle, WA 98105, USA
(2) Nepalese Farming Institute, Maitidevi, Kathmandu 44600, Nepal; cmilanjoshi@gmail.com (P.R.J.); pulu.saroj@gmail.com (S.P); maheshacharya045@gmail.com (M.A.)
(3) Leibniz Institute for Photonic Technologies Leibniz-IPHT), 07745 Jena, Germany; stefan.monecke@leibniz-ipht.de (S.M.); ralf.ehricht@leibniz-ipht.de (R.E.); elke.mueller@leibniz-ipht.de (E.M.); Celia.diezel@leibniz-ipht.de (C.D.); sascha.braun@leibniz-ipht.de (S.D.B.)
(4) InfectoGnostics Research Campus Jena, 07743 Jena, Germany
(5) Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Cams", Technische Universitat Dresden, 01062 Dresden, Germany
(6) Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
(7) PTC--Phage Technology Center GmbH, 59199 Bonen, Germany; darius.gawlik@web.de
(8) Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu 44613, Nepal; lkhanal@cdztu.edu.np
(9) Center for Postgraduate Studies, Nepal Engineering College, Pokhara University, Lalitpur 44800, Nepal; npkoju.2003@gmail.com
(10) Department of Psychology, University of Washington, Seattle, WA 98195, USA
(11) Nepal Biodiversity Research Society and Central Department of Zoology, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal; mukesh57@hotmail.com
(12) Washington National Primate Research Center, Center for Global Field Study, Departments of Psychology, Global Health, Anthropology, University of Washington, Seattle, WA 98195, USA; rkyes@uw.edu
* Correspondence: marilynr@uw.edu; Tel.: +1-206-543-8001
Received: 11 September 2020; Accepted: 10 October 2020; Published: 13 October 2020
Caption: Figure 1. Primate Sampling Locations. Saliva Sampling was conducted at 11 locations in Nepal: 1-Bajrayogini; 2-Nilbarahi; 3-Gokarna; 4-Guheswari; 5-Pashupati; 6-Thapathali; 7-Swayambhu; 8-Hetauda; 9-Chitwan; 10-Ramdi; 11-Rupandehi.
Table 1. Methicillin-resistant S. aureus (MRSA) strains, sample types,
and sampling locations as well as species markers, agr groups, and
capsule types.
Clonal Strain Isolate ID Number
Complex
CC06 CC6-MRSA-IV B 1
CC22 CC22-MRSA-IV (PVL+/tst+) 93, 94, 05, 97, 5
C
CC772 CC772-MRSA-V (PVL+), 91 1
CC15 CC15-MSSA 83 1
CC96 CC96-MSSA 89 1
CC2990 CC2990-MSSA H 1
UNKNOWN 01 ST(4-13-1-105-11-5-x)-MSSA 86, 87 2
UNKNOWN 02 ST(1-421-1-1-12-238-11)-MSSA 52, 53 2
UNKNOWN 03 ST(1-3-1-15-28-x-1)-MSSA 31,32, 71, D 4
UNKNOWN 04 MSSA 01 1
UNKNOWN 05 ST(1-1-1-1-28-4-11)-MSSA 73, F 2
UNKNOWN 06 ST(1-421-1-x-x-1-11)-MSSA 54 1
UNKNOWN 07 ST(12-x-1-66-11-x-x)-MSSA 29, 30, 51 3
UNKNOWN 08 ST(1-38-1-1-x-238-x)-MSSA 81, 88 2
UNKNOWN 09 ST(3-3-2-66-28-x-x)-MSSA 10 1
UNKNOWN 10 ST(3-1-1-66-28-1-x)-MSSA 82, 90 2
UNKNOWN 11 MSSA 50 1
UNKNOWN 12 ST(4-421-1-105-1-5-x)-MSSA 61 1
UNKNOWN 13 ST(1-3-1-x-1-1-11)-MSSA 62, 72 2
UNKNOWN 14 ST(3-38-1-15-1-x-40)-MSSA G 1
UNKNOWN 15 ST(1-421-1-1-12-1-11)-MSSA 11,E 2
UNKNOWN 16 ST(3-3-1-66-4-x-x)-MSSA 49, I 2
UNKNOWN 17 MSSA 13 1
Clonal Sampling Location Host Species gapA, katA, coA,
Complex nucl, spa, sbi, eno,
clfA+B, fnbA
CC06 Nilbarahi Rhesus POS
CC22 2 Gokarna, 1 each 1 Assam, POS
Chitwan, Ramdi 4 Rhesus
and Nilbarahi
CC772 Hetauda Rhesus POS
CC15 Rupandehi Rhesus POS
CC96 Ramdi Assam POS
CC2990 Guheswari Rhesus POS
UNKNOWN 01 Ramdi Assam POS
UNKNOWN 02 Gokarna Rhesus POS
2 Nilbarahi,
1 each
UNKNOWN 03 Chitwan and Rhesus POS
Gokarna
UNKNOWN 04 Pashupati Rhesus POS
UNKNOWN 05 1 Chitwan, POS
1 Gokarna Rhesus
UNKNOWN 06 Gorkarna Rhesus POS
UNKNOWN 07 2 Swayambhu, Rhesus POS
1 Gokarna
e
UNKNOWN 08 1 Ramdi, 1 Assam, POS
1 Rupandehi 1 Rhesus
UNKNOWN 09 Pashupati Rhesus POS
UNKNOWN 10 1 Ramdi, 1 Assam, POS
1 Rupandehi 1 Rhesus
UNKNOWN 11 Bajrayogini Rhesus POS
UNKNOWN 12 Hetauda Rhesus POS
UNKNOWN 13 1 Chitwan, Rhesus POS
1 Hetauda
UNKNOWN 14 Guheswari Rhesus POS
UNKNOWN 15 1 Gokarna, Rhesus POS
1 Thapathali
UNKNOWN 16 1 Bajrayogini, Rhesus POS
1 Guheswari
UNKNOWN 17 Thapathali Rhesus POS
Clonal Staphyloxanthin Operon agr Group Capsule Type
Complex
CC06 not tested I 8
CC22 not tested I 5
CC772 not tested II 5
CC15 not tested II 8
CC96 not tested III 8
CC2990 POS II 8
UNKNOWN 01 POS I 5
UNKNOWN 02 POS I 5
UNKNOWN 03 POS I 8
UNKNOWN 04 POS I 8
UNKNOWN 05 POS I 8
UNKNOWN 06 POS I 8
UNKNOWN 07 POS II 8
UNKNOWN 08 POS II 8
UNKNOWN 09 POS II 8
UNKNOWN 10 POS III 5
UNKNOWN 11 POS III 8
UNKNOWN 12 POS IV 5
UNKNOWN 13 POS IV 5
UNKNOWN 14 POS IV 5
UNKNOWN 15 POS IV 5
UNKNOWN 16 POS IV 8
UNKNOWN 17 POS IV 8
Table 2. Susceptibility tests.
Clonal Strain Number PEN OXA
Complex
CC06 CC6-MRSA-IV 1 R R
CC22 CC22-MRSA-IV (PVL+/tst+) 5 R R
CC772 CC772-MRSA-V (PVL+), "Bengal Bay" 1 R R
CC15 CC15-MSSA 1 R S
CC96 CC96-MSSA 1 S S
CC2990 CC2990-MSSA 1 S S
UNKNOWN 01 ST(4-13-1-105-11-5-x)-MSSA 2 S S
UNKNOWN 02 ST(1-421-1-1-12-238-11)-MSSA 2 S S
UNKNOWN 03 ST(1-3-1-15-28-x-1)-MSSA 4 S S
UNKNOWN 04 MSSA 1 S S
UNKNOWN 05 ST(1-1-1-1-28-4-11)-MSSA 2 S S
UNKNOWN 06 ST(1-421-1-x-x-1-11)-MSSA 1 S S
UNKNOWN 07 ST(12-x-1-66-11-x-x)-MSSA 3 S S
UNKNOWN 08 ST(1-38-1-1-x-238-x)-MSSA 2 S S
UNKNOWN 09 ST(3-3-1-66-28-x-x)-MSSA 1 S S
UNKNOWN 10 ST(3-1-1-66-28-1-x)-MSSA 2 S S
UNKNOWN 11 MSSA 1 S S
UNKNOWN 12 ST(4-421-1-105-1-5-x)-MSSA 1 S S
UNKNOWN 13 ST(1-3-1-x-1-1-11)-MSSA 2 S S
UNKNOWN 14 ST(3-38-1-15-1-x-40)-MSSA 1 S S
UNKNOWN 15 ST(1-421-1-1-12-1-11)-MSSA 2 S S
UNKNOWN 16 ST(3-3-1-66-4-1-x)-MSSA 2 S S
UNKNOWN 17 MSSA 1 S S
Clonal FOX GEN TOB CIP LEV MOX
Complex
CC06 R S S S S S
CC22 R R R R R R
CC772 R R R R R R
CC15 S S S R R R
CC96 S S S S S S
CC2990 S S S S S S
UNKNOWN 01 S S S S S S
UNKNOWN 02 S S S S S S
UNKNOWN 03 S S S S S S
UNKNOWN 04 S S S S S S
UNKNOWN 05 S S S S S S
UNKNOWN 06 S S S S S S
UNKNOWN 07 S S S S S S
UNKNOWN 08 S S S S S S
UNKNOWN 09 S S S S S S
UNKNOWN 10 S S S S S S
UNKNOWN 11 S S S S S S
UNKNOWN 12 S S S S S S
UNKNOWN 13 S S S S S S
UNKNOWN 14 S S S S S S
UNKNOWN 15 S S S S S S
UNKNOWN 16 S S S S S S
UNKNOWN 17 S S S S S S
Clonal ERY CLI LIN TEI VAN TET
Complex
CC06 R R (a) S S S S
CC22 VAR (b) VAR (ab) S S S S
CC772 I S S S S S
CC15 R R (a) S S S S
CC96 R S S S S S
CC2990 S S S S S S
UNKNOWN 01 S S S S S S
UNKNOWN 02 S S S S S S
UNKNOWN 03 S S S S S S
UNKNOWN 04 S S S S S S
UNKNOWN 05 S S S S S S
UNKNOWN 06 S S S S S S
UNKNOWN 07 S S S S S S
UNKNOWN 08 S S S S S S
UNKNOWN 09 S S S S S S
UNKNOWN 10 S S S S S S
UNKNOWN 11 S S S S S S
UNKNOWN 12 S S S S S S
UNKNOWN 13 S S S S S S
UNKNOWN 14 S S S S S S
UNKNOWN 15 S S S S S S
UNKNOWN 16 S S S S S S
UNKNOWN 17 S S S S S S
Clonal FOS NIF FUS MUP RIF TSU
Complex
CC06 S S S S S S
CC22 S S S S S VAR (c)
CC772 S I S S S R
CC15 S S S S S S
CC96 S S S S S S
CC2990 S S S S S S
UNKNOWN 01 S I S S S S
UNKNOWN 02 S S S S S S
UNKNOWN 03 S S S S S S
UNKNOWN 04 S S S S S S
UNKNOWN 05 S S S S S S
UNKNOWN 06 S S S S S S
UNKNOWN 07 S S S S S S
UNKNOWN 08 S I S S S S
UNKNOWN 09 S S S S S S
UNKNOWN 10 S S S S S S
UNKNOWN 11 S S S S S S
UNKNOWN 12 S S S S S S
UNKNOWN 13 S I S S S S
UNKNOWN 14 S S S S S S
UNKNOWN 15 S S S S S S
UNKNOWN 16 S S S S S S
UNKNOWN 17 S S S S S S
PEN, Benzylpenicillin; OXA, Oxacillin; FOX, Cefoxitin; GEN,
Gentamicin; TOB, Tobramycin; CIP, Ciprofloxacin; LEV, Levofloxacin;
MOX, Moxifloxacin; ERY, Erythromycin; CLI, Clindamycin; LIN,
Linezolid; TEI, Teicoplanin; VAN, Vancomycin; TET, Tetracycline; FOS,
Fosfomycin; NIF, Nitrofurantoin; FUS, Fusidic acid; MUP, Mupirocin;
RIF, Rifampicin and TSU, Trimethoprim/Sulfamethoxazole (a) Inducible
clindamycin resistance. (b) Variable, four out of five isolates
resistant (ERY)/inducibly resistant (CLI); one susceptible.
(c) Variable, three out of five isolates resistant, two susceptible.
The actual MICs are found in Supplementary Table S2.
Table 3. SCCmec markers and resistance genes (a).
Clonal Strain N lumber mecA Delta
Complex mecR
CC06 CC6-MRSA-IV 1 POS POS
CC22 CC22-MRSA-IV 5 POS POS
(PVL+/tst+)
CC772 CC772-MRSA-V(PVL+), 1 POS NEG
"Bengal Bay "
CC15 CC15-MSSA 1 NEG NEG
CC96 CC96-MSSA 1 NEG NEG
CC2990 CC2990-MSSA 1 NEG NEG
UNKNOWN 01 ST(4-13-1-105-11-5-x)-MSSA 2 NEG NEG
UNKNOWN 02 ST(1-421-1-1-12-238-11)-MSSA 2 NEG NEG
UNKNOWN 03 ST(1-3-1-15-28-x-1)-MSSA 4 NEG NEG
UNKNOWN 04 MSSA 1 NEG NEG
UNKNOWN 05 ST(1-1-1-1-28-4-11)-MSSA 2 NEG NEG
UNKNOWN 06 ST(1-421-1-x-x-1-11)-MSSA 1 NEG NEG
UNKNOWN 07 ST(12-x-1-66-11-x-x)-MSSA 3 NEG NEG
UNKNOWN 08 ST(1-38-1-1-x-238-x)-MSSA 2 NEG NEG
UNKNOWN 09 MSSA 1 NEG NEG
UNKNOWN 10 ST(3-3-1-66-28-x-x)-MSSA 2 NEG NEG
UNKNOWN 11 MSSA 1 NEG NEG
UNKNOWN 12 ST(4-421-1-105-1-5-x)-MSSA 1 NEG NEG
UNKNOWN 13 ST(1-3-1-x-1-1-11)-MSSA 2 NEG NEG
UNKNOWN 14 ST(3-38-1-15-1-x-40)-MSSA 1 NEG NEG
UNKNOWN 15 ST(1-421-1-1-12-1-11)-MSSA 2 NEG NEG
UNKNOWN 16 ST(3-3-1-66-4-1-x)-MSSA 2 NEG NEG
UNKNOWN 17 MSSA 1 NEG NEG
Clonal ccrA-2 ccrB-2 ccrAA ccrC blaZ/I/R erm(C)
Complex
CC06 POS POS NEG NEG NEG POS
CC22 POS POS NEG NEG POS VAR (b)
CC772 NEG NEG POS POS POS NEG
CC15 NEG NEG NEG NEG POS POS
CC96 NEG NEG NEG NEG NEG NEG
CC2990 NEG NEG NEG NEG NEG NEG
UNKNOWN 01 NEG NEG NEG NEG NEG NEG
UNKNOWN 02 NEG NEG NEG NEG NEG NEG
UNKNOWN 03 NEG NEG NEG NEG NEG NEG
UNKNOWN 04 NEG NEG NEG NEG NEG NEG
UNKNOWN 05 NEG NEG NEG NEG NEG NEG
UNKNOWN 06 NEG NEG NEG NEG NEG NEG
UNKNOWN 07 NEG NEG NEG NEG NEG NEG
UNKNOWN 08 NEG NEG NEG NEG NEG NEG
UNKNOWN 09 NEG NEG NEG NEG NEG NEG
UNKNOWN 10 NEG NEG NEG NEG NEG NEG
UNKNOWN 11 NEG NEG NEG NEG NEG NEG
UNKNOWN 12 NEG NEG NEG NEG NEG NEG
UNKNOWN 13 NEG NEG NEG NEG NEG NEG
UNKNOWN 14 NEG NEG NEG NEG NEG NEG
UNKNOWN 15 NEG NEG NEG NEG NEG NEG
UNKNOWN 16 NEG NEG NEG NEG NEG NEG
UNKNOWN 17 NEG NEG NEG NEG NEG NEG
Clonal lnu(A) msr(A) mpB(C) aacA-aphD aphA3+sat dfrA
Complex
CC06 NEG NEG NEG NEG NEG NEG
CC22 NEG NEG NEG POS NEG POS
CC772 NEG POS POS POS POS NEG
CC15 NEG NEG NEG NEG NEG NEG
CC96 NEG POS NEG NEG NEG NEG
CC2990 NEG NEG NEG NEG NEG NEG
UNKNOWN 01 NEG NEG NEG NEG NEG NEG
UNKNOWN 02 NEG NEG NEG NEG NEG NEG
UNKNOWN 03 NEG NEG NEG NEG NEG NEG
UNKNOWN 04 NEG NEG NEG NEG NEG NEG
UNKNOWN 05 NEG NEG NEG NEG NEG NEG
UNKNOWN 06 NEG NEG NEG NEG NEG NEG
UNKNOWN 07 NEG NEG NEG NEG NEG NEG
UNKNOWN 08 NEG NEG NEG NEG NEG NEG
UNKNOWN 09 NEG NEG NEG NEG NEG NEG
UNKNOWN 10 NEG NEG NEG NEG NEG NEG
UNKNOWN 11 NEG NEG NEG NEG NEG NEG
UNKNOWN 12 NEG NEG NEG NEG NEG NEG
UNKNOWN 13 NEG NEG NEG NEG NEG NEG
UNKNOWN 14 NEG NEG NEG NEG NEG NEG
UNKNOWN 15 NEG NEG NEG NEG NEG NEG
UNKNOWN 16 NEG NEG NEG NEG NEG NEG
UNKNOWN 17 NEG NEG NEG NEG NEG NEG
(a) The table shows only genes that were found at least once in this
study. Genes that were not present in any of the study strains are
other ccrA/B genes, mecR, mecI, kdp-operon genes, heavy metal
resistance genes, mecC, blaZ SCCmec XI, erm(A), erm(B), lnu(A),
mef (A), vat(A), vat(B), vga(A), vga(A), vgb(A), farl, fusC, mupR,
tet(K), tet(M), cat, cfr, fexA, qacA, qacC, vanA, vanB,
and vanZ. (b) Variable, present in four out of five isolates.
Table 4. Virulence-associated genes (a).
Clonal Strain N umber tst sea
Complex
CC06 CC6-MRSA-IV 1 NEG NEG
CC22 CC22-MRSA-IV 5 POS NEG
(PVL+/tst+)
CC772 CC772-MRSA-V (PVL+), 1 NEG POS
"Bengal Bay "
CC15 CC15-MSSA 1 NEG NEG
CC96 CC96-MSSA 1 NEG NEG
CC2990 CC2990-MSSA 1 NEG NEG
UNKNOWN 01 ST(4-13-1-105-11-5-x)-MSSA 2 NEG NEG
UNKNOWN 02 ST(1-421-1-1-12-238-11)-MSSA 2 NEG NEG
UNKNOWN 03 ST(1-3-1-15-28-x-1)-MSSA 4 NEG NEG
UNKNOWN 04 MSSA 1 NEG NEG
UNKNOWN 05 ST(1-1-1-1-28-4-11)-MSSA 2 NEG NEG
UNKNOWN 06 ST(1-421-1-x-x-1-11)-MSSA 1 NEG NEG
UNKNOWN 07 ST(12-x-1-66-11-x-x)-MSSA 3 NEG NEG
UNKNOWN 08 ST(1-38-1-1-x-238-x)-MSSA 2 NEG NEG
UNKNOWN 09 ST(3-3-1-66-28-x-x)-MSSA 1 NEG NEG
UNKNOWN 10 ST(3-1-1-66-28-1-x)-MSSA 2 NEG NEG
UNKNOWN 11 MSSA 1 NEG NEG
UNKNOWN 12 ST(4-421-1-105-1-5-x)-MSSA 1 NEG NEG
UNKNOWN 13 ST(1-3-1-x-1-1-11)-MSSA 2 NEG NEG
UNKNOWN 14 ST(3-38-1-15-1-x-40)-MSSA 1 NEG NEG
UNKNOWN 15 ST(1-421-1-1-12-1-11)-MSSA 2 NEG NEG
UNKNOWN 16 ST(3-3-1-66-4-1-x)-MSSA 2 NEG NEG
UNKNOWN 17 MSSA 1 NEG NEG
Clonal sec+sel egc Genes ORF CM14 PVL lukD/E (b)
Complex
CC06 NEG NEG NEG NEG POS
CC22 POS POS NEG POS NEG
CC772 POS POS POS POS NEG
CC15 NEG NEG NEG NEG POS
CC96 NEG NEG NEG NEG POS
CC2990 POS NEG NEG NEG (POS) (b)
UNKNOWN 01 NEG NEG NEG NEG POS
UNKNOWN 02 NEG POS NEG NEG POS
UNKNOWN 03 NEG NEG NEG NEG POS
UNKNOWN 04 NEG NEG NEG NEG (POS) (b)
UNKNOWN 05 NEG NEG NEG NEG POS
UNKNOWN 06 NEG POS NEG NEG POS
UNKNOWN 07 NEG NEG NEG NEG POS
UNKNOWN 08 NEG NEG NEG NEG POS
UNKNOWN 09 NEG NEG NEG NEG (POS) (b)
UNKNOWN 10 NEG NEG NEG NEG POS
UNKNOWN 11 NEG NEG NEG NEG POS
UNKNOWN 12 NEG NEG NEG NEG POS
UNKNOWN 13 NEG NEG NEG NEG POS
UNKNOWN 14 NEG NEG NEG NEG POS
UNKNOWN 15 NEG POS NEG NEG POS
UNKNOWN 16 NEG NEG NEG NEG POS
UNKNOWN 17 NEG POS NEG NEG POS
Clonal sak chp scn edinB+etD2 cna sasG
Complex
CC06 POS NEG POS NEG POS POS
CC22 POS POS POS NEG POS POS
CC772 NEG NEG POS NEG POS POS
CC15 NEG POS POS NEG NEG POS
CC96 NEG NEG NEG NEG POS POS
CC2990 POS POS POS POS POS POS
UNKNOWN 01 NEG NEG NEG POS NEG POS
UNKNOWN 02 NEG NEG NEG NEG POS POS
UNKNOWN 03 NEG NEG NEG NEG POS NEG
UNKNOWN 04 NEG NEG NEG NEG NEG NEG
UNKNOWN 05 NEG NEG NEG POS POS POS
UNKNOWN 06 NEG NEG NEG NEG POS NEG
UNKNOWN 07 NEG NEG NEG NEG NEG NEG
UNKNOWN 08 NEG NEG NEG NEG POS NEG
UNKNOWN 09 NEG NEG NEG NEG NEG NEG
UNKNOWN 10 NEG NEG NEG NEG NEG POS
UNKNOWN 11 NEG NEG NEG NEG NEG POS
UNKNOWN 12 NEG NEG NEG NEG NEG POS
UNKNOWN 13 NEG NEG NEG POS NEG VAR (c)
UNKNOWN 14 NEG NEG NEG POS POS POS
UNKNOWN 15 NEG NEG NEG NEG NEG POS
UNKNOWN 16 NEG NEG NEG NEG NEG NEG
UNKNOWN 17 NEG NEG NEG NEG POS NEG
(a) Genes that were not present in any of the study strains are seb,
sed, sej, ser, seh, see, lukF-P83+lukM, edinA, edinC, eta, etb, and
etD. Genes present in all strains were hla, hld, lukF/S-hlg, lukX/Y,
aur, and icaA+C+D. See Supplemental File for more details. (b) (POS)
indicates that lukD was detected by array, while the lukE probe
yielded no signals. This is more likely due to allelic variation
rather than due to true absence. (c) Variable, present in one out
of two isolates.
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| Author: | Roberts, Marilyn C.; Joshi, Prabhu Raj; Monecke, Stefan; Ehricht, Ralf; Muller, Elke; Gawlik, Darius |
|---|---|
| Publication: | Antibiotics |
| Article Type: | Report |
| Geographic Code: | 9NEPA |
| Date: | Oct 1, 2020 |
| Words: | 8192 |
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